Contacts of the helix formed by residues 95 - 109 (chain A) in PDB entry 5NS3
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 ARG 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.2 23.6 + - - +
36A LYS* 3.7 30.8 - - + +
66A GLN* 4.9 1.0 + - - -
93A THR* 3.8 16.7 + - + +
94A LEU* 1.3 79.5 - - - +
96A ARG* 1.3 82.1 + - + +
97A ASP 3.4 0.9 + - - -
98A ARG* 3.6 11.8 + - - +
99A MET* 3.3 11.5 + - - -
43D C 2.8 50.6 + - - +
45D A 3.1 54.5 + - - +
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Residues in contact with ARG 96 (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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8A LYS* 6.5 0.2 - - - +
35A GLU 4.9 1.0 + - - -
95A ARG* 1.3 77.6 - - + +
97A ASP* 1.3 71.0 + - - +
99A MET* 3.0 23.0 + - - +
100A TRP* 3.2 19.5 + - - +
33D G 3.0 54.6 + - - -
34D A 5.0 10.5 - - - -
44D G 3.7 13.3 + - - -
45D A 2.7 44.1 + - - +
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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
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5A VAL* 5.3 10.7 - - - +
8A LYS* 3.0 39.1 + - - +
96A ARG* 1.3 83.2 - - - +
98A ARG* 1.3 57.4 + - - +
100A TRP* 3.1 6.1 + - - +
101A ILE* 2.9 46.7 + - + +
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Residues in contact with ARG 98 (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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64A THR 3.8 16.6 - - - +
65A GLY* 3.3 28.7 + - - -
66A GLN* 3.0 25.2 + - - +
94A LEU* 4.0 11.2 - - + +
95A ARG 3.6 10.6 + - - +
96A ARG 3.3 0.2 - - - -
97A ASP* 1.3 74.4 - - - +
99A MET* 1.3 65.3 + - - +
101A ILE* 4.2 9.1 - - + +
102A PHE* 3.1 25.3 + - - +
43D C 3.2 19.8 + - - -
44D G 3.0 27.3 + - - -
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Residues in contact with MET 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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34A LEU* 3.7 34.3 - - + +
35A GLU 3.8 5.2 - - - +
36A LYS* 3.6 35.2 - - - -
37A VAL* 3.6 21.8 - - + -
94A LEU* 3.6 18.7 - - - +
95A ARG* 3.3 12.7 + - - -
96A ARG* 3.0 21.6 + - - +
98A ARG* 1.3 79.8 - - - +
100A TRP* 1.3 83.6 + - + +
102A PHE* 3.4 2.9 + - - +
103A LEU* 3.0 34.9 + - + +
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Residues in contact with TRP 100 (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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5A VAL* 4.5 11.2 - - - +
7A LEU* 3.9 30.2 - - + +
8A LYS* 3.6 56.1 - - + +
11A TYR* 3.7 33.4 - + + -
12A TYR* 5.4 3.1 + + - -
33A ARG* 6.4 0.4 - - + -
34A LEU* 3.7 39.0 - - + -
96A ARG* 3.2 28.1 + - - +
97A ASP* 3.1 8.3 + - - +
99A MET* 1.3 93.8 - - + +
101A ILE* 1.3 65.7 + - - +
103A LEU* 3.4 3.9 + - + +
104A GLU* 3.0 25.1 + - - +
176A LEU* 4.1 15.3 - - + -
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Residues in contact with ILE 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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5A VAL* 4.4 24.9 - - + +
97A ASP* 2.9 34.0 + - + +
98A ARG* 4.2 9.0 - - + +
100A TRP* 1.3 78.1 - - + +
102A PHE* 1.3 62.5 + - - +
104A GLU* 3.4 11.2 + - - +
105A LYS* 3.2 51.7 + - - +
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Residues in contact with PHE 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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37A VAL* 4.1 17.3 - - + -
39A ILE* 3.2 30.3 - - + -
63A ILE* 3.9 36.8 - - + +
64A THR* 4.6 5.4 - - + +
