Contacts of the helix formed by residues 72 - 88 (chain F) in PDB entry 2VT5
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 LYS 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 1.3 58.4 + - + +
74F ASP* 3.4 13.0 + - - -
75F VAL* 3.3 25.2 + - - +
76F LEU* 2.7 54.2 + - + +
79F ASP* 5.4 2.2 + - - -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ALA* 3.9 33.4 - - + +
48F VAL* 4.3 16.8 - - + +
50F LYS* 3.7 26.5 - - - +
72F LYS* 1.3 79.6 - - - +
74F ASP* 1.3 57.2 + - - +
76F LEU* 3.5 11.0 + - + +
77F SER* 3.0 34.3 + - - +
120F LEU* 4.1 11.7 - - + -
123F SER* 6.1 0.4 - - - -
126F ILE* 3.8 34.8 - - + -
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Residues in contact with ASP 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LYS 4.0 7.3 + - - -
73F LEU* 1.3 77.5 - - - +
75F VAL* 1.3 78.5 + - - +
77F SER* 3.8 6.1 - - - -
78F ASN* 3.1 28.1 + - - +
97F GLU* 6.1 0.4 - - - +
98F GLU* 4.0 22.1 - - + +
119F PRO* 4.4 2.8 - - + +
120F LEU* 4.3 12.9 - - + +
123F SER* 3.6 27.8 + - - +
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Residues in contact with VAL 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LYS* 3.3 28.7 + - + +
73F LEU 3.3 0.2 - - - -
74F ASP* 1.3 90.0 + - - +
76F LEU* 1.3 58.1 - - - +
78F ASN* 3.4 3.0 + - - +
79F ASP* 2.9 48.7 + - - +
98F GLU* 3.9 17.5 - - - +
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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
----------------------------------------------------------
47F ALA* 4.0 27.8 - - + -
72F LYS* 2.7 35.5 + - + +
73F LEU* 3.7 12.3 - - + +
75F VAL* 1.3 71.2 - - - +
77F SER* 1.3 54.2 + - - +
79F ASP* 3.1 8.3 + - + +
80F LEU* 2.7 53.5 + - + +
55G HIS* 4.1 17.5 - - + +
60G ALA* 3.9 24.5 - - + -
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Residues in contact with SER 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ILE* 3.5 35.7 - - - +
48F VAL* 5.2 0.2 - - - +
73F LEU* 3.0 20.1 + - - +
74F ASP 3.8 4.9 - - - -
76F LEU* 1.3 74.7 - - - +
78F ASN* 1.3 58.6 + - - +
80F LEU* 3.2 3.0 + - - +
81F VAL* 2.9 34.0 + - - +
119F PRO* 3.7 22.7 - - - -
120F LEU* 3.8 15.6 - - - +
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Residues in contact with ASN 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASP 3.1 16.4 + - - +
75F VAL* 3.6 4.5 - - - +
76F LEU 3.4 0.2 - - - -
77F SER* 1.3 77.4 - - - +
79F ASP* 1.3 64.4 + - - +
81F VAL* 3.5 1.2 + - - +
82F MET* 2.8 39.0 + - - +
96F SER* 2.5 32.6 + - - -
98F GLU* 3.6 20.5 + - + +
99F ASP* 3.2 22.7 + - - +
117F PHE* 3.5 8.4 - - - -
119F PRO* 3.5 13.9 - - + +
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Residues in contact with ASP 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LYS* 5.4 1.7 + - - -
75F VAL* 2.9 33.1 + - - +
76F LEU* 3.5 10.8 - - + +
78F ASN* 1.3 80.1 + - - +
80F LEU* 1.3 61.2 + - - +
82F MET* 4.0 5.1 - - - +
83F ASN* 2.9 33.6 + - - +
60G ALA* 3.4 26.9 - - + +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ALA* 3.9 14.1 - - + +
43F ALA* 3.6 31.0 - - + +
44F ILE* 3.8 23.3 - - + +
47F ALA* 5.7 0.2 - - + -
76F LEU* 2.7 43.7 + - + +
77F SER* 3.6 3.8 - - - +
79F ASP* 1.3 73.1 - - - +
81F VAL* 1.3 63.0 + - - +
83F ASN* 3.9 0.2 - - - -
84F MET* 2.9 28.9 + - - +
55G HIS* 3.9 7.4 - - + -
59G ILE* 3.7 33.5 - - + +
60G ALA* 3.6 18.8 - - + +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 4.0 14.4 - - + -
40F ALA* 3.9 13.5 - - + -
41F VAL* 5.9 0.2 - - + -
44F ILE* 3.7 20.0 - - + -
