Contacts of the helix formed by residues 62 - 83 (chain J) in PDB entry 3V3K
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 LEU 62 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ILE* 4.4 1.1 - - + +
53J TYR* 3.9 46.9 - - + +
56J ALA* 3.6 26.7 - - + +
57J ARG 5.3 3.6 - - - +
58J ASN 3.8 16.2 - - - +
59J ASN* 3.4 18.3 + - - +
60J ASN 3.4 0.8 - - - -
61J GLU* 1.3 74.4 - - - +
63J GLU* 1.3 58.2 + - - +
64J GLU 3.3 3.1 - - - -
65J ILE* 3.2 14.3 + - + +
66J PHE* 2.9 30.2 + - - +
136J CYS* 4.6 11.9 - - - -
138J VAL* 4.1 9.4 - - + +
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Residues in contact with GLU 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ASN 3.8 11.9 + - - +
60J ASN* 3.7 25.8 - - - +
61J GLU 3.3 1.4 - - - -
62J LEU* 1.3 78.9 - - - +
64J GLU* 1.3 61.4 + - + +
66J PHE* 3.9 12.0 - - - +
67J GLN* 3.3 42.8 + - - +
137J LYS* 4.7 18.7 + - - +
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Residues in contact with GLU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ILE* 5.8 6.7 - - + +
61J GLU 4.2 11.1 + - - +
62J LEU 3.3 0.4 - - - -
63J GLU* 1.3 78.9 - - + +
65J ILE* 1.3 68.6 + - + +
67J GLN* 3.7 3.8 + - - +
68J GLU* 3.4 27.7 + - - +
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Residues in contact with ILE 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J MET* 3.6 41.5 - - + +
52J ILE* 3.6 49.4 - - + -
53J TYR* 4.9 8.5 - - + +
61J GLU 5.1 0.7 - - - +
62J LEU* 3.2 22.2 + - + +
64J GLU* 1.3 78.3 - - + +
66J PHE* 1.3 65.2 + - - +
68J GLU* 3.4 14.9 + - - +
69J LEU* 3.3 21.5 + - + +
138J VAL* 4.1 22.0 - - + -
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Residues in contact with PHE 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J LEU 2.9 17.8 + - - +
63J GLU* 3.9 17.0 - - - +
65J ILE* 1.3 76.7 - - - +
67J GLN* 1.3 82.4 + - + +
69J LEU 3.4 1.4 + - - -
70J SER* 3.0 39.4 + - - -
137J LYS* 3.6 46.7 - - + -
138J VAL* 3.9 12.3 - - + +
141J LEU* 3.7 36.0 - - + +
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Residues in contact with GLN 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J GLU* 3.3 27.0 + - - +
64J GLU* 4.2 4.5 - - - +
65J ILE 3.4 0.2 - - - -
66J PHE* 1.3 96.9 - - + +
68J GLU* 1.3 59.6 + - - +
70J SER* 3.5 11.8 + - - -
71J ALA* 3.1 28.2 + - - +
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Residues in contact with GLU 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J LYS* 3.4 21.1 + - - +
48J VAL* 5.6 5.5 - - - +
49J MET* 3.2 33.3 - - + +
52J ILE* 5.7 0.7 - - - +
64J GLU* 3.4 14.8 + - - +
65J ILE* 3.5 25.5 - - - +
66J PHE 3.3 0.6 - - - -
67J GLN* 1.3 76.5 - - - +
69J LEU* 1.3 52.8 + - - +
71J ALA* 3.5 4.7 + - - +
72J PHE* 2.8 35.0 + - - +
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Residues in contact with LEU 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J MET* 4.1 15.9 - - - -
65J ILE* 3.3 7.3 + - + +
66J PHE 3.4 1.8 + - - +
68J GLU* 1.3 78.4 - - - +
70J SER* 1.3 55.1 + - - +
72J PHE* 3.1 5.0 + - + +
73J VAL* 2.6 41.2 + - + +
116J PHE* 4.3 8.7 - - + -
117J LEU* 3.9 27.1 - - + -
120J LEU* 4.0 30.1 - - + -
138J VAL* 3.4 41.1 - - + +
141J LEU* 3.4 17.5 - - + -
142J LEU* 4.2 12.1 - - + -
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Residues in contact with SER 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I GLU* 6.1 0.4 - - - -
66J PHE* 3.0 29.0 + - - -
67J GLN* 3.5 21.7 + - - -
69J LEU* 1.3 77.2 - - - +
71J ALA* 1.3 59.4 + - - +
73J VAL* 4.2 3.8 - - - +
74J SER* 3.2 27.5 + - - -
141J LEU* 3.6 22.6 - - - +
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Residues in contact with ALA 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J GLN* 3.1 19.2 + - - +
68J GLU* 3.7 3.8 - - - +
69J LEU 3.3 0.4 - - - -
70J SER* 1.3 79.0 + - - +
72J PHE* 1.3 63.3 + - - +
74J SER* 3.3 7.3 + - - -
75J GLY* 3.2 19.1 + - - -
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Residues in contact with PHE 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J LEU* 4.5 14.1 - - + -
45J LYS* 3.5 27.1 - - - +
49J MET* 6.4 0.7 - - + -
68J GLU 2.8 19.1 + - - +
69J LEU* 3.4 8.7 - - + +
71J ALA* 1.3 75.6 - - - +
73J VAL* 1.3 53.7 + - - +
75J GLY* 3.5 1.4 + - - -
76J LEU* 2.8 37.3 + - + +
113J ASP* 3.5 52.0 - - + -
116J PHE* 3.6 30.1 - + + -
117J LEU* 3.9 25.1 - - + -
