Contacts of the helix formed by residues 66 - 81 (chain B) in PDB entry 1NMS
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS* 5.9 1.0 - - - +
64B ARG 3.3 0.2 + - - -
65B SER* 1.3 72.6 - - - +
67B THR* 1.3 64.0 + - - +
68B ASP* 3.2 4.1 - - - +
69B VAL* 3.1 24.3 + - - +
70B ASP 3.3 6.8 + - - -
207B ARG* 4.6 2.5 - - - -
208B ASN 3.6 9.6 - - - -
209B SER 3.4 18.6 + - - -
212B GLY* 3.5 12.9 - - - -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 2.6 27.3 + - - +
53B LYS* 3.7 29.2 - - + -
64B ARG* 3.0 51.8 + - - +
65B SER 3.3 0.8 + - - -
66B GLY* 1.3 77.9 - - - +
68B ASP* 1.3 62.8 + - - +
70B ASP* 3.1 9.8 + - - +
71B ALA* 2.9 27.4 + - - +
119B LEU* 3.7 10.2 - - - +
207B ARG* 4.3 3.7 - - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 3.0 22.4 + - - -
53B LYS* 2.9 34.9 + - - +
66B GLY 3.2 2.4 - - - +
67B THR* 1.3 80.6 - - - +
69B VAL* 1.3 61.8 + - + +
71B ALA* 3.8 6.0 - - - +
72B ALA* 3.0 30.3 + - - +
89B ASN* 5.0 0.5 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY* 3.1 16.9 + - - +
68B ASP* 1.3 76.9 - - + +
70B ASP* 1.3 63.4 + - - +
72B ALA* 4.0 4.4 - - - +
73B ASN* 3.0 29.0 + - + +
209B SER 5.3 0.9 - - - +
210B LYS 3.8 20.0 - - - +
211B ASP* 3.6 23.6 - - - +
212B GLY 4.3 2.9 - - - +
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 5.1 2.4 + - - -
66B GLY 3.3 3.4 + - - -
67B THR* 3.1 15.1 + - - +
69B VAL* 1.3 79.9 - - - +
71B ALA* 1.3 57.1 - - - +
73B ASN* 3.1 4.8 + - - +
74B LEU* 2.8 36.7 + - - +
119B LEU* 4.1 13.6 - - + +
161B GLN* 4.3 5.0 - - - +
207B ARG* 5.3 0.9 - - - -
211B ASP 4.5 1.2 - - - +
212B GLY* 3.4 7.1 - - - -
213B SER* 2.7 47.7 + - - +
216B ILE* 3.4 30.4 - - + +
217B GLN* 4.3 2.6 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.5 2.0 - - + -
51B ASN* 3.7 27.1 - - + +
67B THR 2.9 16.6 + - - +
68B ASP* 3.8 5.6 - - - +
70B ASP* 1.3 75.8 - - - +
72B ALA* 1.3 58.4 + - - +
74B LEU* 3.4 5.4 + - - +
75B ARG* 2.9 28.4 + - - +
87B ASN* 3.9 22.5 + - - +
89B ASN* 5.5 0.4 - - - +
119B LEU* 4.1 10.5 - - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP 3.0 18.6 + - - +
69B VAL* 4.0 4.3 - - - +
71B ALA* 1.3 75.6 - - - +
73B ASN* 1.3 64.0 + - - +
75B ARG* 3.3 9.8 + - - +
76B GLU* 3.1 24.1 + - - +
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Residues in contact with ASN 73 (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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69B VAL* 3.0 24.2 + - + +
70B ASP* 3.5 7.5 + - - +
72B ALA* 1.3 75.3 - - - +
74B LEU* 1.3 59.6 + - - +
76B GLU* 3.4 5.2 + - - +
77B THR* 2.8 36.0 + - - -
216B ILE* 4.3 1.4 + - + +
217B GLN* 4.1 22.8 + - - +
220B CYS* 3.4 32.0 - - - +
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Residues in contact with LEU 74 (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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49B ILE* 3.7 16.4 - - + -
70B ASP 2.8 24.6 + - - +
71B ALA* 3.7 4.7 - - - +
