Contacts of the helix formed by residues 110 - 131 (chain A) in PDB entry 5IWG
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 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.2 13.4 - - - -
108A PHE 3.3 1.0 + - - -
109A ASP* 1.3 72.7 - - - +
111A LEU* 1.3 65.0 + - - +
112A PHE 3.3 3.1 - - - -
113A GLU* 3.2 12.0 + - - +
114A PHE 3.0 19.2 + - - -
406A PGE 3.5 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.5 11.4 - - + +
84A ILE* 4.2 28.9 - - + +
101A VAL* 4.9 3.1 - - + -
106A PRO 4.0 9.6 - - - +
107A VAL* 4.4 9.0 - - + -
108A PHE* 3.1 40.9 + - + +
109A ASP 3.4 0.8 + - - -
110A GLY* 1.3 73.9 - - - +
112A PHE* 1.3 65.1 + - - +
114A PHE* 3.3 4.1 + - + +
115A CYS* 3.1 30.4 + - - -
157A TYR* 3.5 58.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 4.8 1.1 - - - -
66A ALA 4.8 7.2 - - - -
69A MET* 3.7 36.3 - - + -
78A ILE* 4.3 8.7 - - + -
81A LEU* 3.6 25.7 + - + +
82A ARG* 3.4 54.3 - - + +
110A GLY 3.3 0.6 - - - -
111A LEU* 1.3 79.5 - - - +
113A GLU* 1.3 59.0 + - + +
115A CYS* 3.1 11.7 + - + +
116A GLN* 2.9 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.4 22.2 + - + +
63A LYS* 2.7 31.7 + - + +
110A GLY* 3.2 11.2 + - - +
112A PHE* 1.3 78.0 - - + +
114A PHE* 1.3 57.0 + - - +
116A GLN* 3.2 21.8 + - - +
117A LEU* 3.0 32.9 + - - +
406A PGE 4.5 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.6 25.4 - - + -
27A TYR* 3.6 38.0 - + + -
29A TYR* 3.5 21.3 - + - -
35A MET* 5.5 0.2 - - + -
37A PRO* 3.8 34.8 - - + -
108A PHE* 3.8 16.8 - + + -
110A GLY 3.0 13.3 + - - +
111A LEU* 3.4 12.8 - - + +
113A GLU* 1.3 74.2 - - - +
115A CYS* 1.3 64.4 + - - +
117A LEU* 3.4 4.7 + - - +
118A SER* 3.2 25.9 + - - -
144A LEU* 5.3 3.1 - - + -
157A TYR* 5.2 3.6 - + - -
403A IWX 3.1 32.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 4.0 6.5 - - + -
81A LEU* 4.6 6.3 - - - -
111A LEU* 3.1 31.2 + - - -
112A PHE* 3.1 11.9 + - + +
114A PHE* 1.3 76.4 - - - +
116A GLN* 1.3 55.9 + - - +
118A SER* 3.2 6.9 + - - -
119A THR* 2.7 38.3 + - - -
144A LEU* 6.2 2.7 - - - -
157A TYR* 3.7 33.0 - - - -
158A VAL* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS 3.7 0.9 - - - +
63A LYS* 3.8 26.5 + - + +
64A ALA* 2.9 45.2 + - - +
65A THR* 4.4 4.8 - - - +
69A MET* 3.8 9.9 - - + -
112A PHE* 2.9 44.9 + - + +
113A GLU* 3.2 29.7 + - - +
115A CYS* 1.3 76.5 - - - +
117A LEU* 1.3 56.4 + - - +
120A GLY* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 3.2 38.4 - - + +
23A ASP* 4.5 3.6 - - + +
24A ILE* 3.9 28.7 - - + +
27A TYR* 3.6 37.2 - - + +
61A PRO* 4.0 19.0 - - + +
62A HIS 4.8 2.0 - - - +
63A LYS* 4.2 25.4 - - + -
113A GLU 3.0 15.9 + - - +
114A PHE* 3.7 4.0 - - - +
115A CYS 3.3 0.2 - - - -
116A GLN* 1.3 74.5 - - - +
118A SER* 1.3 66.2 + - - +
120A GLY* 3.4 0.5 + - - -
121A GLY* 3.4 18.0 + - - -
139A ASN* 5.0 1.7 + - - +
141A ALA* 5.3 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.6 4.4 - - - +
114A PHE* 3.2 12.0 + - - -
115A CYS* 3.2 13.9 + - - -
117A LEU* 1.3 78.2 - - - +
119A THR* 1.3 64.1 + - - +
122A SER* 3.5 4.9 + - - -
139A ASN* 2.9 26.2 + - - -
141A ALA* 3.4 35.0 - - - -
142A GLY* 4.3 0.3 - - - -
144A LEU* 4.1 22.8 - - - +
158A VAL* 5.2 1.2 + - - +
160A ASP* 4.0 4.8 - - - +
403A IWX 4.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 3.6 21.3 - - + -
68A GLU* 5.7 1.3 - - + -
69A MET* 4.6 4.0 - - + -
115A CYS 2.7 22.9 + - - -
118A SER* 1.3 76.9 + - - +
120A GLY* 1.3 63.5 + - - +
122A SER* 3.2 4.3 + - - -
123A VAL* 3.1 31.9 + - + +
158A VAL* 3.3 23.5 + - + +
160A ASP* 3.8 15.0 - - - +
163A LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.7 6.3 - - - -
62A HIS* 3.3 28.7 - - - -
64A ALA* 3.9 4.0 - - - +
116A GLN 2.9 12.7 + - - -
117A LEU 3.4 1.3 + - - -
