Contacts of the helix formed by residues 109 - 133 (chain A) in PDB entry 2FY4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE 3.9 3.1 - - - +
108A PRO* 1.3 75.2 - - - +
110A THR* 1.3 66.8 - - - -
111A ASP* 3.1 4.5 - - - -
112A ASP* 2.7 33.7 + - - +
113A GLN 3.6 2.3 + - - -
314A ARG* 3.3 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY* 1.3 71.0 - - - -
111A ASP* 1.3 66.0 + - - +
113A GLN* 3.0 15.9 + - - +
114A LEU* 3.0 40.1 + - + +
219A VAL* 4.7 17.3 - - + -
314A ARG* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY* 3.1 2.1 - - - -
110A THR* 1.3 80.0 - - - +
112A ASP* 1.3 56.9 + - - +
114A LEU* 3.3 3.9 + - - +
115A ARG* 2.8 58.4 + - - +
212A PHE* 3.4 13.2 - - + -
216A ARG* 3.0 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS 4.6 0.7 - - - +
107A PHE* 3.8 24.7 - - + -
108A PRO* 3.1 18.8 - - + +
109A GLY* 2.7 35.8 + - - +
111A ASP* 1.3 78.6 - - - +
113A GLN* 1.3 62.4 + - - +
115A ARG* 3.4 19.1 + - - +
116A PHE* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.5 29.5 - - + -
109A GLY 3.6 1.4 + - - -
110A THR* 3.0 21.5 + - - +
112A ASP* 1.3 79.7 - - - +
114A LEU* 1.3 65.2 + - + +
116A PHE* 3.3 4.9 + - - +
117A ALA* 3.0 25.1 + - - +
219A VAL* 5.6 1.4 - - - +
272A LEU* 3.9 20.1 - - + +
273A ASP 3.8 5.1 + - - -
312A VAL* 2.8 36.2 + - + +
313A GLY* 3.8 0.4 - - - -
314A ARG* 3.0 41.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.0 27.9 + - + +
111A ASP* 3.3 11.4 + - - +
113A GLN* 1.3 81.9 - - - +
115A ARG* 1.3 59.3 + - - +
117A ALA* 4.3 2.7 - - - -
118A ALA* 2.8 29.6 + - - +
212A PHE* 3.8 12.5 - - + -
215A LEU* 3.4 18.2 - - + +
216A ARG* 3.8 40.4 - - + +
219A VAL* 3.8 22.7 - - + -
272A LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 2.8 70.4 + - - +
112A ASP* 3.5 21.6 + - - +
113A GLN 3.3 0.2 - - - -
114A LEU* 1.3 70.4 - - - +
116A PHE* 1.3 66.6 + - - +
118A ALA* 3.2 5.3 + - - +
119A SER* 3.0 24.1 + - - -
208A GLU* 4.1 3.5 - - - +
212A PHE* 3.8 26.7 - - + -
216A ARG* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.8 3.4 - + - -
105A GLN* 3.3 37.7 - - + -
107A PHE* 3.6 20.9 - + + -
112A ASP 3.2 6.2 + - - +
113A GLN 3.4 9.2 - - - +
115A ARG* 1.3 79.6 - - - +
117A ALA* 1.3 56.5 + - - +
119A SER* 3.1 5.9 + - - -
120A LEU* 2.8 47.2 + - + +
312A VAL* 3.6 20.4 - - + -
318A CYS* 3.8 20.2 - - + -
340A LEU* 4.7 11.2 - - + -
343A MET* 3.4 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLN 3.0 13.1 + - - +
114A LEU* 3.7 5.4 - - - +
115A ARG 3.3 0.2 - - - -
116A PHE* 1.3 79.7 - - - +
118A ALA* 1.3 57.5 + - - +
120A LEU* 3.4 7.3 + - - +
121A ILE* 2.9 35.2 + - - +
