Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 3KVT
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 VAL 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A HIS* 3.2 24.9 + - + +
60A GLY* 1.3 73.0 - - - +
62A PHE* 1.3 64.2 + - - +
64A GLN* 3.0 18.6 + - + +
65A ILE* 3.1 10.0 + - + +
77A PRO* 5.0 4.9 - - + -
79A ASP* 5.6 1.3 - - - +
80A VAL* 4.0 19.5 - - + -
84A LEU* 3.7 25.6 - - + -
85A PHE* 3.4 30.5 - - + -
88A GLU* 3.7 22.4 - - + -
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Residues in contact with PHE 62 (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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14A ILE* 3.8 16.8 - - + -
16A VAL* 3.6 20.2 - - + -
21A HIS* 3.4 41.1 - + + +
36A LEU* 3.9 25.6 - - + -
58A HIS 3.5 12.1 + - - +
59A PRO 3.7 12.1 - - - +
60A GLY 3.2 0.8 - - - -
61A VAL* 1.3 76.5 - - - +
63A ALA* 1.3 56.6 + - - +
65A ILE* 3.0 11.3 + - + +
66A ILE* 2.7 51.9 + - + +
92A TRP* 3.4 47.8 - + - +
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Residues in contact with ALA 63 (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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21A HIS* 3.8 18.0 - - + +
59A PRO 5.2 0.2 - - - +
60A GLY 3.5 12.2 + - - +
61A VAL 3.2 0.8 - - - -
62A PHE* 1.3 78.3 - - - +
64A GLN* 1.3 60.7 + - - +
66A ILE* 3.1 12.7 - - + +
67A ASN* 2.9 29.7 + - - +
70A ARG* 4.7 3.0 + - - +
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Residues in contact with GLN 64 (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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60A GLY 4.5 1.1 + - - +
61A VAL* 3.0 13.0 + - - +
63A ALA* 1.3 79.6 - - - +
65A ILE* 1.3 65.7 + - - +
67A ASN* 3.3 16.5 + - - +
68A TYR* 3.5 9.9 + - - +
74A LEU* 5.3 1.6 - - - +
75A HIS* 3.5 36.5 + - - +
76A TYR 3.5 22.8 + - - -
77A PRO* 3.6 29.1 - - + +
85A PHE* 3.9 11.8 - - + -
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Residues in contact with ILE 65 (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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36A LEU* 4.5 7.6 - - + -
61A VAL* 3.1 19.1 + - + +
62A PHE* 3.0 25.7 + - + +
64A GLN* 1.3 76.7 - - - +
66A ILE* 1.3 62.9 + - - +
68A TYR* 3.2 21.6 + - - +
69A TYR* 3.5 7.6 - - + -
74A LEU* 6.2 0.7 - - - -
85A PHE* 3.8 12.1 - - + -
88A GLU* 4.2 1.8 - - + -
89A LEU* 3.6 37.9 - - + +
92A TRP* 3.8 37.0 - - + +
94A LEU* 3.7 18.9 - - + +
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Residues in contact with ILE 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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14A ILE* 4.9 3.4 - - + -
21A HIS* 4.4 13.2 - - + +
22A GLU 4.8 0.2 - - - +
23A THR* 4.1 21.5 - - + +
27A THR* 5.6 0.4 - - + -
28A LEU* 4.8 12.1 - - + -
36A LEU* 5.2 1.3 - - + -
62A PHE* 2.7 44.5 + - + +
63A ALA* 3.1 25.4 - - - +
65A ILE* 1.3 73.0 - - - +
67A ASN* 1.3 63.7 + - - +
69A TYR* 3.1 12.3 + - + +
70A ARG* 3.1 63.2 + - + +
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Residues in contact with ASN 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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63A ALA 2.9 18.7 + - - +
64A GLN* 3.6 15.4 - - - +
65A ILE 3.2 0.6 - - - -
66A ILE* 1.3 77.9 - - - +
68A TYR* 1.3 53.7 + - - +
69A TYR 3.3 0.2 - - - -
70A ARG* 3.8 23.2 - - - +
71A SER* 2.8 50.8 + - - -
73A LYS 4.4 1.3 - - - -
75A HIS* 4.8 10.4 - - - -
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Residues in contact with TYR 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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31A ILE* 3.6 29.0 - - + +
64A GLN 3.5 6.8 + - - +
65A ILE* 3.2 13.8 + - - +
66A ILE 3.1 0.2 - - - -
67A ASN* 1.3 78.8 - - - +
69A TYR* 1.3 56.9 + - + +
72A GLY* 2.8 37.8 + - - -
73A LYS 3.4 24.0 - - - +
74A LEU* 3.8 43.5 - - + -
94A LEU* 3.8 32.1 - - + -
95A ASP 4.9 3.1 - - - -
98A GLN* 3.3 27.9 - - + +
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Residues in contact with TYR 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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27A THR* 3.5 24.9 - - + +
28A LEU* 3.4 35.7 - - + -
30A LYS* 2.9 33.1 + - - +
31A ILE* 3.7 30.5 - - + -
34A THR* 2.7 32.2 + - - -
36A LEU* 3.6 33.0 + - + +
65A ILE 3.5 17.9 - - - -
66A ILE* 3.1 12.6 + - + +
68A TYR* 1.3 79.7 - - - +
70A ARG* 1.3 58.6 + - - +
71A SER 3.6 0.2 + - - -
72A GLY* 3.8 1.0 + - - -
92A TRP* 4.4 2.3 + - - +
94A LEU* 3.6 28.7 - - + +
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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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21A HIS* 5.4 3.6 + - - +
22A GLU 2.9 30.1 + - - +
23A THR* 4.0 9.0 + - - +
27A THR* 3.8 19.7 - - + +
30A LYS* 2.9 17.1 + - - +
63A ALA* 4.7 4.2 + - - +
66A ILE* 3.1 57.4 + - + +
67A ASN* 3.9 21.5 - - - +
69A TYR* 1.3 77.2 - - - +
71A SER* 1.3 57.5 + - - +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 4.6 2.5 - - - -
67A ASN* 2.8 34.5 + - - -
70A ARG* 1.3 75.6 - - - +
72A GLY* 1.3 59.9 + - - +
73A LYS* 3.1 35.6 + - - +
75A HIS* 4.8 3.7 - - - -
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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
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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