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Residues in contact with VAL 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J LEU* 2.6 27.5 + - + +
70J SER* 4.2 6.3 - - - +
72J PHE* 1.3 71.0 - - - +
74J SER* 1.3 60.2 + - - +
76J LEU* 3.2 9.0 + - + +
77J MET* 2.9 38.7 + - + +
117J LEU* 4.1 24.2 - - + -
141J LEU* 4.8 26.0 - - + +
142J LEU* 5.5 0.2 - - + -
150J LEU* 4.1 23.3 - - + -
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Residues in contact with SER 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I ARG* 4.3 9.5 + - - +
70J SER 3.2 18.2 + - - -
71J ALA* 3.3 9.5 + - - -
73J VAL* 1.3 79.6 - - - +
75J GLY* 1.3 59.9 + - - +
77J MET* 3.5 11.2 + - - +
78J ASP* 3.0 34.5 + - - +
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Residues in contact with GLY 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J ALA 3.2 11.5 + - - -
72J PHE 3.7 3.4 - - - -
74J SER* 1.3 80.5 + - - +
76J LEU* 1.3 57.3 + - - +
78J ASP* 3.4 10.6 + - - +
79J LYS* 2.9 28.1 + - - +
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Residues in contact with LEU 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J PHE* 2.8 26.5 + - + +
73J VAL* 3.2 10.3 + - - +
75J GLY* 1.3 70.6 - - - +
77J MET* 1.3 62.6 + - - +
79J LYS* 3.3 7.8 + - + +
80J ARG* 3.1 23.1 + - + +
110J TYR* 3.4 48.2 - - + +
113J ASP* 3.4 37.0 - - + +
114J LEU* 4.5 1.8 - - + +
117J LEU* 4.2 15.0 - - + -
150J LEU* 4.0 24.2 - - + -
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Residues in contact with MET 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I ARG* 3.5 72.5 - - - +
73J VAL* 2.9 26.6 + - + +
74J SER* 3.6 11.0 - - - +
75J GLY 3.3 0.2 - - - -
76J LEU* 1.3 79.2 - - - +
78J ASP* 1.3 62.2 + - - +
80J ARG* 3.6 8.3 + - + +
81J ASN* 3.3 29.2 + - - +
149J GLU* 4.2 20.9 - - + +
150J LEU* 6.4 2.0 - - + -
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Residues in contact with ASP 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I ARG* 2.7 36.8 + - - +
74J SER 3.0 17.0 + - - +
75J GLY* 3.5 12.1 - - - +
76J LEU 3.3 0.2 - - - -
77J MET* 1.3 75.6 - - - +
79J LYS* 1.3 62.1 + - - +
81J ASN* 3.3 6.0 + - - +
82J SER* 3.3 22.5 + - - -
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Residues in contact with LYS 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J GLY 2.9 17.6 + - - +
76J LEU* 3.3 9.6 + - + +
78J ASP* 1.3 73.1 - - - +
80J ARG* 1.3 62.2 + - - +
82J SER* 3.1 18.9 + - - +
83J VAL* 3.1 29.4 - - + +
106J ASP 4.6 1.3 - - - -
109J SER* 3.2 41.7 + - - -
110J TYR* 3.8 22.9 - - + +
113J ASP* 3.2 30.2 + - - +
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Residues in contact with ARG 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J LEU* 3.1 8.6 + - + +
77J MET* 3.7 12.3 - - + +
78J ASP 3.3 0.2 - - - -
79J LYS* 1.3 77.7 - - - +
81J ASN* 1.3 65.3 + - - +
83J VAL 3.3 0.2 + - - -
84J PHE* 2.8 50.0 + - + +
86J VAL* 5.0 0.8 - - - +
110J TYR* 3.8 29.2 + - + +
149J GLU* 3.2 43.9 + - - +
153J ASP* 2.8 34.7 + - - -
178J ASP 3.7 3.4 + - - -
179J LEU* 3.7 37.6 + - - +
181J TYR 5.7 1.2 + - - -
183J LYS* 3.6 24.5 - - - +
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Residues in contact with ASN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I ARG* 3.4 22.6 - - - +
77J MET* 3.3 21.7 + - - +
78J ASP* 3.3 6.7 + - - +
80J ARG* 1.3 81.0 - - - +
82J SER* 1.3 57.2 + - - +
84J PHE 4.1 4.5 - - - -
99J ARG* 3.2 28.2 + - - +
149J GLU* 4.0 20.3 + - - +
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Residues in contact with SER 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J ASP 3.3 12.3 + - - -
79J LYS* 3.1 15.4 + - - +
81J ASN* 1.3 77.5 - - - +
83J VAL* 1.3 69.4 + - - +
99J ARG* 3.4 25.0 - - - +
102J MET* 3.6 19.1 - - - +
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Residues in contact with VAL 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J LYS* 3.1 30.1 + - + +
82J SER* 1.3 83.4 + - - +
84J PHE* 1.3 93.7 + - + +
98J LEU* 3.6 15.2 - - + -
99J ARG* 2.9 24.8 + - - +
102J MET* 3.6 29.2 - - + +
106J ASP* 3.8 29.4 - - + +
110J TYR* 5.1 0.4 - - + -
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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
------------------------------------------------------------
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