Contacts of the helix formed by residues 82 - 101 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 2.9 21.4 + - - -
80D GLN 3.7 0.6 + - - -
81D ASP* 1.3 73.8 - - - +
83D CYS* 1.3 59.7 + - - +
85D SER* 4.2 5.8 - - - -
86D GLN* 2.8 38.8 + - - +
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Residues in contact with CYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG 4.5 5.4 - - - +
58C GLY* 3.5 27.4 - - - +
59C CYS* 5.5 0.2 - - - -
83C CYS* 5.7 3.6 - - - -
54D LEU* 3.6 6.0 - - - +
57D ARG* 4.1 3.1 - - - +
58D GLY 5.1 0.7 - - - -
59D CYS* 2.0 54.2 - - + +
60D GLY 5.1 0.2 - - - +
64D LEU* 4.2 4.5 - - + +
81D ASP* 3.3 9.0 + - - +
82D SER* 1.3 82.5 + - - +
84D ARG* 1.3 58.4 + - - +
87D LEU* 3.0 29.1 + - - +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLU* 3.0 26.6 + - - +
56C LYS* 2.7 29.7 + - - +
58C GLY* 3.4 10.3 - - - +
64D LEU* 3.4 24.4 - - + +
65D SER* 2.9 35.9 + - - +
66D TYR* 3.8 7.2 - - + +
80D GLN* 3.6 28.3 - - + -
81D ASP* 3.1 28.9 + - - +
83D CYS* 1.3 77.5 - - - +
85D SER* 1.3 61.8 + - - +
87D LEU* 3.8 4.7 - - - +
88D CYS* 2.9 30.8 + - - +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D CYS* 4.8 2.6 - - - +
78D ALA 4.3 5.0 + - - -
79D LYS* 5.0 0.7 - - - -
80D GLN* 2.8 30.6 + - - +
81D ASP 2.8 21.2 + - - -
82D SER* 3.8 6.7 - - - -
84D ARG* 1.3 78.5 - - - +
86D GLN* 1.3 65.4 + - - +
88D CYS* 3.4 5.4 + - - +
89D GLU* 3.0 30.7 + - - +
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ARG* 5.6 4.0 + - - -
54D LEU* 3.4 22.6 - - + +
57D ARG* 3.7 26.0 + - - +
82D SER* 2.8 28.7 + - - +
85D SER* 1.3 80.6 - - - +
87D LEU* 1.3 62.2 + - - +
89D GLU* 3.3 12.2 + - - +
90D CYS* 3.1 27.2 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASN 4.5 0.4 - - - +
51D TYR* 3.4 42.0 - - + +
54D LEU* 3.7 18.5 - - + +
60D GLY 3.8 6.1 - - - +
61D THR* 3.3 37.5 - - - +
64D LEU* 3.3 27.8 - - + +
66D TYR* 4.0 15.5 - - + -
83D CYS 3.0 16.9 + - - +
84D ARG* 3.8 4.3 - - - +
85D SER 3.3 0.2 - - - -
86D GLN* 1.3 72.4 - - - +
88D CYS* 1.3 66.5 + - - +
90D CYS* 3.1 12.7 + - - +
91D ASP* 3.1 15.2 + - - +
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Residues in contact with CYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D MET* 4.4 3.6 - - - +
66D TYR* 3.7 39.9 - - + -
67D LYS 4.2 1.6 - - - -
68D PHE* 3.9 9.6 - - - -
77D CYS* 2.0 54.0 - - + -
80D GLN* 4.5 2.5 - - - +
84D ARG 2.9 19.6 + - - +
85D SER* 3.6 5.2 - - - +
87D LEU* 1.3 76.3 - - - +
89D GLU* 1.3 54.6 + - - +
91D ASP* 3.3 4.5 + - - +
92D LYS* 2.9 23.2 + - - +
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Residues in contact with GLU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D CYS* 3.5 27.9 + - + +
85D SER* 3.0 23.0 + - - +
86D GLN* 3.8 12.1 - - - +
87D LEU 3.2 0.2 - - - -
88D CYS* 1.3 73.6 - - - +
90D CYS* 1.3 61.9 + - - +
92D LYS* 3.8 20.5 + - - +
93D ALA* 3.0 27.2 + - - +
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Residues in contact with CYS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D HIS* 3.2 15.0 - - + -
50D CYS* 2.0 53.2 - - + -
51D TYR* 4.3 11.7 - - + -
53D ARG* 4.9 5.4 - - - -
86D GLN 3.1 12.7 + - - +
87D LEU* 3.1 10.2 + - - +
89D GLU* 1.3 76.4 - - - +
91D ASP* 1.3 65.8 + - - +
93D ALA* 3.4 6.5 + - - +
94D ALA 3.1 17.0 + - - -
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Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASN 4.2 1.6 - - - +
5D PHE* 3.4 34.3 - - + +
8D MET* 3.6 5.6 - - - -
47D HIS* 2.9 12.9 + - - -