77F SER 2.9 19.3 + - - +
80F LEU* 1.3 75.0 - - - +
82F MET* 1.3 57.0 + - - +
84F MET* 4.1 0.2 - - - +
85F LEU* 3.0 48.2 + - + +
117F PHE* 3.6 36.3 - - + -
119F PRO* 4.4 9.4 - - + -
134F THR* 4.5 11.9 - - + -
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Residues in contact with MET 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASN* 2.8 32.7 + - - +
79F ASP* 4.0 5.6 - - - +
81F VAL* 1.3 73.0 - - - +
83F ASN* 1.3 64.6 + - - +
85F LEU* 4.2 2.8 - - - +
86F LYS* 3.0 45.3 + - - +
94F LEU* 3.8 33.2 - - + +
96F SER* 3.7 7.4 - - - -
99F ASP* 3.2 24.0 - - - +
103F ILE* 3.5 27.4 - - + -
117F PHE* 3.7 23.3 - - + -
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Residues in contact with ASN 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ASP 2.9 19.5 + - - +
82F MET* 1.3 79.5 - - - +
84F MET* 1.3 60.6 + - - +
86F LYS* 3.8 8.3 - - - +
87F SER* 2.9 29.5 + - - -
58G GLY 3.0 24.0 + - - +
59G ILE 3.0 17.2 + - - +
60G ALA 3.9 1.1 - - - +
61G GLY* 3.5 22.4 - - - +
9H ASP* 5.1 7.0 - - - +
10H VAL* 3.7 16.6 - - - +
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Residues in contact with MET 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F SER* 3.4 31.2 - - - +
37F LEU* 5.3 0.2 - - - -
39F THR* 3.5 26.9 - - + +
40F ALA* 3.9 17.9 - - + +
80F LEU 2.9 20.0 + - - +
81F VAL 4.1 0.4 - - - +
83F ASN* 1.3 75.2 - - - +
85F LEU* 1.3 65.6 + - + +
87F SER* 3.2 3.6 + - - -
88F SER 3.2 4.9 + - - -
59G ILE* 3.7 31.6 - - + +
10H VAL* 3.8 17.7 - - + -
12H THR* 5.1 7.6 - - + +
15H ARG* 3.1 49.0 + - - +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.6 40.8 - - + +
36F SER* 4.6 0.7 - - - -
37F LEU* 4.2 18.2 - - + +
81F VAL* 3.0 39.4 + - + +
82F MET 4.2 1.8 - - - +
84F MET* 1.3 76.1 - - + +
86F LYS* 1.3 59.2 + - - +
88F SER* 2.7 23.5 + - - -
89F PHE 4.3 0.5 + - - -
91F THR* 3.3 15.0 + - + +
94F LEU* 3.8 25.6 - - + -
115F VAL* 3.7 28.7 - - + -
117F PHE* 4.0 5.8 - - + -
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Residues in contact with LYS 86 (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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82F MET* 3.0 37.8 + - - +
83F ASN* 3.8 8.3 - - - +
84F MET 3.3 0.2 - - - -
85F LEU* 1.3 77.2 - - - +
87F SER* 1.3 61.1 + - - +
88F SER 3.2 0.9 + - - -
89F PHE 3.7 5.4 + - - -
91F THR* 4.3 5.4 + - - -
94F LEU* 3.9 13.7 - - + -
103F ILE* 3.9 30.2 - - - +
105F VAL* 4.3 15.7 - - + +
106F GLU 6.2 0.4 - - - +
109F LYS* 3.2 44.1 - - + +
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Residues in contact with SER 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ASN* 2.9 25.1 + - - -
84F MET* 3.2 2.1 + - - -
86F LYS* 1.3 75.2 - - - +
88F SER* 1.3 59.6 + - - +
89F PHE* 3.1 21.5 + - - -
109F LYS* 4.2 3.6 - - - -
9H ASP* 3.7 31.0 - - - -
10H VAL* 4.4 2.9 - - - +
15H ARG* 2.7 45.9 + - - -
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Residues in contact with SER 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F GLN* 3.6 32.5 - - - +
33F LEU* 4.0 9.1 - - - +
36F SER* 3.1 29.6 - - - -
84F MET 3.2 4.3 + - - -
85F LEU* 2.7 22.6 + - - -
87F SER* 1.3 76.6 - - - +
89F PHE* 1.3 67.9 + - - +
90F ALA* 3.2 18.8 + - - +
91F THR* 4.3 1.0 + - - +
15H ARG* 3.9 8.2 - - - +
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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
------------------------------------------------------------
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