Contacts of the helix formed by residues 39 - 57 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 1.3 75.1 - - - +
40A THR* 1.3 65.4 + - - +
42A ARG* 3.2 19.3 + - - +
43A CYS* 3.1 26.4 + - - -
101A ASN* 3.4 30.6 + - + +
104A THR* 4.6 13.2 - - + +
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Residues in contact with THR 40 (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 TYR* 3.7 32.1 - - + -
24A TYR* 3.7 32.8 + - + -
28A CYS* 4.7 0.9 - - - -
38A ASP* 3.4 6.9 + - - -
39A ALA* 1.3 77.3 - - - +
41A ASP* 1.3 58.0 + - - +
43A CYS* 2.9 34.0 + - - +
44A CYS* 3.3 6.9 + - - -
98A PHE* 4.0 11.5 + - + -
101A ASN* 3.6 22.7 + - - +
104A THR 4.8 0.5 - - - -
105A TYR* 4.3 8.4 + - + +
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Residues in contact with ASP 41 (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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24A TYR* 3.7 5.7 - - + +
25A GLY* 3.5 7.8 - - - -
26A CYS* 2.9 24.3 + - - +
27A HIS* 2.9 25.6 + - - +
28A CYS* 3.6 13.6 + - - -
36A PRO* 3.3 11.2 - - + +
37A LYS* 2.8 27.0 + - - +
38A ASP* 3.1 23.4 + - - +
40A THR* 1.3 76.1 - - - +
42A ARG* 1.3 57.3 + - - +
44A CYS* 3.0 15.9 + - - +
45A VAL* 3.1 13.2 + - - +
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Residues in contact with ARG 42 (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 PRO* 3.6 35.2 + - + +
38A ASP* 2.9 28.3 + - - +
39A ALA* 3.4 18.5 - - - +
40A THR 3.2 0.4 - - - -
41A ASP* 1.3 72.2 - - - +
43A CYS* 1.3 60.9 + - - +
44A CYS 3.2 0.2 - - - -
45A VAL* 3.5 9.9 + - + +
46A THR* 3.0 26.8 + - - +
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Residues in contact with CYS 43 (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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39A ALA 3.1 19.9 + - - -
40A THR* 2.9 15.4 + - - +
42A ARG* 1.3 76.2 - - - +
44A CYS* 1.3 55.7 + - - +
46A THR* 3.3 8.7 + - - -
47A HIS* 3.1 25.9 + - - +
94A ALA* 4.8 5.8 - - - +
97A CYS* 2.0 64.8 - - + -
98A PHE* 3.5 20.4 - - + -
101A ASN* 3.5 7.2 - - - -
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Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.8 1.8 - - - -
28A CYS* 2.0 64.8 - - - +
40A THR 3.7 0.7 - - - -
41A ASP 3.0 8.0 + - - +
43A CYS* 1.3 79.5 - - - +
45A VAL* 1.3 58.9 + - - +
47A HIS* 3.2 0.6 + - - -
48A ASP* 2.9 36.8 + - - +
98A PHE* 3.5 28.3 - - - -
190A OAP 3.7 15.1 - - + +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.4 42.1 - - + +
36A PRO* 4.2 7.6 - - + -
41A ASP 3.1 13.8 + - - +
42A ARG* 3.8 15.9 - - + +
43A CYS 3.4 0.4 - - - -
44A CYS* 1.3 76.0 - - - +
46A THR* 1.3 59.6 + - - +
48A ASP* 3.5 6.1 + - - +
49A CYS* 3.1 36.5 + - - -
121A THR* 5.6 1.6 - - + -
122A PRO* 3.8 34.8 - - + +
123A ARG 5.5 0.7 - - - +
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Residues in contact with THR 46 (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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42A ARG* 3.0 16.2 + - - +
43A CYS* 3.3 10.7 + - - -
44A CYS 3.2 0.2 - - - -
45A VAL* 1.3 79.0 - - - +
47A HIS* 1.3 59.7 + - - +
49A CYS* 3.3 8.3 + - + +
50A CYS* 3.0 27.3 + - + +
93A ALA* 6.2 3.4 - - + -
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Residues in contact with HIS 47 (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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5A PHE* 3.7 16.8 - + - -
43A CYS 3.1 13.4 + - - +
44A CYS 3.2 0.2 + - - -
46A THR* 1.3 74.3 - - - +
48A ASP* 1.3 66.9 + - - +
50A CYS* 3.2 4.5 + - - +
51A TYR* 3.0 52.9 + + - +
90A CYS* 3.2 30.5 - - + -
91A ASP* 2.8 25.0 + - - -
94A ALA* 3.6 19.1 - - + -
190A OAP 2.8 41.8 + - + +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.4 9.8 + - - +
31A GLY 3.0 12.0 - - - +
32A GLY* 4.5 1.6 - - - -
44A CYS 2.9 20.3 + - - +
45A VAL* 3.6 8.5 - - - +
47A HIS* 1.3 76.7 - - - +
49A CYS* 1.3 62.8 + - - +
51A TYR* 3.5 2.4 + - - +
52A LYS* 3.1 24.1 + - - +
190A OAP 2.8 38.1 - - - +
191A CA 2.2 32.0 - - - -
