Contacts of the helix formed by residues 74 - 92 (chain B) in PDB entry 2NS7
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 SER 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLY 3.6 3.0 + - - -
73B GLU* 1.3 78.6 - - - +
75B TRP* 1.3 60.0 + - - +
76B GLN* 3.4 17.7 + - - +
77B ASP* 3.0 33.7 + - - +
78B PHE* 2.9 26.7 + - - +
119B PHE* 4.2 0.2 - - - -
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Residues in contact with TRP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU 3.8 0.4 + - - -
74B SER* 1.3 74.1 - - - +
76B GLN* 1.3 100.5 + - + +
78B PHE* 3.7 1.6 - - - +
79B LEU* 3.1 48.9 + - + +
119B PHE* 3.7 13.4 - - + -
120B LEU* 3.8 13.2 - - + -
123B GLN* 3.7 46.6 + - + +
125B PHE* 3.8 26.6 - + - -
194B ILE* 3.7 13.5 - - + -
197B PHE* 3.7 28.5 - + + -
198B GLU* 3.8 16.8 - - + -
201B LEU* 4.8 5.8 - - + +
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 3.4 18.9 - - - +
75B TRP* 1.3 113.9 + - + +
77B ASP* 1.3 65.3 + - - +
79B LEU* 3.4 4.2 + - - +
80B ARG* 3.1 44.7 + - - +
194B ILE* 3.6 25.6 - - + +
198B GLU* 3.4 29.2 + - - +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.4 22.3 - - + +
74B SER* 3.0 25.6 + - - +
76B GLN* 1.3 74.3 - - - +
78B PHE* 1.3 67.0 + - - +
80B ARG* 2.6 36.4 + - - +
81B ASN* 3.0 32.8 + - - +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B HIS* 3.9 12.8 - + - -
67B PHE 3.5 28.7 - - - -
68B SER 3.5 3.1 - - - -
69B PRO* 3.5 33.0 - - + -
73B GLU* 3.4 17.1 - - - +
74B SER 2.9 16.6 + - - +
75B TRP 3.7 4.7 - - - +
77B ASP* 1.3 75.8 - - - +
79B LEU* 1.3 77.6 + - + +
81B ASN* 3.8 0.7 - - - +
82B ASN* 2.8 47.6 + - + +
116B GLN* 3.8 21.8 - - + -
119B PHE* 3.9 23.3 - + + -
120B LEU* 4.9 3.8 - - + -
134B LEU* 4.2 12.3 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TRP* 3.1 44.2 + - + +
76B GLN 3.6 5.2 - - - +
78B PHE* 1.3 95.6 - - + +
80B ARG* 1.3 65.7 + - - +
82B ASN* 3.7 5.5 - - - +
83B ALA* 3.1 25.6 + - - +
120B LEU* 4.6 10.5 - - + -
125B PHE* 5.2 0.4 - - + -
133B ALA* 4.9 5.2 - - + -
134B LEU* 3.8 25.6 - - + +
137B VAL* 4.2 22.5 - - + +
190B LEU* 4.9 0.9 - - - -
194B ILE* 4.1 11.2 - - + -
197B PHE* 3.9 21.3 - - + -
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLN* 3.1 26.8 + - - +
77B ASP* 2.6 50.8 + - - +
79B LEU* 1.3 75.3 - - - +
81B ASN* 1.3 65.3 + - - +
83B ALA* 3.4 2.6 + - - +
84B LYS* 3.0 48.9 + - - +
190B LEU* 3.7 9.3 - - + +
191B GLU* 2.6 37.8 + - - +
194B ILE* 3.3 29.3 - - + +
198B GLU* 5.5 2.0 + - - -
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B HIS* 3.6 29.3 - - + +
70B LEU* 5.6 1.0 - - - +
73B GLU* 3.0 22.8 + - - -
77B ASP* 3.0 18.1 + - - +
80B ARG* 1.3 81.9 - - - +
82B ASN* 1.3 64.5 + - - +
84B LYS* 3.9 19.5 + - - +
85B SER* 3.0 25.8 + - - -
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.3 30.3 + - - -
66B HIS* 2.9 29.2 + - - +
67B PHE* 3.6 10.3 + - - +
78B PHE* 2.8 37.5 + - + +
79B LEU* 3.7 6.8 - - - +
81B ASN* 1.3 76.7 - - - +
83B ALA* 1.3 57.3 + - - +
85B SER 3.2 1.4 + - - -
86B PHE* 2.9 27.7 + - - +
116B GLN* 4.2 9.9 + - - +
134B LEU* 5.1 5.7 - - - +
137B VAL* 5.3 5.5 - - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 3.1 18.4 + - - +
80B ARG 3.7 3.8 - - - +
82B ASN* 1.3 74.0 + - - +
