Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 3KVF
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 SER 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.7 25.1 - - - -
84A GLN* 3.5 13.1 - - - +
86A ILE* 2.5 36.0 + - - +
88A ASN* 1.3 77.7 - - - +
90A CYS* 1.3 66.5 + - - +
91A GLY 2.8 5.4 + - - -
92A THR* 2.9 15.6 + - - -
93A MET* 2.9 16.4 + - - +
133A PHE* 4.2 12.8 - - - -
143A HIS* 4.6 1.3 - - - -
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Residues in contact with CYS 90 (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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84A GLN* 3.3 23.2 + - - +
88A ASN 4.7 0.2 - - - -
89A SER* 1.3 77.9 + - - +
91A GLY* 1.3 64.1 + - - +
93A MET* 3.4 6.5 - - - +
94A GLY* 2.9 24.8 + - - -
161A HIS* 3.5 13.7 - - + +
162A PHE* 3.6 29.1 - - + +
75B GLY 3.6 3.1 - - - -
76B GVE 1.8 61.9 - - + +
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Residues in contact with GLY 91 (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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6A MET* 4.5 17.3 - - - -
13A LEU* 6.4 0.2 - - - -
50A LEU* 5.4 0.2 - - - +
88A ASN 4.8 0.6 + - - -
89A SER 2.8 5.8 + - - -
90A CYS* 1.3 81.4 - - - +
92A THR* 1.3 59.2 + - - -
94A GLY* 3.2 10.6 + - - -
95A LEU* 3.2 22.3 + - - +
143A HIS* 4.6 2.1 - - - -
162A PHE* 3.8 27.8 - - - -
75B GLY 5.0 0.8 + - - -
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Residues in contact with THR 92 (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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3A LEU* 5.3 0.7 - - - -
6A MET* 4.7 0.7 - - - +
16A VAL* 4.3 11.0 - - + +
20A LEU* 5.4 5.2 - - + -
89A SER* 2.9 8.9 + - - -
91A GLY* 1.3 69.2 - - - -
93A MET* 1.3 57.3 + - - +
95A LEU* 2.9 11.1 + - + +
96A ILE* 2.7 48.0 + - + +
133A PHE* 4.0 11.0 - - + -
139A ILE* 3.8 28.2 + - + -
143A HIS* 2.6 41.4 + - + +
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Residues in contact with MET 93 (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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82A MET* 3.3 53.4 - - + +
83A LYS 3.4 21.1 - - - +
84A GLN* 3.7 15.7 - - + +
89A SER* 2.9 31.4 + - - +
90A CYS* 3.4 13.9 - - - +
92A THR* 1.3 76.5 - - - +
94A GLY* 1.3 58.1 + - - +
96A ILE* 3.7 6.2 - - - +
97A HIS* 2.8 50.0 + - + +
133A PHE* 4.4 18.6 - - + -
177A GLY* 4.2 4.3 - - - +
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Residues in contact with GLY 94 (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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50A LEU* 4.1 22.3 - - - +
90A CYS 2.9 15.5 + - - -
91A GLY 3.2 4.5 + - - -
92A THR 3.1 0.6 - - - -
93A MET* 1.3 73.7 - - - +
95A LEU* 1.3 53.0 + - - +
97A HIS* 3.2 9.3 + - - +
98A ALA* 2.7 34.7 + - - +
162A PHE* 5.3 2.9 - - - -
163A ILE* 5.9 0.7 - - - -
164A LEU* 4.1 9.0 - - - +
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Residues in contact with LEU 95 (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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13A LEU* 3.6 51.1 - - + +
16A VAL* 3.8 25.6 - - + -
17A LEU* 3.8 18.8 - - + +
20A LEU* 5.6 6.3 - - + -
28A PHE* 3.9 20.2 - - + -
50A LEU* 4.5 5.6 - - + -
91A GLY 3.2 20.2 + - - +
92A THR* 2.9 11.7 + - + +
