Contacts of the helix formed by residues 125 - 140 (chain A) in PDB entry 2DFD
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 PRO 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 3.7 34.3 - - + +
93A ASP* 4.3 11.7 - - - +
95A LEU 4.6 0.2 - - - +
96A PHE* 3.8 41.3 - - + +
99A ASN* 4.9 0.4 - - + -
124A ASN* 1.4 86.4 - - + +
126A VAL* 1.3 66.7 + - - +
127A ASN* 3.2 6.3 - - + +
128A SER* 2.9 19.6 + - - +
129A THR* 3.0 19.7 + - + -
182A HIS 5.9 0.9 - - - +
308A SER* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL 4.3 6.1 - - - +
122A ILE 3.5 26.5 - - - +
123A ALA 3.6 4.7 - - - +
124A ASN* 3.2 13.5 + - - +
125A PRO* 1.3 70.5 - - - +
127A ASN* 1.3 62.6 + - - +
128A SER 3.0 1.6 + - - -
129A THR* 3.3 8.7 - - - +
130A ILE* 3.3 20.0 + - + +
150A GLY* 4.0 29.8 - - - -
151A VAL 4.4 1.8 - - - +
152A THR* 4.8 2.0 - - + -
182A HIS* 4.0 24.0 + - + -
259A PHE* 3.7 19.4 - - + -
3003A NAD 3.6 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.1 5.2 + - + +
126A VAL* 1.3 75.0 - - - +
128A SER* 1.3 58.6 + - - +
131A PRO* 3.4 18.4 - - - +
181A GLY* 3.4 5.9 - - - -
182A HIS* 2.7 29.3 + - - +
183A ALA* 3.8 16.3 - - + +
186A THR* 3.2 27.5 + - - +
259A PHE* 3.7 18.1 - - - -
304A GLU* 4.8 1.2 + - - -
305A LEU* 3.5 20.5 - - + +
308A SER* 3.7 21.9 + - - +
309A ILE* 3.8 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 5.0 1.9 + - - -
96A PHE* 3.5 34.3 - - - -
125A PRO* 2.9 13.4 + - - +
127A ASN* 1.3 76.5 - - - +
129A THR* 1.3 64.3 + - - +
130A ILE 3.3 2.2 - - - -
131A PRO* 3.3 8.3 - - - +
132A ILE* 3.1 24.6 + - - +
308A SER* 2.7 35.2 + - - -
311A LYS* 4.2 6.1 - - - +
312A GLY* 3.8 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 5.6 0.9 - - + -
99A ASN* 4.8 6.5 - - + +
100A ALA 5.2 0.2 - - - +
103A VAL* 3.8 22.9 - - + +
121A VAL* 3.5 14.8 - - - +
123A ALA 3.0 26.5 + - - +
124A ASN 3.9 14.4 - - - +
125A PRO* 3.0 17.7 + - + +
126A VAL* 3.3 13.2 + - - -
128A SER* 1.3 74.9 - - - +
130A ILE* 1.3 62.6 + - - +
132A ILE* 3.4 15.6 + - + +
133A THR* 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 3.8 19.7 - - + -
126A VAL* 3.3 13.6 + - + +
129A THR* 1.3 74.1 + - - +
131A PRO* 1.3 74.0 - - + +
133A THR* 3.1 4.3 + - - +
134A ALA* 3.0 21.3 + - - +
148A ILE* 3.7 24.9 - - + +
149A PHE 3.4 12.1 - - - +
150A GLY* 3.3 38.6 - - - +
259A PHE* 3.8 20.4 - - + +
260A VAL* 4.9 2.2 - - - -
261A LYS 5.2 0.4 - - - +
269A TYR* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 3.4 25.6 - - - +
128A SER 3.3 11.0 - - - +
130A ILE* 1.3 95.9 - - + +
132A ILE* 1.3 60.4 + - - +
134A ALA* 3.4 1.4 + - - +
135A GLU* 3.1 29.6 + - - +
259A PHE* 4.1 2.9 - - + -
269A TYR* 3.8 33.7 - - + -
309A ILE* 3.8 32.5 - - + +
312A GLY 4.9 1.8 - - - -
313A GLU* 4.3 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.9 16.4 - - + -
100A ALA* 3.7 36.3 - - + -
103A VAL* 4.0 6.3 - - + -
