Contacts of the helix formed by residues 82 - 100 (chain F) in PDB entry 1KVO
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 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F ARG* 2.6 35.7 + - - -
80F GLN 3.8 0.4 + - - -
81F ASP* 1.3 72.2 - - - +
83F CYS* 1.3 57.3 + - - +
85F SER* 3.7 5.7 - - - -
86F GLN* 3.0 31.9 + - - +
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Residues in contact with CYS 83 (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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57E ARG 5.1 2.5 - - - -
58E GLY* 3.4 25.8 - - - +
59E CYS* 5.4 0.2 - - - -
83E CYS* 5.8 3.1 - - - -
54F LEU* 3.9 3.8 - - - +
57F ARG* 3.9 10.5 - - - +
58F GLY 5.1 0.9 - - - -
59F CYS* 2.0 53.6 - - + +
64F LEU* 4.1 6.1 - - + -
81F ASP* 3.1 8.7 + - - +
82F SER* 1.3 77.9 - - - +
84F ARG* 1.3 58.7 + - - +
86F GLN* 3.3 1.9 + - - +
87F LEU* 2.8 32.4 + - - +
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Residues in contact with ARG 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E GLU* 2.9 19.2 + - - +
56E LYS* 2.7 35.7 + - - +
58E GLY 3.5 5.8 - - - +
64F LEU* 3.4 38.8 - - + +
65F SER* 2.8 38.5 + - - +
66F TYR* 3.7 13.4 - - + +
67F LYS* 4.6 7.7 - - - +
80F GLN* 3.8 20.1 + - + +
81F ASP* 3.0 27.9 + - - +
83F CYS* 1.3 79.6 - - - +
85F SER* 1.3 56.4 + - - +
87F LEU* 3.8 3.3 - - - +
88F CYS* 3.0 28.9 + - - +
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Residues in contact with SER 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F CYS* 4.6 3.1 - - - +
78F ALA 4.3 3.2 + - - -
79F LYS* 5.0 0.7 - - - -
80F GLN* 2.6 44.5 + - - +
81F ASP 2.9 9.2 + - - -
82F SER* 3.7 5.6 - - - -
84F ARG* 1.3 76.3 - - - +
86F GLN* 1.3 58.3 + - - +
88F CYS* 3.5 5.6 + - - +
89F GLU* 3.1 32.3 + - - +
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Residues in contact with GLN 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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50F CYS 4.9 0.8 + - - -
53F ARG* 4.3 26.5 - - - +
54F LEU* 3.5 26.2 - - + +
57F ARG* 2.4 42.6 + - - +
82F SER 3.0 15.8 + - - +
85F SER* 1.3 74.0 - - - +
87F LEU* 1.3 60.1 + - - +
89F GLU* 3.5 7.4 + - - +
90F CYS* 3.0 36.3 + - - -
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Residues in contact with LEU 87 (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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51F TYR* 3.5 34.1 - - + +
54F LEU* 3.6 17.6 - - + +
60F GLY 4.2 2.2 - - - +
61F THR* 3.7 25.1 - - - +
64F LEU* 3.2 46.7 - - + +
66F TYR* 3.4 19.5 - - + -
83F CYS 2.8 17.7 + - - +
84F ARG* 3.8 3.1 - - - +
86F GLN* 1.3 72.3 - - - +
88F CYS* 1.3 66.4 + - - +
90F CYS* 3.1 5.5 + - - +
91F ASP* 3.0 25.0 + - - +
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Residues in contact with CYS 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F MET* 4.2 3.8 - - - +
66F TYR* 3.7 38.1 - - + -
67F LYS 4.3 1.1 - - - -
68F PHE* 4.1 8.5 - - - -
77F CYS* 2.0 51.8 - - + -
80F GLN* 4.3 2.9 - - - +
84F ARG 3.0 19.2 + - - +
85F SER 3.6 3.8 - - - +
86F GLN 3.3 0.2 - - - -
87F LEU* 1.3 77.5 - - - +
89F GLU* 1.3 55.9 + - - +
91F ASP* 3.1 3.8 + - - +
92F LYS* 2.7 29.5 + - - +
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Residues in contact with GLU 89 (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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77F CYS* 3.8 23.2 + - + +
85F SER* 3.1 18.4 + - - +
86F GLN* 4.0 7.0 - - + +
87F LEU 3.3 0.2 - - - -
88F CYS* 1.3 74.9 - - - +
90F CYS* 1.3 62.0 + - - +
92F LYS* 3.6 29.0 + - - +
93F ALA* 2.9 25.5 + - - +
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Residues in contact with CYS 90 (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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47F HIS* 3.3 13.2 - - + -
50F CYS* 2.0 64.9 - - + -
51F TYR* 4.2 13.2 - - + -
54F LEU* 3.8 10.8 - - - -
86F GLN* 3.0 27.0 + - - -
87F LEU 3.1 9.6 + - - +
89F GLU* 1.3 79.3 - - - +
91F ASP* 1.3 56.8 + - - +
93F ALA* 3.5 4.5 + - - +
94F ALA 3.1 20.1 + - - -
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Residues in contact with ASP 91 (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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1F ASN 4.4 2.1 + - - +