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Residues in contact with CYS 49 (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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45A VAL* 3.1 32.3 + - - -
46A THR* 3.5 12.6 - - + +
47A HIS 3.1 0.4 - - - -
48A ASP* 1.3 75.8 - - - +
50A CYS* 1.3 64.9 + - - +
52A LYS* 3.3 7.4 + - - +
53A ARG* 3.2 25.0 + - - +
122A PRO 5.2 0.9 - - - -
123A ARG 4.7 0.9 - - - -
124A CYS* 2.0 65.1 - - + +
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.0 13.9 + - + +
47A HIS* 3.2 10.5 + - - +
49A CYS* 1.3 76.3 - - - +
51A TYR* 1.3 61.1 + - - +
53A ARG* 3.2 50.8 + - - +
54A LEU* 3.2 6.4 + - - +
86A GLN 4.6 0.2 - - - -
90A CYS* 2.0 55.6 - - + -
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Residues in contact with TYR 51 (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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1A ASN* 5.3 3.1 + - - -
2A LEU* 4.9 4.9 - - + +
5A PHE* 4.5 5.5 - - - +
47A HIS* 3.0 42.4 + + - +
48A ASP 3.8 3.8 - - - +
50A CYS* 1.3 76.8 - - - +
52A LYS* 1.3 57.7 + - - +
54A LEU* 3.3 6.9 + - - +
55A GLU* 3.0 35.0 + - + +
61A THR* 3.7 29.7 + - + +
62A LYS* 4.4 11.3 - - + -
87A LEU* 3.5 25.4 - - + +
90A CYS* 4.1 12.3 - - + -
91A ASP* 2.9 25.7 + - - -
190A OAP 3.6 44.2 - - + -
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Residues in contact with LYS 52 (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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48A ASP 3.1 18.3 + - - +
49A CYS* 3.4 7.2 - - - +
51A TYR* 1.3 75.3 - - - +
53A ARG* 1.3 66.1 + - + +
55A GLU* 3.6 12.5 + - - +
56A LYS* 3.1 46.4 + - + +
124A CYS* 4.5 21.7 - - + +
115C LYS* 6.2 4.5 - - + +
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Residues in contact with ARG 53 (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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49A CYS 3.2 9.1 + - - +
50A CYS* 3.2 47.4 + - - +
52A LYS* 1.3 77.2 - - + +
54A LEU* 1.3 82.7 + - + +
56A LYS* 3.5 9.1 + - - +
57A ARG* 3.2 25.6 + - - +
86A GLN* 4.4 21.3 + - - +
90A CYS* 3.9 1.8 - - - -
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Residues in contact with LEU 54 (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 CYS 3.2 13.7 + - - +
51A TYR* 3.6 8.5 - - - +
52A LYS 3.2 0.2 - - - -
53A ARG* 1.3 84.1 - - - +
55A GLU* 1.3 65.3 + - - +
57A ARG* 3.1 26.4 + - - +
59A CYS* 3.1 40.9 + - + +
60A GLY 5.0 1.3 - - - +
61A THR* 4.0 12.3 - - + -
83A CYS 4.5 1.8 - - - +
86A GLN* 3.6 26.7 - - + -
87A LEU* 3.7 33.2 - - + +
90A CYS* 3.6 25.6 - - - -
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Residues in contact with GLU 55 (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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51A TYR* 3.0 21.6 + - - +
52A LYS* 4.0 11.9 - - - +
54A LEU* 1.3 75.2 - - - +
56A LYS* 1.3 52.3 + - - +
58A GLY* 2.9 12.5 + - - -
59A CYS 4.0 11.0 + - - +
61A THR* 4.1 23.1 + - + +
62A LYS* 4.4 10.9 + - - -
63B PHE* 4.7 9.7 - - - +
64B LEU* 3.7 8.4 - - + +
84B ARG* 2.6 28.4 + - - +
115C LYS* 3.5 39.9 + - - +
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Residues in contact with LYS 56 (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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52A LYS* 3.1 38.8 + - + +
53A ARG* 3.5 11.2 - - - +
54A LEU 3.2 0.2 - - - -
55A GLU* 1.3 79.8 - - - +
57A ARG* 1.3 56.4 + - - +
58A GLY 3.3 0.2 - - - -
81B ASP* 4.7 3.3 - - - +
84B ARG* 3.3 19.7 + - - +
116C HIS* 5.8 6.8 + - - -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 3.2 18.8 - - - +
54A LEU* 3.2 23.1 - - - +
56A LYS* 1.3 77.5 - - - +
58A GLY* 1.3 59.6 + - - +
59A CYS* 3.7 21.5 + - - -
82A SER* 3.2 25.7 + - - -
83A CYS* 4.5 2.4 - - - -
86A GLN* 2.9 40.6 + - - +
81B ASP* 4.2 14.3 - - - +
83B CYS* 5.0 3.5 - - - -
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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
------------------------------------------------------------
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