Contacts of the helix formed by residues 62 - 83 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ILE* 4.4 1.3 - - + +
53F TYR* 4.2 43.1 - - + +
56F ALA* 3.5 27.8 - - + -
57F ARG 5.8 1.8 - - - +
58F ASN 3.8 15.0 - - - +
59F ASN* 3.5 18.0 + - - +
60F ASN 3.4 0.6 - - - -
61F GLU* 1.3 72.3 - - - +
63F GLU* 1.3 58.3 + - - +
64F GLU 3.2 3.4 - - - -
65F ILE* 3.0 17.1 + - + +
66F PHE* 2.9 28.0 + - - +
136F CYS* 4.5 12.8 - - - -
138F VAL* 4.3 11.7 - - + -
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ASN* 3.8 14.2 + - - +
60F ASN* 3.7 24.5 - - - +
61F GLU 3.3 2.0 - - - -
62F LEU* 1.3 76.9 - - - +
64F GLU* 1.3 61.5 + - + +
66F PHE* 4.0 17.1 - - - +
67F GLN* 3.3 41.0 + - + +
137F LYS* 4.8 17.8 + - - +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ILE* 5.7 7.5 - - + +
61F GLU 4.2 10.5 + - - +
62F LEU 3.2 0.4 - - - -
63F GLU* 1.3 77.0 - - + +
65F ILE* 1.3 68.0 + - + +
67F GLN* 3.7 3.9 + - - +
68F GLU* 3.4 30.5 + - - +
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Residues in contact with ILE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F VAL* 5.8 0.4 - - + -
49F MET* 3.7 41.1 - - + +
52F ILE* 3.4 48.7 - - + -
53F TYR* 5.0 7.6 - - + +
61F GLU 5.2 0.4 - - - +
62F LEU* 3.0 20.5 + - + +
64F GLU* 1.3 81.7 - - + +
66F PHE* 1.3 64.1 + - - +
68F GLU* 3.3 14.6 + - - +
69F LEU* 3.2 23.0 + - + +
124F ILE* 6.4 0.2 - - + -
138F VAL* 4.0 23.6 - - + -
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Residues in contact with PHE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU 2.9 15.3 + - - +
63F GLU* 4.2 19.7 - - - +
65F ILE* 1.3 78.4 - - - +
67F GLN* 1.3 78.9 + - + +
69F LEU 3.5 1.2 + - - -
70F SER* 2.9 38.3 + - - -
137F LYS* 3.5 52.3 - - + -
138F VAL* 4.0 10.9 - - + +
141F LEU* 3.8 33.0 - - + +
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Residues in contact with GLN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLU* 3.3 27.6 + - - +
64F GLU* 3.7 4.2 + - - +
65F ILE 3.4 0.2 - - - -
66F PHE* 1.3 94.0 - - + +
68F GLU* 1.3 59.7 + - - +
70F SER* 3.5 9.3 + - - -
71F ALA* 3.2 27.4 + - - +
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Residues in contact with GLU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LYS* 3.7 19.7 + - - +
48F VAL* 5.9 3.5 - - - +
49F MET* 3.2 34.6 - - + +
52F ILE* 6.0 0.9 - - - +
64F GLU* 3.4 19.5 + - - +
65F ILE* 3.3 16.0 + - - +
66F PHE 3.3 0.4 - - - -
67F GLN* 1.3 77.6 - - - +
69F LEU* 1.3 54.3 - - - +
71F ALA* 3.3 4.9 + - - +
72F PHE* 2.8 35.9 + - - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F MET* 4.2 15.5 - - + -
65F ILE* 3.2 10.3 + - + +
68F GLU* 1.3 78.6 - - - +
70F SER* 1.3 53.3 + - - +
72F PHE* 3.5 5.1 - - + +
73F VAL* 2.7 41.8 + - + +
116F PHE* 4.6 8.3 - - + -
117F LEU* 3.9 28.3 - - + -
120F LEU* 4.2 29.2 - - + -
138F VAL* 3.4 40.4 - - + +
141F LEU* 3.5 16.4 - - + -
142F LEU* 3.9 11.7 - - + -
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Residues in contact with SER 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E GLU* 5.8 3.5 + - - -
66F PHE* 2.9 30.0 + - - -
67F GLN* 3.5 16.8 + - - -
69F LEU* 1.3 76.5 - - - +
71F ALA* 1.3 51.1 + - - +
73F VAL* 4.5 4.4 - - - +
74F SER* 2.8 34.8 + - - -
141F LEU* 3.6 20.8 - - - +
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLN 3.2 18.5 + - - +
68F GLU* 3.5 4.7 - - - +
69F LEU 3.3 0.2 - - - -
70F SER* 1.3 79.6 + - - +
72F PHE* 1.3 58.9 + - - +
74F SER* 2.9 17.7 + - - -
75F GLY* 3.0 14.4 + - - -
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Residues in contact with PHE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 4.6 11.7 - - + -
45F LYS* 3.8 25.1 - - + +
68F GLU 2.8 21.7 + - - +
69F LEU* 3.5 8.7 - - + +
71F ALA* 1.3 71.8 - - - +
73F VAL* 1.3 56.6 + - - +
75F GLY* 3.3 2.5 + - - -
76F LEU* 2.7 38.6 + - + +
113F ASP* 3.6 49.4 - - + -
116F PHE* 3.5 34.3 - + + -
117F LEU* 4.0 23.3 - - + -
