Contacts of the helix formed by residues 95 - 113 (chain A) in PDB entry 6H25
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 GLN 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 4.9 9.5 - - + +
89A ALA* 3.6 13.7 - - - +
90A PHE* 3.6 40.8 - - + -
91A GLU 4.0 4.6 + - - +
93A GLY* 4.6 1.3 - - - +
94A ARG* 1.3 105.2 + - - +
96A SER* 1.3 62.5 + - - +
97A ASP* 3.4 3.3 - - - +
98A LEU* 4.6 16.8 - - + +
99A LEU* 3.3 21.8 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.6 19.6 + - - -
94A ARG 3.3 5.4 + - - -
95A GLN* 1.3 74.4 - - - +
97A ASP* 1.3 67.1 + - - +
99A LEU* 3.4 8.8 + - - +
100A VAL* 3.0 38.4 + - - +
97B CYS* 6.5 1.1 - - - -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN* 3.4 0.8 - - - +
96A SER* 1.3 83.5 - - - +
98A LEU* 1.3 59.2 + - - +
100A VAL 3.4 1.2 + - - -
101A LYS* 2.9 29.4 + - - +
101B LEU* 3.8 33.0 - - + +
104B ARG* 3.6 24.8 + - - -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 21.5 - - + -
90A PHE* 4.5 13.5 - - + -
95A GLN* 4.3 20.8 + - + +
97A ASP* 1.3 77.8 - - - +
99A LEU* 1.3 57.2 + - - +
101A LYS* 4.3 15.0 - - + +
102A LEU* 3.0 66.6 + - + +
141A HIS* 6.2 0.2 - - + -
145A ILE* 4.7 13.0 - - + -
146A ILE* 6.3 0.2 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.3 26.7 - - + +
81A GLU* 4.6 1.8 - - - -
82A LEU* 4.2 29.8 - - + +
95A GLN 3.3 20.8 + - - +
96A SER* 3.4 10.3 + - - +
97A ASP 3.2 0.2 - - - -
98A LEU* 1.3 80.8 - - - +
100A VAL* 1.3 60.1 + - + +
102A LEU* 4.0 3.6 - - + +
103A ASN* 2.9 37.0 + - + +
94B ARG* 5.8 4.9 - - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 3.0 21.0 + - - +
97A ASP* 4.0 2.9 - - - +
99A LEU* 1.3 78.3 - - + +
101A LYS* 1.3 58.4 + - - +
103A ASN* 4.3 5.2 - - - +
104A ARG* 3.0 31.7 + - + +
94B ARG* 4.0 24.2 - - + +
97B CYS* 3.7 37.2 - - + -
98B GLU* 3.8 20.9 - - + +
101B LEU* 4.9 5.4 - - + -
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP 2.9 18.2 + - - +
98A LEU* 3.9 18.8 - - + +
99A LEU 3.3 0.4 - - - -
100A VAL* 1.3 79.2 - - - +
102A LEU* 1.3 64.2 + - + +
104A ARG* 5.0 2.1 - - - +
105A LEU* 3.5 22.7 + - + +
146A ILE* 4.2 16.0 - - - +
220A LEU* 3.4 32.9 - - - +
222A VAL* 5.1 3.0 - - - +
235A GLN* 4.6 23.9 + - - +
237A SER* 3.5 25.5 + - - -
98B GLU* 5.9 4.7 - - - -
101B LEU* 5.2 7.6 - - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.7 21.1 - - + +
82A LEU* 4.4 9.4 - - + -
98A LEU* 3.0 50.0 + - + +
99A LEU* 4.0 4.5 - - + +
101A LYS* 1.3 82.4 - - + +
103A ASN* 1.3 64.4 + - - +
105A LEU* 3.3 4.5 + - - +
106A MET* 3.0 24.8 + - - +
145A ILE* 3.7 33.9 - - + -
146A ILE* 3.6 38.8 - - + +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.4 13.0 + - - +
79A ASN* 5.2 2.4 + - - -
80A LEU* 4.4 29.7 + - - +
99A LEU* 2.9 22.5 + - + +
100A VAL* 3.9 5.6 - - - +
102A LEU* 1.3 78.2 - - - +
104A ARG* 1.3 58.2 + - - +
106A MET* 3.5 5.5 + - - +
107A GLU* 3.0 29.4 + - - +
94B ARG* 2.1 61.0 + - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.0 19.5 + - + +
101A LYS* 5.0 0.9 - - - +
103A ASN* 1.3 77.4 - - - +
105A LEU* 1.3 57.5 + - - +
107A GLU* 3.4 31.0 + - - +
108A ARG* 2.9 52.3 + - + +
111A ARG* 5.5 2.4 - - - +
112A ASN* 5.8 1.2 + - - -
94B ARG* 4.9 15.5 - - + +
95B LYS* 2.9 48.9 - - - +
98B GLU* 3.2 46.7 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LYS* 3.5 23.2 + - - +
102A LEU 3.3 4.0 + - - +
103A ASN 3.3 0.6 - - - -
104A ARG* 1.3 79.8 - - - +
