Contacts of the helix formed by residues 39 - 56 (chain B) 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 ALA 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ASP* 1.3 75.4 - - - +
40B THR* 1.3 65.6 + - - +
41B ASP 3.1 1.8 - - - -
42B ARG* 3.1 15.8 + - - +
43B CYS* 3.0 27.5 + - - -
97B CYS* 4.6 0.2 - - - -
101B ASN* 3.4 29.8 + - + +
104B THR* 4.8 10.2 - - + +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.5 37.0 - - + -
24B TYR* 3.8 22.2 - - + -
28B CYS* 4.6 1.6 - - - -
38B ASP* 3.4 14.4 + - - -
39B ALA* 1.3 76.3 - - - +
41B ASP* 1.3 57.4 + - - +
43B CYS* 3.1 31.8 + - - +
44B CYS* 3.5 2.9 + - - -
98B PHE* 3.4 14.1 + - + -
101B ASN* 3.6 23.3 + - - +
104B THR* 4.8 0.7 - - - +
105B TYR* 4.2 11.6 + - - +
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.6 7.1 - - + +
25B GLY* 4.0 6.1 - - - -
26B CYS 2.9 23.2 + - - -
27B HIS* 2.9 25.6 + - - +
28B CYS* 3.6 11.5 + - - -
36B PRO* 3.3 9.8 - - + +
37B LYS* 2.9 27.1 + - - +
38B ASP* 3.0 23.7 + - - +
40B THR* 1.3 76.6 - - - +
42B ARG* 1.3 62.9 + - - +
43B CYS 3.2 0.2 - - - -
44B CYS* 3.3 3.0 + - - +
45B VAL* 3.2 20.4 + - - +
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 3.4 40.2 + - + +
37B LYS 5.3 1.2 + - - -
38B ASP* 3.1 26.4 + - - +
39B ALA* 3.1 17.0 + - - +
41B ASP* 1.3 74.3 - - - +
43B CYS* 1.3 66.4 + - - +
44B CYS 3.1 0.2 - - - -
45B VAL* 3.2 9.0 + - + +
46B THR* 3.1 26.1 + - - -
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Residues in contact with CYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA 3.0 23.7 + - - -
40B THR* 3.1 12.8 - - - +
42B ARG* 1.3 77.9 - - - +
44B CYS* 1.3 54.2 + - - +
46B THR* 3.4 9.2 + - - -
47B HIS* 3.1 25.6 + - - +
94B ALA* 4.4 7.0 - - - +
97B CYS* 2.0 62.1 - - + -
98B PHE* 3.4 19.3 - - + -
101B ASN* 3.2 11.9 - - - -
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Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 3.5 18.8 - - - +
28B CYS* 2.0 51.6 - - - -
40B THR 3.8 0.7 - - - -
41B ASP 3.3 6.9 + - - +
42B ARG 3.1 0.4 - - - -
43B CYS* 1.3 74.3 - - - +
45B VAL* 1.3 53.8 + - - +
47B HIS* 3.0 1.8 + - - +
48B ASP* 2.7 40.2 + - - +
98B PHE* 3.4 25.8 - - - -
190B OAP 3.7 13.7 - - + -
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 3.3 38.3 - - + +
36B PRO* 4.1 11.4 - - + -
41B ASP 3.2 11.2 + - - +
42B ARG* 3.2 10.8 + - + +
44B CYS* 1.3 76.2 - - - +
46B THR* 1.3 65.4 + - - +
48B ASP* 3.3 5.8 + - - +
49B CYS* 3.2 33.3 + - - -
122B PRO* 3.3 36.8 - - + +
123B ARG 5.6 1.3 - - - +
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG 3.1 13.7 + - - -
43B CYS* 3.6 10.3 - - - -
44B CYS 3.2 0.2 - - - -
45B VAL* 1.3 78.4 - - - +
47B HIS* 1.3 57.5 + - - +
49B CYS* 3.3 8.0 + - + +
50B CYS* 3.1 28.4 + - + +
93B ALA* 6.0 6.7 - - + -
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.5 24.6 - + - -
43B CYS 3.1 13.4 + - - +
44B CYS 3.0 8.2 + - - +
46B THR* 1.3 75.6 - - - +
48B ASP* 1.3 65.2 + - - +
49B CYS 3.1 0.2 - - - -
50B CYS* 3.2 4.8 + - - +
51B TYR* 3.1 50.4 + + - +
90B CYS* 3.5 28.5 - - + -
91B ASP* 2.8 22.2 + - - -
94B ALA* 3.5 17.7 - - + -