119A THR* 1.3 76.5 - - - +
121A GLY* 1.3 55.3 + - - +
123A VAL* 3.6 9.4 - - - +
124A ALA* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.8 19.9 - - - -
61A PRO* 3.3 21.3 - - - +
117A LEU 3.4 6.4 + - - -
118A SER 3.8 0.2 + - - -
119A THR 3.3 1.0 - - - -
120A GLY* 1.3 73.9 - - - +
122A SER* 1.3 56.8 + - - +
125A GLY* 3.0 24.8 + - - -
139A ASN* 3.6 24.1 - - - +
301A LEU* 5.1 0.5 - - - +
----------------------------------------------------------
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 SER 3.5 0.3 + - - -
119A THR 3.2 8.7 + - - -
121A GLY* 1.3 73.8 - - - +
123A VAL* 1.3 60.0 + - - +
125A GLY* 3.4 1.9 + - - -
126A ALA* 3.0 27.2 + - - +
139A ASN* 2.9 20.3 + - - +
160A ASP* 2.6 46.4 + - - -
164A ALA* 3.7 13.5 - - - +
301A LEU* 3.8 4.6 - - - +
303A LEU* 3.4 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 3.7 9.6 - - + +
64A ALA* 4.9 0.4 - - + -
68A GLU* 3.4 30.1 - - + +
119A THR* 3.1 27.2 + - + +
120A GLY* 3.6 7.4 - - - +
122A SER* 1.3 71.5 - - - +
124A ALA* 1.3 63.7 + - - +
126A ALA* 3.2 8.1 + - - +
127A VAL* 3.0 34.3 + - + +
160A ASP 4.8 0.9 - - - +
163A LEU* 3.9 39.5 - - + +
164A ALA* 4.1 2.2 - - - +
167A GLU* 4.3 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.5 31.5 + - + -
61A PRO* 5.2 3.6 - - + -
62A HIS* 4.2 15.3 - - + +
120A GLY 2.9 20.4 + - - +
121A GLY 4.0 1.1 - - - +
123A VAL* 1.3 78.2 - - - +
125A GLY* 1.3 57.9 + - - +
127A VAL* 3.3 8.4 + - - +
128A LYS* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.7 14.0 - - - -
121A GLY 3.0 16.3 + - - -
122A SER 3.7 1.8 - - - -
124A ALA* 1.3 75.9 - - - +
126A ALA* 1.3 54.8 + - - +
128A LYS* 3.3 3.8 + - - +
129A LEU* 3.0 34.2 + - - +
137A ALA* 3.6 24.9 - - - +
301A LEU* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 3.0 14.0 + - - +
123A VAL 3.2 9.2 + - - +
125A GLY* 1.3 72.0 - - - +
127A VAL* 1.3 60.4 + - - +
129A LEU* 3.3 6.5 + - - +
130A ASN* 2.9 33.1 + - - +
164A ALA* 3.5 28.5 - - + +
167A GLU* 3.7 14.1 - - + -
168A LEU* 3.8 15.6 - - + +
301A LEU* 4.4 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 3.0 20.9 + - + +
124A ALA* 3.3 10.3 + - - +
126A ALA* 1.3 74.2 - - - +
128A LYS* 1.3 58.2 + - - +
130A ASN* 3.3 7.3 + - + +
131A ARG* 2.9 65.1 + - + +
167A GLU* 3.5 28.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A LYS* 5.0 2.0 - - - +
17A CYS* 3.9 15.0 - - + -
19A TYR* 3.5 24.7 - - + +
57A GLU* 4.5 2.0 + - - -
59A TYR* 3.3 29.4 + - + -
124A ALA 3.0 6.4 + - - +
125A GLY* 3.3 10.1 + - - +
127A VAL* 1.3 78.7 - - - +
129A LEU* 1.3 60.2 + - - +
131A ARG* 3.5 5.4 + - - +
132A GLN 3.4 2.6 + - - -
133A GLN* 2.8 67.5 + - + +
134A THR* 3.5 22.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 3.0 21.4 + - - +
126A ALA* 3.7 6.1 - - - +
128A LYS* 1.3 73.8 - - - +
130A ASN* 1.3 58.8 - - - +
132A GLN* 3.0 23.9 + - - +
134A THR* 3.6 27.5 - - + +
135A ASP 3.4 26.7 - - - +
136A MET 4.1 0.2 - - - +
137A ALA* 4.1 5.4 - - + +
168A LEU* 4.2 17.7 - - + -
172A HIS* 4.9 5.2 + - - +
262A VAL 5.4 0.2 - - - +
299A PRO* 4.1 18.3 - - + +
300A LEU 3.6 34.1 - - - +
301A LEU* 3.8 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 2.9 19.7 + - - +
127A VAL* 3.3 6.2 + - - +
129A LEU* 1.3 75.3 - - - +
131A ARG* 1.3 62.6 + - + +
132A GLN* 3.2 9.6 + - - +
167A GLU* 2.8 43.0 + - - +
168A LEU* 3.6 8.9 - - - +
171A TYR* 3.4 46.6 - - + +
172A HIS* 3.3 30.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 2.9 43.3 + - + +
128A LYS* 3.9 4.5 - - - +
129A LEU 3.3 0.2 - - - -
130A ASN* 1.3 76.3 - - + +
132A GLN* 1.3 69.8 + - - +
133A GLN* 3.2 39.1 + - + +
171A TYR* 6.3 2.2 - - + -
----------------------------------------------------------
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