215A LEU* 3.7 14.8 - - + -
270A VAL* 4.4 8.5 - - + -
272A LEU* 4.2 21.5 - - + -
312A VAL* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU 2.8 18.1 + - - +
115A ARG* 3.5 6.7 - - - +
117A ALA* 1.3 76.6 - - - +
119A SER* 1.3 63.3 + - - +
121A ILE* 3.3 3.3 + - - -
122A SER* 3.0 24.3 + - - -
208A GLU* 3.6 27.6 - - + +
211A LEU* 3.5 13.0 - - + +
212A PHE* 3.8 20.2 - - + +
215A LEU* 3.7 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG 3.0 10.1 + - - -
116A PHE* 3.5 9.0 - - - -
118A ALA* 1.3 75.3 - - - +
120A LEU* 1.3 58.1 + - - +
122A SER* 3.1 4.4 + - - -
123A GLY* 2.8 26.7 + - - -
208A GLU* 2.9 32.1 + - - -
342A HIS* 4.6 4.0 + - - -
343A MET* 3.3 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.5 13.0 - - + -
116A PHE* 2.8 29.4 + - + +
117A ALA* 3.6 5.8 - - - +
119A SER* 1.3 77.7 - - - +
121A ILE* 1.3 59.1 + - + +
123A GLY* 3.1 3.2 + - - -
124A VAL* 2.9 43.3 + - + +
270A VAL* 5.9 2.9 - - + -
310A PHE* 3.9 35.0 - - + -
311A VAL 5.5 0.7 - - - +
312A VAL* 3.9 25.4 - - + -
339A LEU* 4.2 10.5 - - + +
340A LEU* 5.7 0.4 - - + -
343A MET* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 2.9 27.0 + - - +
118A ALA* 3.3 5.6 + - - +
120A LEU* 1.3 76.0 - - + +
122A SER* 1.3 62.4 + - - +
124A VAL* 3.1 11.3 + - + +
125A LEU* 3.0 30.8 + - + +
186A VAL* 4.4 12.1 - - + -
197A LEU* 4.1 22.9 - - + -
199A VAL* 4.0 25.6 - - + -
211A LEU* 4.2 13.9 - - + -
215A LEU* 4.5 12.8 - - + -
270A VAL* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 3.0 15.5 + - - -
119A SER* 3.3 11.9 - - - -
121A ILE* 1.3 72.3 - - - +
123A GLY* 1.3 68.1 + - - +
125A LEU* 3.0 19.0 + - - +
126A SER 3.0 11.1 + - - -
205A ARG* 3.3 17.6 + - - +
206A LEU 4.8 2.1 + - - -
207A SER 4.7 0.3 - - - -
208A GLU* 3.5 23.9 + - - +
211A LEU* 3.3 16.0 - - - +
342A HIS* 4.3 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER 2.8 12.4 + - - -
120A LEU* 3.1 4.5 + - - -
122A SER* 1.3 76.4 - - - +
124A VAL* 1.3 62.1 + - - +
126A SER* 3.0 5.3 + - - -
127A TYR* 2.9 24.3 + - - +
338A HIS* 5.6 0.5 + - - -
339A LEU* 3.6 14.3 - - - +
342A HIS* 3.5 29.9 - - - +
343A MET* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 2.9 35.9 + - + +
121A ILE* 3.3 13.0 - - + +
123A GLY* 1.3 75.5 - - - +
125A LEU* 1.3 61.5 + - + +
127A TYR* 3.4 2.3 + - - +
128A LYS* 2.9 29.0 + - + +
159A PHE* 3.7 25.1 - - + -
267A ILE* 4.2 17.5 - - + -
268A CYS* 4.6 9.4 - - - -
270A VAL* 6.5 0.7 - - + -
310A PHE* 4.2 13.2 - - + -
339A LEU* 3.6 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.0 25.4 + - + +
122A SER* 3.4 13.7 - - - +
124A VAL* 1.3 80.5 - - + +