51D TYR* 2.7 32.1 + - - -
66D TYR* 2.6 39.2 + - - +
87D LEU 3.1 8.3 + - - -
88D CYS 3.6 5.6 - - - +
90D CYS* 1.3 73.8 - - - +
92D LYS* 1.3 60.8 + - - +
94D ALA* 3.1 2.8 + - - +
95D ALA* 2.8 31.7 + - - +
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Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D MET* 3.4 15.6 - - - -
74D ARG* 6.0 0.2 - - - +
75D ILE* 2.5 49.1 + - + +
76D THR* 4.4 4.0 - - - +
77D CYS* 4.4 8.2 - - - +
88D CYS 2.9 16.8 + - - +
89D GLU* 3.8 25.6 + - - +
90D CYS 3.3 0.2 - - - -
91D ASP* 1.3 79.1 - - - +
93D ALA* 1.3 56.6 + - - +
95D ALA* 4.1 1.1 - - - +
96D THR* 3.0 41.2 + - - +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 6.0 7.2 - - + -
89D GLU 3.0 17.8 + - - +
90D CYS* 3.7 7.9 - - - +
91D ASP 3.2 0.2 - - - -
92D LYS* 1.3 76.4 - - - +
94D ALA* 1.3 60.9 - - - +
96D THR* 3.9 3.9 - - - +
97D CYS* 2.9 30.0 + - - +
100D ARG* 5.1 3.0 + - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.7 13.9 - - + -
43D CYS* 5.0 7.4 - - - +
47D HIS* 3.4 39.5 - - + -
90D CYS 3.1 4.9 + - - -
91D ASP 3.1 5.6 + - - +
93D ALA* 1.3 75.1 - - - +
95D ALA* 1.3 63.4 + - - +
97D CYS* 2.9 18.3 + - - +
98D PHE* 2.9 27.2 + - + -
190D OAP 5.5 0.2 - - + -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.3 1.0 - - + -
8D MET* 3.9 27.6 - - + +
9D ILE* 4.2 12.8 - - + -
12D THR* 3.0 32.0 + - + +
91D ASP 2.8 20.4 + - - +
92D LYS* 4.1 3.1 - - - +
94D ALA* 1.3 70.8 - - - +
96D THR* 1.3 62.1 + - - +
98D PHE* 3.7 13.1 + - - +
99D ALA 3.2 13.7 + - - -
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 4.8 9.4 - - - +
75D ILE* 6.0 1.4 - - - +
92D LYS* 3.0 30.8 + - - +
93D ALA* 3.9 4.7 - - - -
94D ALA 3.2 0.2 - - - -
95D ALA* 1.3 75.4 - - - +
97D CYS* 1.3 59.5 + - - +
99D ALA* 3.2 8.3 + - + +
100D ARG* 2.9 62.9 + - + +
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Residues in contact with CYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA 4.4 0.7 - - - -
43D CYS* 2.0 51.6 - - + -
93D ALA 2.9 18.6 + - - +
94D ALA* 2.9 6.1 + - - +
96D THR* 1.3 76.7 - - - +
98D PHE* 1.3 62.3 + - - +
100D ARG* 3.1 27.2 + - - +
101D ASN* 3.0 37.5 + - - -
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.8 2.7 - + - -
9D ILE* 4.3 19.7 - - + -
13D THR* 3.7 16.6 - - + -
21D TYR* 3.8 41.5 + + + +
40D THR* 3.4 46.1 + - + -
43D CYS* 3.7 14.1 - - + -
44D CYS* 3.5 24.0 - - - -
94D ALA* 2.9 22.4 + - + -
95D ALA* 3.7 5.4 - - - +
97D CYS* 1.3 75.7 - - - +
99D ALA* 1.3 61.3 + - - +
101D ASN 3.2 2.9 + - - -
102D LYS* 3.0 23.7 + - - +
190D OAP 4.2 19.1 - - + -
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 3.6 28.9 - - - +
13D THR* 3.6 8.7 - - - +
73D SER* 6.5 0.4 - - - -
95D ALA 3.2 11.8 + - - +
96D THR* 3.2 12.4 + - + +
98D PHE* 1.3 78.0 - - - +
100D ARG* 1.3 63.4 + - + +
101D ASN 3.1 1.4 + - - -
102D LYS* 3.2 21.5 + - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA* 5.1 2.6 + - - +
96D THR* 2.9 43.0 + - + +
97D CYS* 3.1 35.3 + - - +
99D ALA* 1.3 72.9 - - + +
101D ASN* 1.3 69.3 + - - +
102D LYS 3.6 0.6 + - - -
103D THR* 4.5 6.6 + - - -
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA* 3.2 32.9 + - + +
40D THR* 3.7 17.3 + - - +
43D CYS* 3.8 3.6 - - - -
97D CYS* 3.0 42.1 + - - +
98D PHE 3.5 2.9 - - - -
99D ALA 3.1 0.2 - - - -
100D ARG* 1.3 88.8 - - - +
102D LYS* 1.3 61.7 + - - +
103D THR* 3.1 7.6 - - - +
104D THR* 3.0 22.7 + - - +
105D TYR 3.4 5.4 + - - -
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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