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Residues in contact with VAL 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU* 2.7 29.5 + - + +
70F SER* 4.5 4.0 - - - +
72F PHE* 1.3 71.6 - - - +
74F SER* 1.3 57.9 + - - +
76F LEU* 3.3 8.7 + - + +
77F MET* 2.9 34.8 + - + +
117F LEU* 3.9 28.9 - - + -
141F LEU* 4.8 21.5 - - + +
142F LEU* 5.1 0.7 - - + -
150F LEU* 3.7 26.9 - - + -
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Residues in contact with SER 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ARG* 4.6 11.3 + - - -
70F SER 2.8 23.0 + - - -
71F ALA* 2.9 18.7 + - - -
73F VAL* 1.3 77.6 - - - +
75F GLY* 1.3 56.6 + - - +
77F MET* 3.4 15.5 + - - +
78F ASP* 3.1 34.2 + - - +
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ALA 3.0 16.6 + - - -
72F PHE* 3.5 4.0 - - - -
74F SER* 1.3 75.4 + - - +
76F LEU* 1.3 57.7 + - - +
78F ASP* 3.4 10.6 + - - +
79F LYS* 2.9 28.1 + - - +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F PHE* 2.7 24.0 + - + +
73F VAL* 3.3 10.7 + - - +
75F GLY* 1.3 72.6 - - - +
77F MET* 1.3 59.8 + - - +
79F LYS* 3.4 5.6 + - + +
80F ARG* 3.1 22.6 + - + +
110F TYR* 3.4 50.4 - - + +
113F ASP* 3.5 37.9 - - + +
114F LEU* 4.4 2.2 - - + +
117F LEU* 4.3 13.9 - - + -
150F LEU* 4.0 24.2 - - + -
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Residues in contact with MET 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ARG* 3.3 82.1 - - - +
73F VAL* 2.9 19.9 + - + +
74F SER* 3.6 14.6 - - - +
76F LEU* 1.3 76.3 - - - +
78F ASP* 1.3 63.7 + - - +
80F ARG* 3.6 6.3 + - - +
81F ASN* 3.2 37.8 + - - +
149F GLU* 4.7 10.9 - - - +
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Residues in contact with ASP 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ARG* 2.7 42.2 + - - +
74F SER* 3.1 18.5 + - - +
75F GLY* 3.6 10.5 - - - +
76F LEU 3.4 0.2 - - - -
77F MET* 1.3 75.0 - - - +
79F LYS* 1.3 62.9 - - - +
81F ASN* 3.5 3.1 + - - +
82F SER* 3.2 24.1 + - - -
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Residues in contact with LYS 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F GLY 2.9 17.2 + - - +
76F LEU* 3.6 10.5 - - + +
77F MET 3.3 0.2 - - - -
78F ASP* 1.3 75.4 - - - +
80F ARG* 1.3 62.4 + - - +
82F SER* 2.9 19.8 + - - +
83F VAL* 3.1 27.1 + - + +
106F ASP 4.7 1.3 - - - -
109F SER* 3.5 38.1 + - - -
110F TYR* 3.9 22.7 - - + +
112F ARG* 5.9 0.6 - - - +
113F ASP* 3.4 27.4 + - - +
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Residues in contact with ARG 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F LEU* 3.1 11.1 + - + +
77F MET* 3.8 7.9 - - - +
78F ASP 3.4 0.2 - - - -
79F LYS* 1.3 75.9 - - - +
81F ASN* 1.3 64.2 + - - +
83F VAL 3.2 0.5 + - - -
84F PHE* 2.8 52.3 + - + +
86F VAL* 4.8 2.2 - - - +
110F TYR* 3.6 29.8 - - + +
149F GLU* 3.6 42.3 + - - +
153F ASP* 2.8 41.6 + - - -
178F ASP 3.8 4.9 + - - -
179F LEU* 3.7 34.8 + - - +
181F TYR 5.8 0.6 + - - -
183F LYS* 3.5 24.9 - - - +
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Residues in contact with ASN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ARG* 3.1 32.0 - - - +
77F MET* 3.2 20.9 + - - +
78F ASP 3.5 4.5 + - - +
79F LYS 3.4 0.4 - - - -
80F ARG* 1.3 78.6 - - - +
82F SER* 1.3 55.1 + - - +
84F PHE 4.1 4.0 - - - -
99F ARG* 2.8 31.7 + - - +
149F GLU* 3.8 22.3 + - - +
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Residues in contact with SER 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP 3.2 14.0 + - - -
79F LYS* 2.9 21.7 + - - +
81F ASN* 1.3 78.3 - - - +
83F VAL* 1.3 64.9 + - - +
99F ARG* 3.2 27.7 + - - +
102F MET* 4.0 15.6 - - - +
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F LYS* 3.1 28.7 + - + +
82F SER* 1.3 78.6 + - - +
84F PHE* 1.3 80.3 + - + +
98F LEU* 3.7 20.8 - - + -
99F ARG* 2.8 34.0 + - - +
102F MET* 3.4 34.7 - - + +
106F ASP* 4.2 13.9 - - + +
107F ARG 4.3 11.4 - - - +
110F TYR* 5.3 0.7 - - + -
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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