5F PHE* 3.4 34.4 - - + +
8F MET* 3.5 4.0 - - - -
47F HIS* 2.8 28.2 + - - -
51F TYR* 2.9 22.3 + - - -
66F TYR* 2.8 38.8 + - - +
87F LEU* 3.0 9.8 + - - +
88F CYS 3.7 3.8 - - - +
90F CYS* 1.3 73.9 - - - +
92F LYS* 1.3 60.2 + - - +
94F ALA 3.2 0.2 + - - -
95F ALA* 2.8 32.1 + - - +
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Residues in contact with LYS 92 (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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8F MET* 3.5 9.8 - - - -
75F ILE* 3.1 53.5 + - + +
76F THR* 4.7 4.0 - - - +
77F CYS* 4.4 1.8 - - - +
88F CYS 2.7 20.6 + - - +
89F GLU* 3.6 35.2 + - - +
91F ASP* 1.3 73.4 - - - +
93F ALA* 1.3 62.5 + - - +
95F ALA* 3.7 1.9 - - - +
96F THR* 2.9 39.2 + - - +
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F THR* 6.2 4.7 - - + -
50F CYS* 6.0 1.3 - - - -
89F GLU 2.9 19.4 + - - +
90F CYS* 3.6 6.5 - - - +
92F LYS* 1.3 78.1 - - - +
94F ALA* 1.3 60.4 + - - +
96F THR* 4.0 3.6 - - - -
97F CYS* 3.1 23.6 + - - +
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Residues in contact with ALA 94 (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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5F PHE* 3.7 16.2 - - + -
43F CYS* 4.9 5.4 - - - +
47F HIS* 3.5 39.9 - - + -
90F CYS 3.1 5.9 + - - -
91F ASP 3.2 1.5 + - - +
93F ALA* 1.3 75.5 - - - +
95F ALA* 1.3 58.5 + - - +
97F CYS* 3.1 7.9 + - - +
98F PHE* 3.0 44.6 + - + -
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Residues in contact with ALA 95 (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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5F PHE* 4.3 0.8 - - - -
8F MET* 3.8 31.2 - - + -
9F ILE* 4.4 8.3 - - + +
12F THR* 2.9 33.7 + - + +
75F ILE* 6.0 0.4 - - + -
91F ASP 2.8 20.0 + - - +
92F LYS 3.7 4.7 - - - +
94F ALA* 1.3 72.7 - - - +
96F THR* 1.3 61.4 + - - +
98F PHE* 3.6 11.5 + - - +
99F ALA 3.3 12.8 + - - -
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Residues in contact with THR 96 (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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12F THR* 4.8 7.3 - - - +
75F ILE* 5.8 1.0 - - - +
92F LYS* 2.9 28.2 + - - +
93F ALA* 4.0 4.5 - - - -
95F ALA* 1.3 74.1 - - - +
97F CYS* 1.3 61.3 + - - +
99F ALA* 3.1 10.0 + - + +
100F ARG* 2.8 59.2 + - - +
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Residues in contact with CYS 97 (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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39F ALA 4.7 0.2 - - - -
43F CYS* 2.0 52.7 - - + -
46F THR* 6.0 0.7 - - - -
93F ALA 3.1 16.3 + - - +
94F ALA* 3.1 10.3 + - - +
96F THR* 1.3 78.1 - - - +
98F PHE* 1.3 59.1 + - - +
100F ARG* 3.3 11.4 + - - +
101F ASN* 3.0 38.1 + - - -
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Residues in contact with PHE 98 (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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5F PHE* 4.5 4.3 - + - -
9F ILE* 4.1 28.0 - - + -
13F THR* 3.5 17.9 - - + +
21F TYR* 3.8 32.7 + + - +
40F THR* 3.8 25.7 + - + -
43F CYS* 3.6 26.7 - - + -
44F CYS* 3.6 27.8 - - - -
94F ALA* 3.0 26.8 + - + -
95F ALA* 3.8 4.5 - - - +
97F CYS* 1.3 75.6 - - - +
99F ALA* 1.3 56.8 + - - +
101F ASN* 3.2 5.7 + - - +
102F LYS* 3.0 28.2 + - - +
190F OAP 4.4 16.4 - - + -
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Residues in contact with ALA 99 (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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12F THR* 3.7 26.0 - - - +
13F THR* 3.5 2.8 - - - +
95F ALA 3.3 11.4 + - - +
96F THR* 3.1 13.4 + - + +
98F PHE* 1.3 77.0 - - - +
100F ARG* 1.3 66.7 + - - +
102F LYS* 3.1 29.8 + - + +
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Residues in contact with ARG 100 (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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96F THR* 2.8 41.0 + - - +
97F CYS* 3.3 16.5 - - - +
99F ALA* 1.3 76.3 - - - +
101F ASN* 1.3 69.6 + - - +
102F LYS 3.7 0.3 + - - -
103F THR* 4.0 9.5 + - - +
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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