Contacts of the helix formed by residues 91 - 100 (chain A) in PDB entry 5NVN
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 VAL 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A HIS* 2.9 37.4 + - + +
56A LEU* 3.7 17.9 - - + +
90A SER* 1.3 71.2 - - - +
92A GLU* 1.3 64.8 + - - +
94A PHE* 3.2 10.5 + - + +
95A TRP* 3.2 36.7 + - - +
54B TYR* 3.8 9.2 - - + -
59B LEU* 3.5 35.7 - - + -
62B CYS* 3.7 28.5 - - + -
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Residues in contact with GLU 92 (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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52A ALA 5.0 1.6 - - - +
53A GLU* 3.1 22.5 - - + +
54A HIS* 2.7 54.0 + - - +
90A SER* 3.2 3.1 - - - +
91A VAL* 1.3 79.3 + - - +
93A GLN* 1.3 63.2 + - - +
95A TRP* 3.1 15.8 + - - +
96A ARG* 3.1 17.5 + - - +
62B CYS* 4.1 16.7 - - - +
65B SER* 4.4 17.0 - - - +
67B VAL* 4.0 21.3 - - + -
68B THR* 3.9 8.0 - - + +
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Residues in contact with GLN 93 (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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53A GLU* 4.5 7.7 + - - +
87A THR 4.8 1.8 + - - +
88A PHE* 3.4 27.6 - - + -
89A ALA 4.5 1.1 - - - +
90A SER* 2.9 23.6 + - - +
92A GLU* 1.3 77.1 - - - +
94A PHE* 1.3 62.3 + - - +
96A ARG* 3.2 23.9 + - - +
97A PHE* 3.2 39.7 + - + -
301A FMT 2.8 36.8 + - - +
67B VAL* 5.4 0.7 - - - +
72B PRO* 4.1 3.2 - - - +
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Residues in contact with PHE 94 (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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56A LEU* 4.9 0.4 - - + -
62A PHE* 3.8 24.0 - + - -
88A PHE* 3.5 34.2 - + + -
90A SER 2.9 11.0 + - - +
91A VAL* 3.3 15.9 - - + +
92A GLU 3.1 0.2 - - - -
93A GLN* 1.3 76.5 - - - +
95A TRP* 1.3 84.7 + + - +
97A PHE* 3.1 4.2 + - - +
98A TYR* 2.8 40.8 + + + +
115A LEU* 4.6 0.7 - - + -
149A GLU* 6.3 0.4 - - + -
152A ILE* 3.8 22.7 - - + -
153A LEU* 3.6 28.3 - - + -
156A LEU* 3.3 29.4 - - + -
59B LEU* 6.4 0.4 - - + -
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Residues in contact with TRP 95 (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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91A VAL* 3.2 35.3 + - + +
92A GLU* 3.1 8.5 + - - +
94A PHE* 1.3 87.9 - + - +
96A ARG* 1.3 52.2 + - - +
98A TYR* 3.6 33.2 - + - -
99A SER* 2.7 42.5 + - - -
149A GLU* 4.9 2.5 - - + -
153A LEU* 3.7 28.3 - - + -
59B LEU* 2.8 33.3 + - - +
60B MET* 3.7 27.4 - - + -
62B CYS 4.2 3.4 - - - -
63B ARG* 3.6 50.9 - - + +
68B THR* 3.7 17.7 - - + -
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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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53A GLU* 5.8 0.8 + - - -
92A GLU 3.1 9.1 + - - +
93A GLN* 3.4 24.2 + - - +
94A PHE 3.2 0.2 - - - -
95A TRP* 1.3 76.7 - - - +
97A PHE* 1.3 60.0 + - - +
99A SER* 3.5 4.2 + - - -
100A HIS* 2.6 31.5 + - - +
301A FMT 2.8 30.2 + - - -
67B VAL* 3.1 36.8 + - - +
68B THR* 3.5 13.2 - - - -
70B THR* 3.0 37.2 + - - +
71B PRO 3.0 20.4 + - - -
72B PRO* 3.8 12.4 - - + +
73B ARG 4.8 0.4 - - - +
197C ARG* 4.6 3.0 - - - +
198C ASP* 2.9 31.1 + - - -
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Residues in contact with PHE 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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62A PHE* 4.0 18.4 - + + -
85A ILE* 3.9 17.5 - - + -
86A GLY* 3.6 26.5 - - - -
87A THR 3.6 20.2 - - - -
88A PHE* 4.1 13.9 - + + -
93A GLN* 3.2 34.3 + - + -
94A PHE 3.1 6.8 + - - +
96A ARG* 1.3 78.2 - - - +
98A TYR* 1.3 64.9 + - - +
100A HIS* 3.2 11.9 + - - +
101A MET* 3.3 20.5 + - - +
72B PRO* 3.6 29.6 - - + -
74B ASP* 3.6 22.9 - - - -
75B LEU* 4.0 18.2 - - + +
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Residues in contact with TYR 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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62A PHE* 4.4 10.5 - + - -
94A PHE* 2.8 36.4 + + + +
95A TRP* 3.6 28.9 - + - +
97A PHE* 1.3 74.0 - - - +
99A SER* 1.3 66.1 + - - +
100A HIS 3.0 1.4 + - - -
101A MET* 3.0 26.6 + - + +
103A ARG* 4.0 24.6 + - + +
104A PRO* 5.6 2.0 - - + +
145A SER 4.4 2.1 + - - -
148A TRP* 4.3 14.7 - + - -
149A GLU* 2.9 42.7 + - + +
152A ILE* 3.8 29.8 - - + -
63B ARG* 4.6 6.7 - - - -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TRP* 2.7 28.0 + - - -
98A TYR* 1.3 78.3 - - - +
100A HIS* 1.3 80.2 + - - +
101A MET 3.5 2.9 + - - +
63B ARG* 5.2 15.3 - - - +
68B THR* 3.8 9.1 + - - -
83B SER* 4.0 4.9 + - - -
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Residues in contact with HIS 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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96A ARG 2.6 26.1 + - - +
97A PHE 3.2 5.9 + - - +
98A TYR 3.0 1.4 + - - -
99A SER* 1.3 96.5 + - - +
101A MET* 1.3 57.8 + - - +
68B THR 3.8 9.0 - - - -
69B LYS 4.5 4.7 + - - -
70B THR* 3.6 10.9 - - - -
71B PRO* 3.4 45.4 - - + +
75B LEU* 3.7 15.7 - - + +
82B THR* 3.3 9.2 - - - -
83B SER* 2.9 46.0 + - - +
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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