84B LYS* 1.3 61.6 + - - +
86B PHE* 3.3 7.0 + - - +
87B ARG* 2.9 28.8 + - - +
137B VAL* 3.6 24.5 - - + -
141B THR* 3.8 15.9 - - - +
186B PHE* 4.0 2.9 - - + -
190B LEU* 3.7 18.6 - - + -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.0 37.2 + - - +
81B ASN* 3.9 20.8 + - - +
83B ALA* 1.3 75.6 - - - +
85B SER* 1.3 57.6 + - - +
87B ARG* 3.4 7.9 + - - +
88B ASN* 2.9 40.9 + - - +
186B PHE* 4.3 16.2 - - + -
187B LEU* 3.7 26.8 - - + +
190B LEU* 4.5 3.6 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS 3.3 9.2 - - - +
64B HIS* 2.5 26.1 + - - -
65B THR* 2.8 25.5 + - - -
66B HIS* 3.0 15.3 + - - -
81B ASN 3.0 19.2 + - - -
82B ASN 3.5 3.4 - - - -
84B LYS* 1.3 76.5 - - - +
86B PHE* 1.3 63.4 + - - +
88B ASN* 3.3 10.0 + - - +
89B ALA* 3.1 17.7 + - - +
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 6.1 0.2 - - - -
60B LEU* 4.0 18.4 - - + -
64B HIS* 3.3 18.1 + + + +
82B ASN* 2.9 17.5 + - - +
83B ALA* 3.6 6.3 - - - +
85B SER* 1.3 76.7 - - - +
87B ARG* 1.3 61.9 + - - +
89B ALA* 3.2 5.1 + - - +
90B LEU* 3.0 55.8 + - + +
100B HIS* 3.5 41.5 - + - -
138B GLY* 4.0 26.5 - - - -
141B THR* 3.7 22.4 - - + -
142B LEU* 4.3 4.9 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 2.9 17.6 + - - +
84B LYS* 3.5 7.0 - - - +
85B SER 3.3 0.2 - - - -
86B PHE* 1.3 76.9 - - - +
88B ASN* 1.3 68.8 + - - +
90B LEU* 3.0 4.0 + - - +
91B LEU* 2.9 43.7 + - + +
141B THR* 3.8 13.4 - - + +
144B SER* 5.7 1.4 - - - -
145B VAL* 3.8 20.2 - - + +
148B ASP* 3.8 18.8 + - - -
182B ALA* 4.2 5.5 + - - +
183B GLU* 3.6 50.0 + - - +
186B PHE* 3.5 38.2 - - + +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS* 4.3 10.2 - - + +
84B LYS* 2.9 35.1 + - - +
85B SER* 3.7 9.0 - - - +
87B ARG* 1.3 81.1 + - - +
89B ALA* 1.3 62.8 + - - +
91B LEU* 3.4 8.7 + - - +
92B SER* 3.0 23.2 + - - -
58C GLU* 5.9 0.2 + - - -
62C ARG* 4.9 33.0 + - + +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 2.9 25.7 - - + +
60B LEU* 4.2 13.5 - - + -
63B HIS* 3.7 29.7 + - - +
64B HIS* 4.2 10.1 - - + -
85B SER 3.1 9.7 + - - +
86B PHE* 3.4 9.2 - - + +
88B ASN* 1.3 77.4 - - - +
90B LEU* 1.3 59.7 + - + +
92B SER* 2.8 22.5 + - - -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 4.1 4.5 - - + -
60B LEU* 5.5 2.0 - - + -
86B PHE* 3.0 55.3 + - + +
87B ARG 3.0 7.6 + - - +
89B ALA* 1.3 77.4 - - + +
91B LEU* 1.3 60.1 + - - +
92B SER 3.5 0.3 + - - -
93B HIS 3.5 1.4 - - - +
96B GLY* 3.2 25.1 - - - +
97B ALA* 4.0 5.2 - - + +
100B HIS* 3.7 30.5 - - + +
141B THR* 4.6 0.9 - - + +
142B LEU* 4.0 19.1 - - + -
145B VAL* 3.8 29.6 - - + -
149B GLN* 2.9 17.2 + - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 2.9 57.2 + - + +
88B ASN* 3.7 8.3 - - - +
90B LEU* 1.3 75.2 - - - +
92B SER* 1.3 62.1 + - - +
93B HIS* 3.2 8.0 + - - +
145B VAL* 3.6 23.1 - - + -
148B ASP* 3.5 20.0 - - - +
149B GLN* 3.6 8.6 + - + +
152B GLN* 3.9 16.2 - - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASN* 5.0 2.1 + - - -
59B MET* 3.3 2.9 - - - +
63B HIS* 3.2 39.3 - - - -
88B ASN 3.0 11.3 + - - -
89B ALA 2.8 20.0 + - - -
91B LEU* 1.3 77.4 - - - +
93B HIS* 1.3 81.7 + - - +
63C HIS* 5.9 0.7 - - - -
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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