126A SER* 1.3 57.1 + - - +
128A LYS* 3.5 8.1 + - + +
129A ALA* 3.0 25.1 + - - +
186A VAL* 5.3 0.4 - - + -
199A VAL* 3.5 49.6 - - + +
200A VAL* 4.4 7.6 - - + -
205A ARG* 3.7 35.0 + - + +
206A LEU 4.7 5.8 - - - +
211A LEU* 4.7 5.4 - - + -
267A ILE* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 3.0 5.3 + - - -
123A GLY 3.0 8.7 + - - -
125A LEU* 1.3 73.7 - - - +
127A TYR* 1.3 68.0 + - - +
129A ALA* 3.2 5.4 + - - +
130A LEU* 3.0 28.9 + - - +
205A ARG* 2.9 37.4 + - - +
338A HIS* 4.9 4.0 - - - -
342A HIS* 3.4 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 2.9 17.0 + - - +
124A VAL 3.6 4.7 - - - +
126A SER* 1.3 79.6 + - - +
128A LYS* 1.3 62.0 + - - +
130A LEU* 3.1 15.0 + - + +
131A LEU* 3.0 51.2 + - + +
136A ILE* 3.4 16.1 - - + +
155A TYR* 3.3 27.9 - - - -
158A LEU* 4.0 4.9 - - + -
159A PHE* 4.0 6.3 - + + -
334A GLN* 4.5 1.8 - - - +
335A CYS* 3.6 37.5 + - + -
338A HIS* 3.4 53.2 - + + +
339A LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 2.9 18.3 + - + +
125A LEU* 3.8 8.7 - - + +
127A TYR* 1.3 73.9 - - - +
129A ALA* 1.3 57.9 + - - +
131A LEU* 3.6 11.3 - - + +
132A ASP* 2.7 73.5 + - - +
159A PHE* 4.2 28.0 - - + -
160A SER* 6.6 0.4 - - - -
180A MET* 4.7 8.5 - - - +
184A GLU* 2.8 35.0 + - - +
267A ILE* 4.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 3.0 14.4 + - - +
126A SER* 3.3 13.2 - - - +
127A TYR 3.1 0.4 - - - -
128A LYS* 1.3 74.0 - - - +
130A LEU* 1.3 59.2 + - + +
132A ASP* 3.3 7.1 + - - +
133A SER* 2.7 35.3 + - - -
205A ARG* 4.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.0 19.9 + - - +
127A TYR* 3.3 12.6 - - + +
129A ALA* 1.3 78.0 - - + +
131A LEU* 1.3 59.2 + - + +
133A SER* 3.0 9.6 + - - +
135A SER* 2.8 49.4 + - - +
136A ILE* 3.8 12.9 + - + +
338A HIS* 3.6 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.0 33.6 + - + +
128A LYS* 3.6 8.5 - - + +
129A ALA 3.1 0.2 - - - -
130A LEU* 1.3 73.6 - - + +
132A ASP* 1.3 64.0 + - - +
133A SER 3.0 1.8 - - - -
134A HIS* 2.9 17.8 + - - +
136A ILE* 4.0 37.7 - - + -
155A TYR* 3.9 30.3 - - + +
156A TYR* 3.3 33.8 - - + -
158A LEU* 4.4 0.4 - - + -
159A PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 2.7 61.4 + - - +
129A ALA* 3.9 7.5 - - - +
131A LEU* 1.3 76.4 - - - +
133A SER* 1.3 58.5 + - - +
134A HIS* 3.3 13.9 + - - -
156A TYR* 5.3 2.0 - - - -
180A MET* 5.0 14.8 - - + +
184A GLU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 2.7 22.0 + - - -
130A LEU* 3.0 9.0 + - - +
132A ASP* 1.3 76.5 - - - +
134A HIS* 1.3 74.5 + - - +
135A SER* 2.7 24.8 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il