104A ALA* 3.9 33.0 - - + +
128A SER 3.1 15.2 + - - +
129A THR* 3.6 14.8 - - + +
130A ILE 3.2 0.4 - - - -
131A PRO* 1.3 73.9 - - - +
133A THR* 1.3 58.9 + - - +
135A GLU* 3.2 2.3 + - - -
136A VAL* 2.8 30.5 + - + +
312A GLY* 3.5 18.8 - - - +
315A PHE* 3.8 7.4 - - + -
316A VAL* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.5 5.5 - - - +
107A THR* 3.5 39.5 - - + +
119A ILE* 4.1 14.1 - - + -
121A VAL* 3.7 9.4 - - + +
129A THR 2.8 15.4 + - - -
130A ILE* 3.4 9.0 - - - -
132A ILE* 1.3 76.2 - - - +
134A ALA* 1.3 62.4 + - - +
136A VAL* 3.3 1.4 + - - +
137A PHE* 3.0 29.9 + - + -
148A ILE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE 3.0 11.3 + - - +
131A PRO 3.6 5.4 - - - +
133A THR* 1.3 77.8 - - - +
135A GLU* 1.3 58.0 + - - +
137A PHE* 3.3 3.5 + - - +
138A LYS* 2.9 34.8 + - - +
143A TYR* 3.6 31.8 - - + +
148A ILE* 4.2 5.3 - - + +
269A TYR* 3.3 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO 3.1 17.2 + - - +
132A ILE 3.8 1.6 - - - +
134A ALA* 1.3 78.1 - - + +
136A VAL* 1.3 65.1 + - - +
138A LYS* 2.9 40.9 + - - +
139A LYS* 3.0 26.3 + - - +
269A TYR* 4.3 3.7 + - - +
313A GLU* 4.0 37.4 - - + +
316A VAL* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 4.0 22.4 - - + +
107A THR* 3.6 20.2 - - - +
108A ALA* 3.5 41.1 - - + +
132A ILE* 2.8 24.4 + - + +
133A THR 3.6 2.0 - - - +
135A GLU* 1.3 74.9 - - - +
137A PHE* 1.3 65.9 + - + +
139A LYS* 3.1 14.9 + - + +
140A HIS* 2.9 29.5 + - + +
316A VAL* 4.3 12.3 - - + -
319A LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.4 32.5 - - - -
110A CYS* 4.0 9.2 - - + -
111A ALA* 3.7 27.4 - - + -
115A PRO* 3.9 21.5 - - + -
117A ALA 5.3 1.1 - - - -
119A ILE* 3.8 29.8 - - + -
133A THR* 3.0 28.0 + - + +
134A ALA 3.6 4.9 - - - +
136A VAL* 1.3 77.8 - - - +
138A LYS* 1.3 60.9 + - - +
140A HIS* 3.1 12.3 + - - +
141A GLY 3.1 9.0 + - - -
142A VAL* 3.1 34.2 + - + +
143A TYR* 3.8 18.6 - - + -
144A ASN 4.9 1.1 - - - -
148A ILE* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 2.9 22.4 + - - +
135A GLU* 2.9 41.9 + - - +
136A VAL 3.3 0.2 - - - -
137A PHE* 1.3 74.4 - - - +
139A LYS* 1.3 61.7 + - - +
141A GLY* 3.1 14.0 + - - +
142A VAL 4.9 0.2 - - - +
143A TYR* 3.6 45.4 - - + +
261A LYS* 6.3 1.0 - - - +
269A TYR* 4.6 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU 3.0 10.7 + - - +
136A VAL* 3.1 13.4 + - - +
138A LYS* 1.3 76.4 - - - +
140A HIS* 1.3 71.3 + - + +
141A GLY 3.6 0.3 + - - -
316A VAL* 3.6 33.7 + - + +
319A LEU* 4.1 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.8 22.9 - - + -
111A ALA* 3.7 21.1 - - + +
112A GLN* 3.4 40.4 + - + +
136A VAL* 2.9 27.5 + - + -
137A PHE 3.1 8.4 + - - +
139A LYS* 1.3 89.4 - - + +
141A GLY* 1.3 60.6 + - - +
142A VAL* 3.3 13.1 + - + +
----------------------------------------------------------
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