94A GLY* 1.3 71.7 - - - +
96A ILE* 1.3 61.8 + - + +
98A ALA* 3.1 7.1 + - - +
99A VAL* 2.8 35.9 + - + +
114A LEU* 5.6 1.1 - - + -
162A PHE* 6.1 0.4 - - + -
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Residues in contact with ILE 96 (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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20A LEU* 5.4 2.5 - - + -
80A TYR* 4.3 7.4 - - + -
82A MET* 3.6 30.5 - - + -
92A THR* 2.7 32.0 + - + +
93A MET* 3.7 5.4 - - - +
95A LEU* 1.3 72.0 - - + +
97A HIS* 1.3 59.4 + - + +
99A VAL* 4.0 1.7 - - - +
100A ALA* 2.8 34.8 + - - +
114A LEU* 3.8 24.7 - - + -
117A PHE* 4.3 5.8 - - + -
118A LEU* 4.1 21.8 - - + -
133A PHE* 3.6 33.0 - - + -
139A ILE* 4.5 5.8 - - + -
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Residues in contact with HIS 97 (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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80A TYR* 3.6 24.5 - + - -
81A PHE* 3.8 9.4 - + - -
82A MET* 3.1 45.2 + - + +
93A MET* 2.8 37.1 + - + +
94A GLY* 3.5 8.5 + - - +
96A ILE* 1.3 77.3 - - + +
98A ALA* 1.3 61.3 + - - +
100A ALA* 4.6 2.0 - - - -
101A ASN* 3.3 28.3 + - - +
164A LEU* 3.5 18.0 - - + +
175A LEU* 3.8 23.5 + - + +
177A GLY 4.1 14.3 + - - -
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Residues in contact with ALA 98 (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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28A PHE* 4.6 7.6 - - + -
48A ALA* 4.2 2.0 - - + -
50A LEU* 5.4 0.2 - - + -
94A GLY 2.7 19.7 + - - +
95A LEU* 3.4 9.4 - - - +
97A HIS* 1.3 77.0 - - - +
99A VAL* 1.3 63.8 + - + +
102A ASN* 3.2 27.7 + - - +
164A LEU* 3.5 24.2 - - + +
166A ASN* 3.7 2.8 + - - +
219A LEU* 3.9 24.0 - - + +
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Residues in contact with VAL 99 (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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17A LEU* 3.8 28.3 - - + -
22A VAL* 4.2 2.0 - - + -
95A LEU 2.8 21.6 + - - +
96A ILE 4.0 0.7 - - - +
98A ALA* 1.3 70.4 - - + +
100A ALA* 1.3 59.4 + - - +
101A ASN 3.1 2.0 - - - -
102A ASN 2.8 31.8 + - - -
103A GLN* 3.4 3.7 - - + +
106A LEU* 3.8 28.9 - - + -
108A PHE* 3.5 37.0 - - + -
114A LEU* 3.8 19.3 - - + -
118A LEU* 3.9 2.0 - - + -
219A LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 100 (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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80A TYR* 3.5 40.6 - - + +
96A ILE 2.8 21.9 + - - +
97A HIS 4.2 2.7 - - - +
99A VAL* 1.3 73.3 - - - +
101A ASN* 1.3 59.5 + - - +
103A GLN* 3.0 25.6 + - - +
118A LEU* 3.6 26.6 - - + +
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Residues in contact with ASN 101 (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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78A LYS 3.5 6.8 - - - +
79A VAL* 3.5 10.4 - - - +
80A TYR* 3.0 46.9 + - - +
97A HIS* 3.3 18.3 + - - +
99A VAL 3.1 1.2 - - - -
100A ALA* 1.3 77.1 - - - +
102A ASN* 1.3 67.1 + - - +
103A GLN 3.8 1.8 - - - -
104A ASP* 4.2 4.0 - - - +
105A LYS* 5.2 0.5 + - - -
166A ASN* 3.4 26.7 - - - +
167A ASN 4.5 4.9 - - - +
168A VAL* 3.6 16.8 - - + +
175A LEU* 3.3 16.7 - - - +
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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