Contacts of the helix formed by residues 65 - 75 (chain B) in PDB entry 1JVN
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 PHE 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.3 21.8 - - + -
8B ASP 5.2 1.1 - - - -
9B VAL* 5.5 0.7 - - + -
31B VAL* 3.6 26.7 - - + -
32B LYS 3.6 17.0 - - - -
33B SER* 3.4 28.7 - - - -
34B PRO* 3.7 19.1 - - + -
37B PHE* 4.1 13.0 - + - -
60B LEU* 3.3 49.9 + - + +
61B PHE* 4.2 0.8 + - - -
63B ARG* 3.7 20.6 - - + -
64B GLY* 1.3 74.4 - - - +
66B GLU* 1.3 66.3 + - - +
68B PRO* 3.0 6.6 - - + +
69B ILE* 2.9 31.7 + - + +
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Residues in contact with GLU 66 (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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61B PHE* 3.4 51.5 - - + +
64B GLY 3.5 2.2 - - - -
65B PHE* 1.3 76.6 - - - +
67B LYS* 1.3 69.9 + - + +
69B ILE* 3.2 4.4 + - - +
70B ARG* 3.0 60.3 + - - +
100B THR* 5.7 0.9 - - - +
101B GLY 5.2 0.9 - - - +
102B LEU* 4.0 11.1 - - + +
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Residues in contact with LYS 67 (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 GLY 4.6 0.6 + - - +
66B GLU* 1.3 82.3 - - + +
68B PRO* 1.3 73.6 - - + +
70B ARG* 3.2 8.6 + - - +
71B GLU* 2.9 39.3 + - + +
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Residues in contact with PRO 68 (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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34B PRO* 4.1 14.6 - - + -
37B PHE* 3.9 27.6 - - + -
39B ILE* 4.0 5.7 - - + +
64B GLY 3.1 24.0 - - - +
65B PHE* 3.0 16.6 - - + +
67B LYS* 1.3 96.2 - - + +
69B ILE* 1.3 62.2 + - - +
71B GLU* 3.0 11.9 + - + +
72B TYR* 2.8 24.9 + - - +
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Residues in contact with ILE 69 (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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7B ILE* 3.9 30.1 - - + -
37B PHE* 5.5 1.6 - - + -
45B LEU* 5.0 5.2 - - + -
47B LEU* 4.2 11.4 - - + -
60B LEU* 4.1 20.9 - - + -
61B PHE* 5.6 0.4 - - + -
65B PHE* 2.9 40.3 + - + +
66B GLU* 3.7 4.5 - - - +
68B PRO* 1.3 72.6 - - - +
70B ARG* 1.3 58.1 + - - +
72B TYR* 3.4 6.2 + - - +
73B ILE* 2.9 46.6 + - + +
79B ILE* 4.2 12.3 - - + -
89B LEU* 6.2 0.2 - - + -
102B LEU* 3.9 21.5 - - + -
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Residues in contact with ARG 70 (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 GLU* 3.0 46.6 + - - +
67B LYS* 3.6 10.8 - - - +
69B ILE* 1.3 75.2 - - - +
71B GLU* 1.3 57.0 + - + +
73B ILE* 3.2 3.5 + - - +
74B GLU* 2.8 42.7 + - - +
101B GLY 4.1 3.6 + - - -
102B LEU* 2.8 50.6 + - + +
103B ASN* 5.1 1.0 - - - +
104B TYR* 3.5 31.0 + - + +
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Residues in contact with GLU 71 (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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39B ILE* 3.9 23.8 - - + +
67B LYS* 2.9 30.4 + - + +
68B PRO* 3.4 10.8 - - - +
70B ARG* 1.3 74.1 - - + +
72B TYR* 1.3 64.7 + - - +
74B GLU* 3.1 18.5 + - - +
75B SER* 3.0 22.0 + - - -
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Residues in contact with TYR 72 (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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37B PHE* 5.0 4.0 - + + -
39B ILE* 3.5 22.6 - - + +
42B THR* 3.4 38.8 - - + -
43B SER 3.0 24.1 + - - -
44B ARG 3.5 0.9 + - - -
45B LEU* 3.5 34.5 - - + -
68B PRO 2.8 16.1 + - - +
69B ILE 3.7 4.0 - - - +
71B GLU* 1.3 76.4 - - - +
73B ILE* 1.3 63.9 + - - +
75B SER* 2.5 28.5 + - - -
76B GLY 3.6 2.1 + - - -
77B LYS* 3.3 31.9 + - + +
78B PRO 2.6 32.3 + - - -
79B ILE* 3.9 10.3 - - + -
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Residues in contact with ILE 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 ILE* 2.9 34.5 + - + +
70B ARG 3.4 4.7 - - - +
72B TYR* 1.3 76.8 - - - +
74B GLU* 1.3 58.2 + - + +
76B GLY* 3.2 6.9 + - - -
79B ILE* 4.2 27.6 - - + -
89B LEU* 4.8 5.6 - - + -
104B TYR* 3.4 45.1 - - + +
186B ASN* 2.9 29.8 + - - +
187B ILE* 3.8 29.2 - - + -
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Residues in contact with GLU 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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70B ARG* 2.8 27.7 + - + +
71B GLU* 3.1 20.5 + - - +
73B ILE* 1.3 74.1 - - + +
75B SER* 1.3 61.0 + - - +
76B GLY* 2.9 7.9 + - - -
104B TYR* 5.5 1.8 - - + +
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Residues in contact with SER 75 (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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39B ILE* 3.8 21.0 - - - +
71B GLU 3.0 11.2 + - - -
72B TYR* 2.5 22.3 + - - -
74B GLU* 1.3 76.4 - - - +
76B GLY* 1.3 59.9 + - - +
77B LYS* 3.3 33.1 + - - +
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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