190B OAP 2.8 35.3 + - + +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 3.2 12.9 + - - +
31B GLY 2.8 13.3 - - - +
32B GLY* 4.3 2.3 - - - -
44B CYS 2.7 21.4 + - - +
45B VAL* 3.3 7.6 + - - +
47B HIS* 1.3 72.7 - - - +
49B CYS* 1.3 58.7 + - - +
51B TYR* 4.0 1.6 - - - +
52B LYS* 3.1 34.4 + - + +
124B CYS* 5.3 0.2 - - - -
190B OAP 2.9 32.2 - - + +
191B CA 2.4 31.2 - - - -
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Residues in contact with CYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.2 26.6 + - - +
46B THR* 3.5 11.7 - - - +
47B HIS 3.1 0.6 - - - -
48B ASP* 1.3 77.6 - - - +
50B CYS* 1.3 64.1 + - - +
52B LYS* 3.9 3.3 - - - +
53B ARG* 3.1 26.0 + - - +
122B PRO 5.2 1.8 - - - -
123B ARG 4.8 0.4 - - - -
124B CYS* 2.0 66.2 - - + +
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 3.1 15.8 + - - +
47B HIS* 3.5 11.4 - - - +
49B CYS* 1.3 78.2 - - - +
51B TYR* 1.3 61.5 + - - +
53B ARG* 3.5 28.9 + - - +
54B LEU* 3.1 25.5 + - - +
90B CYS* 2.0 55.9 - - + -
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 5.2 1.9 + - - -
2B LEU* 4.8 4.3 - - - +
5B PHE* 4.5 5.4 - - - +
47B HIS* 3.1 43.8 + + - +
48B ASP 4.0 3.8 - - - +
50B CYS* 1.3 75.5 - - - +
52B LYS* 1.3 66.6 + - - +
54B LEU* 2.9 7.4 + - + +
55B GLU* 2.9 35.3 + - - +
61B THR* 3.7 28.4 + - + -
62B LYS* 4.1 13.2 - - + -
87B LEU* 3.5 25.8 - - + +
90B CYS* 4.4 8.3 - - + -
91B ASP* 2.9 26.6 + - - -
190B OAP 3.4 42.4 - - + +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP* 3.1 23.1 + - - +
49B CYS* 3.9 6.5 - - - +
50B CYS 3.4 0.2 - - - -
51B TYR* 1.3 75.0 - - - +
53B ARG* 1.3 58.2 + - - +
55B GLU* 3.3 14.8 + - - +
56B LYS* 2.8 53.1 + - + +
124B CYS* 5.4 11.0 - - - -
115F LYS* 3.1 35.8 + - + +
117F CYS 5.1 5.1 + - - -
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B CYS 3.1 15.7 + - - +
50B CYS* 3.5 30.3 - - - +
52B LYS* 1.3 79.6 - - - +
54B LEU* 1.3 64.5 + - + +
56B LYS* 3.4 19.4 - - - +
57B ARG* 3.4 19.2 + - - +
86B GLN* 3.5 34.9 + - - +
90B CYS* 4.9 0.4 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B CYS 3.1 15.5 + - - +
51B TYR* 2.9 10.1 + - + +
53B ARG* 1.3 80.6 - - + +
55B GLU* 1.3 64.8 + - - +
57B ARG* 3.3 24.4 + - - +
59B CYS* 2.9 38.1 + - + -
60B GLY 5.1 0.2 - - - +
61B THR* 3.9 12.3 - - + -
83B CYS 4.8 1.6 - - - +
86B GLN* 3.5 33.4 - - + -
87B LEU* 3.6 45.5 - - + +
90B CYS* 3.9 15.0 - - - -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE 5.7 2.2 - - - +
64A LEU* 3.6 6.8 - - + +
84A ARG* 3.0 17.8 + - - +
51B TYR* 2.9 30.5 + - - +
52B LYS* 3.6 12.5 + - - +
54B LEU* 1.3 76.7 - - - +
56B LYS* 1.3 58.9 + - + +
58B GLY* 2.7 21.8 + - - -
59B CYS 3.8 10.7 + - - +
61B THR* 4.0 22.7 + - + +
62B LYS* 5.3 6.1 + - - -
190B OAP 5.2 5.5 - - - +
115F LYS* 5.7 5.2 - - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 4.5 1.2 - - - +
84A ARG* 3.2 23.4 + - - +
52B LYS* 2.8 38.6 + - + +
53B ARG* 3.4 11.2 - - - +
54B LEU 3.2 0.2 - - - -
55B GLU* 1.3 77.3 - - + +
57B ARG* 1.3 56.6 + - - +
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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