106A MET* 1.3 64.3 + - - +
108A ARG* 3.4 12.6 + - + +
109A CYS* 3.0 48.1 + - - -
146A ILE* 3.7 37.0 - - + -
193A CYS* 5.3 0.9 - - - -
222A VAL* 3.9 23.8 - - + -
233A THR* 4.3 7.0 - - - +
235A GLN* 3.3 33.1 + - + +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.7 40.4 - - + -
79A ASN 5.3 1.3 - - - +
80A LEU* 4.4 22.2 - - + -
102A LEU 3.0 16.9 + - - +
103A ASN* 3.8 5.2 - - - +
105A LEU* 1.3 77.6 - - - +
107A GLU* 1.3 62.1 + - - +
109A CYS* 3.4 4.6 + - - +
110A LEU* 3.0 29.6 + - + +
134A VAL* 3.8 18.6 - - + -
136A LEU* 3.7 33.9 - - + -
149A ALA* 5.3 6.3 - - + +
150A SER* 6.3 1.3 - - - -
153A ALA* 4.0 12.1 - - + -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.7 21.3 - - + -
103A ASN* 3.0 18.4 + - - +
104A ARG* 3.7 28.4 + - - +
105A LEU 3.3 0.2 - - - -
106A MET* 1.3 78.0 - - - +
108A ARG* 1.3 57.2 + - + +
111A ARG* 2.8 82.0 + - + +
94B ARG* 4.1 25.4 + - - -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 2.9 51.4 + - - +
105A LEU* 4.0 10.0 - - + +
107A GLU* 1.3 75.9 - - - +
109A CYS* 1.3 64.1 + - - +
112A ASN* 2.9 39.2 + - - +
113A SER 3.8 0.7 + - - -
233A THR* 4.4 7.0 - - + +
234A ILE 4.6 3.2 + - - -
235A GLN* 2.9 43.6 + - - +
98B GLU* 3.9 13.0 + - - -
200B GLU* 2.3 29.8 + - - -
201B MET 4.8 1.2 - - - +
202B ASP* 2.9 45.1 + - - +
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Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.0 37.0 + - - +
106A MET* 3.8 4.9 - - - +
108A ARG* 1.3 74.7 - - - +
110A LEU* 1.3 68.9 + - + +
113A SER* 2.7 38.3 + - - -
191A PRO* 5.6 2.2 - - + -
193A CYS* 3.9 24.7 - - - -
224A ALA* 4.1 4.7 - - + -
232A CYS* 5.7 1.8 - - + -
233A THR* 2.7 38.4 - - - -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 4.1 6.8 - - - +
78A PHE* 3.5 33.6 - - + -
106A MET* 3.0 18.3 + - + +
107A GLU 3.9 0.2 - - - -
109A CYS* 1.3 82.5 - - + +
111A ARG* 1.3 59.2 + - - +
113A SER 4.6 0.4 - - - -
115A CYS* 3.3 29.2 + - - -
150A SER* 5.1 9.4 - - - +
153A ALA* 3.7 30.5 - - + -
154A ILE* 3.7 21.3 - - + -
157A LEU* 6.1 3.4 - - + -
191A PRO* 3.7 32.5 - - + +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 6.0 0.4 - - - +
76A LEU* 3.5 34.4 + - + +
77A PHE* 5.2 5.9 - - - +
78A PHE* 5.2 6.6 - - + +
104A ARG* 5.5 2.4 - - - +
107A GLU* 2.8 54.7 + - + +
110A LEU* 1.3 78.8 - - - +
112A ASN* 1.3 73.8 + - - +
113A SER 3.1 4.3 - - - -
114A LYS* 3.1 27.5 + - - +
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Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 5.8 1.2 + - - -
108A ARG* 2.9 35.1 + - - +
111A ARG* 1.3 86.7 - - - +
113A SER* 1.3 62.5 + - - +
114A LYS* 3.2 10.1 + - - +
202B ASP* 4.8 19.7 - - + +
203B ALA* 4.3 13.7 - - - +
204B ARG* 5.6 0.9 - - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG 3.8 0.6 + - - -
109A CYS* 2.7 24.6 + - - -
111A ARG 3.1 0.2 - - - -
112A ASN* 1.3 78.9 - - - +
114A LYS* 1.3 67.5 + - - +
115A CYS* 4.4 4.7 - - - -
189A HIS* 3.3 19.6 + - - -
191A PRO* 3.9 8.7 - - - +
232A CYS* 3.0 36.8 - - - -
233A THR* 5.8 1.5 - - - +
203B ALA 4.3 8.5 - - - -
204B ARG* 4.3 12.2 - - - +
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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
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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) + - + + + + + -
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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