73B ASN* 1.3 76.1 - - - +
75B ARG* 1.3 66.8 + - - +
77B THR* 4.3 0.9 - - - -
78B PHE* 3.0 51.2 + - + +
117B VAL* 3.7 31.6 - - + -
119B LEU* 4.2 12.1 - - + -
216B ILE* 3.6 31.2 - - + -
219B LEU* 4.5 8.7 - - + -
220B CYS* 3.8 16.8 - - - -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.8 8.0 - - - +
71B ALA 2.9 18.5 + - - +
72B ALA* 3.6 9.2 - - - +
73B ASN 3.3 0.2 - - - -
74B LEU* 1.3 77.1 - - - +
76B GLU* 1.3 58.8 + - - +
79B ARG* 2.9 33.8 + - + +
85B VAL* 3.9 28.1 + - + +
86B ARG* 4.9 0.2 - - - +
87B ASN* 2.8 54.8 + - - +
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Residues in contact with GLU 76 (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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72B ALA 3.1 13.4 + - - +
73B ASN* 3.9 5.2 - - - +
75B ARG* 1.3 79.6 - - - +
77B THR* 1.3 65.3 + - - +
79B ARG* 2.9 46.9 + - - +
80B ASN* 3.0 39.4 + - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 2.8 23.8 + - - -
74B LEU* 3.7 3.8 - - - -
76B GLU* 1.3 78.5 - - - +
78B PHE* 1.3 64.9 + - + +
80B ASN* 3.3 9.5 + - - +
81B LEU* 3.2 24.3 + - + +
220B CYS* 3.4 31.5 + - - +
223B LEU* 3.8 40.6 - - + -
224B LYS* 4.8 5.6 - - + +
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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
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47B CYS* 3.7 27.6 - - + -
74B LEU* 3.0 46.4 + - + +
77B THR* 1.3 77.5 - - + +
79B ARG* 1.3 66.6 + - - +
80B ASN 3.2 0.2 - - - -
81B LEU* 3.1 22.4 + - + +
82B LYS 3.2 0.2 + - - -
83B TYR* 3.0 51.3 + + + +
85B VAL* 3.9 8.5 - - + -
115B VAL* 4.1 20.2 - - + -
117B VAL* 4.9 0.7 - - + -
157B LEU* 5.7 1.6 - - + -
159B ILE* 3.8 26.2 - - + -
223B LEU* 3.9 24.2 - - + -
232B PHE* 6.3 1.8 - + - -
275B PHE* 5.2 7.4 - + - -
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Residues in contact with ARG 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 ARG* 2.9 23.6 + - + +
76B GLU* 2.9 43.2 + - - +
78B PHE* 1.3 76.2 - - - +
80B ASN* 1.3 74.7 + - - +
82B LYS* 2.9 26.9 + - - +
83B TYR 4.1 11.2 - - - +
85B VAL* 4.0 4.6 - - + +
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Residues in contact with ASN 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 GLU* 3.0 43.6 + - - +
77B THR* 3.6 8.1 - - - +
78B PHE 3.2 0.2 - - - -
79B ARG* 1.3 99.2 + - - +
81B LEU* 1.3 63.5 + - + +
82B LYS* 3.2 20.8 + - - +
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Residues in contact with LEU 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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44B MET* 3.4 18.2 - - + +
77B THR* 3.2 16.9 + - + +
78B PHE* 3.1 32.3 + - + +
80B ASN* 1.3 76.9 - - + +
82B LYS* 1.3 73.6 + - - +
83B TYR* 3.6 12.6 + - + -
223B LEU* 4.4 25.8 - - + +
227B ALA* 3.6 26.2 - - + -
275B PHE* 4.1 27.6 - - + +
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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