Contacts of the helix formed by residues 65 - 75 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 23.1 - - + -
8A ASP 5.2 1.1 - - - -
9A VAL* 5.3 1.1 - - + -
31A VAL* 3.6 32.3 - - + -
32A LYS* 3.5 15.0 - - - -
33A SER* 3.5 27.1 - - - -
34A PRO* 3.7 16.4 - - + -
37A PHE* 4.1 5.8 - + - -
60A LEU* 3.2 49.1 + - + +
61A PHE 4.2 0.4 + - - -
63A ARG* 3.7 21.1 - - + -
64A GLY* 1.3 74.8 - - - +
66A GLU* 1.3 66.1 + - - +
68A PRO* 3.0 13.7 - - + +
69A ILE* 2.9 30.9 + - + +
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Residues in contact with GLU 66 (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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61A PHE* 3.6 51.8 - - + +
64A GLY 3.5 2.0 - - - -
65A PHE* 1.3 76.9 - - - +
67A LYS* 1.3 71.5 + - + +
69A ILE* 3.1 4.4 + - - +
70A ARG* 2.9 66.4 + - - +
101A GLY 5.0 0.9 - - - +
102A LEU* 4.3 5.3 - - + -
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Residues in contact with LYS 67 (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 GLY 4.6 1.3 + - - +
66A GLU* 1.3 81.4 - - + +
68A PRO* 1.3 67.8 - - + +
70A ARG* 3.1 8.0 + - - +
71A GLU* 2.8 51.3 + - + +
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Residues in contact with PRO 68 (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 PRO* 4.3 9.6 - - + -
37A PHE* 3.7 28.1 - - + -
39A ILE* 3.6 9.7 - - + +
64A GLY 3.2 23.3 - - - +
65A PHE* 3.0 27.6 - - + +
67A LYS* 1.3 97.0 - - + +
69A ILE* 1.3 55.5 + - - -
71A GLU* 4.3 8.7 - - + -
72A TYR* 3.1 27.9 + - - +
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Residues in contact with ILE 69 (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 ILE* 3.9 27.6 - - + -
37A PHE* 5.7 0.4 - - + -
45A LEU* 5.1 5.4 - - + -
47A LEU* 4.2 11.2 - - + -
60A LEU* 4.1 21.5 - - + -
65A PHE* 2.9 39.2 + - + +
66A GLU* 3.1 6.0 + - - +
68A PRO* 1.3 73.7 - - + +
70A ARG* 1.3 60.2 + - + +
72A TYR* 3.4 5.3 + - - +
73A ILE* 2.9 45.8 + - + +
79A ILE* 4.2 12.3 - - + -
102A LEU* 4.0 22.9 - - + -
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Residues in contact with ARG 70 (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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66A GLU* 2.9 53.8 + - + +
67A LYS* 3.7 6.5 - - - +
69A ILE* 1.3 74.8 - - + +
71A GLU* 1.3 58.7 + - + +
73A ILE* 3.2 3.8 + - - +
74A GLU* 2.8 42.7 + - - +
101A GLY 4.3 1.6 + - - -
102A LEU* 2.7 48.1 + - + +
103A ASN* 5.2 0.6 - - - +
104A TYR* 3.5 33.4 + - - +
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Residues in contact with GLU 71 (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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39A ILE* 4.0 26.9 - - + +
67A LYS* 2.8 41.7 + - + +
68A PRO* 4.0 3.3 - - + +
70A ARG* 1.3 73.2 - - + +
72A TYR* 1.3 61.5 + - - +
74A GLU* 3.2 18.2 + - - +
75A SER* 3.0 22.2 + - - -
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.9 2.9 - + + -
39A ILE* 3.6 22.1 - - + +
42A THR* 3.4 41.5 - - + -
43A SER 3.2 23.2 + - - -
44A ARG 3.6 0.9 + - - -
45A LEU* 3.5 33.7 - - + -
68A PRO 3.1 20.2 + - - +
69A ILE 3.6 3.4 - - - +
71A GLU* 1.3 76.4 - - - +
73A ILE* 1.3 63.9 + - - +
75A SER* 2.5 28.0 + - - -
76A GLY 3.7 1.4 + - - -
77A LYS* 3.3 32.7 + - + +
78A PRO 2.7 31.0 + - - -
79A ILE* 3.9 10.3 - - + -
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Residues in contact with ILE 73 (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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69A ILE* 2.9 31.5 + - + +
70A ARG 3.4 4.9 - - - +
72A TYR* 1.3 77.9 - - - +
74A GLU* 1.3 60.2 + - + +
76A GLY* 3.1 7.8 + - - -
79A ILE* 4.1 28.0 - - + -
89A LEU* 4.9 6.3 - - + -
104A TYR* 3.4 43.5 - - + +
186A ASN* 2.8 31.0 + - - +
187A ILE* 3.9 29.8 - - + -
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Residues in contact with GLU 74 (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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70A ARG* 2.8 27.5 + - - +
71A GLU* 3.2 19.2 + - - +
73A ILE* 1.3 74.9 - - + +
75A SER* 1.3 60.5 + - - +
76A GLY* 3.0 7.0 + - - -
104A TYR* 5.8 1.3 - - - +
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Residues in contact with SER 75 (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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39A ILE* 3.8 19.5 - - - -
71A GLU 3.0 11.7 + - - -
72A TYR* 2.5 21.9 + - - -
74A GLU* 1.3 75.9 - - - +
76A GLY* 1.3 58.8 + - - +
77A LYS* 3.3 31.6 + - - +
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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