94A LEU* 3.7 22.4 - - + -
98A ARG 3.1 19.6 + - - +
99A MET 3.8 3.1 - - - +
101A ILE* 1.3 78.0 - - - +
103A LEU* 1.3 63.1 + - + +
105A LYS* 3.2 12.9 + - + +
106A LEU* 2.9 49.6 + - + +
155A MET* 4.6 7.4 - - + -
157A ILE* 4.5 17.7 - - + -
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Residues in contact with LEU 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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7A LEU* 3.6 21.5 - - + -
34A LEU* 3.3 35.2 - - + -
37A VAL* 4.3 22.2 - - + -
99A MET* 3.0 21.6 + - + +
100A TRP* 3.8 4.0 - - + +
101A ILE 3.4 0.2 - - - -
102A PHE* 1.3 82.7 - - + +
104A GLU* 1.3 56.3 + - - +
106A LEU* 3.1 19.4 + - + +
107A LEU* 2.9 36.7 + - + +
157A ILE* 6.2 0.2 - - + -
159A VAL* 4.9 5.8 - - + -
176A LEU* 5.5 0.2 - - + -
178A PHE* 3.8 31.2 - - + -
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Residues in contact with GLU 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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5A VAL* 3.6 16.3 + - - +
6A ALA* 2.9 34.5 + - - +
7A LEU* 3.1 27.1 + - + +
100A TRP 3.0 16.0 + - - +
101A ILE* 3.6 8.8 - - - +
102A PHE 3.2 0.2 - - - -
103A LEU* 1.3 75.5 - - - +
105A LYS* 1.3 58.9 + - + +
107A LEU* 4.9 2.5 - - - -
108A ASN* 2.9 57.9 + - - +
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Residues in contact with LYS 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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62A LEU 5.2 5.3 + - - -
63A ILE* 4.5 24.2 + - + +
64A THR 6.1 1.4 - - - -
101A ILE* 3.2 35.7 + - + +
102A PHE* 3.4 12.7 - - + +
104A GLU* 1.3 74.2 - - + +
106A LEU* 1.3 59.9 + - - +
109A VAL* 2.9 41.9 + - + +
110A ALA* 3.1 9.9 + - - +
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Residues in contact with LEU 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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102A PHE* 2.9 34.9 + - + +
103A LEU* 3.1 27.3 + - + +
105A LYS* 1.3 74.7 - - - +
107A LEU* 1.3 65.2 + - + +
110A ALA* 3.5 16.8 + - + -
111A LEU* 3.0 54.3 + - + +
120A LEU* 6.4 0.2 - - + -
133A LEU* 4.7 14.8 - - + -
135A LEU* 4.3 22.0 - - + -
157A ILE* 4.6 14.4 - - + -
178A PHE* 5.3 5.4 - - + -
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Residues in contact with LEU 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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7A LEU* 4.0 22.4 - - + -
103A LEU* 2.9 19.9 + - + +
104A GLU* 4.2 2.0 - - - +
106A LEU* 1.3 82.8 - - + +
108A ASN* 1.3 66.2 + - - +
111A LEU* 4.3 18.9 - - + +
112A PRO* 3.3 22.5 - - - +
176A LEU* 4.0 14.6 - - + +
177A GLY 4.3 10.8 - - - +
178A PHE* 3.8 57.9 - - + -
179A PRO* 4.4 4.5 - - + +
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Residues in contact with ASN 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 GLU* 2.9 44.2 + - - +
107A LEU* 1.3 84.9 - - - +
109A VAL* 1.3 67.3 + - + +
112A PRO* 3.8 9.2 - - - +
113A ARG* 3.7 9.2 + - - -
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Residues in contact with VAL 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 LYS* 2.9 27.8 + - + +
107A LEU 3.6 0.2 - - - -
108A ASN* 1.3 89.2 - - + +
110A ALA* 1.3 65.9 + - + +
111A LEU 3.6 0.9 - - - -
112A PRO* 3.5 4.7 - - - +
113A ARG* 2.7 46.6 + - - +
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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
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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