Contacts of the helix formed by residues 39 - 57 (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 ALA 39 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 1.3 76.8 - - - +
40F THR* 1.3 61.3 + - - +
42F ARG* 3.1 41.3 + - - +
43F CYS* 3.2 17.5 + - - -
97F CYS* 4.7 0.3 - - - -
101F ASN* 3.2 31.8 + - - +
104F THR* 3.7 15.5 - - + +
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Residues in contact with THR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F TYR* 3.8 29.3 - - + -
24F TYR* 3.5 38.0 + - + -
28F CYS* 4.4 1.3 - - - -
38F ASP* 3.3 2.9 + - - -
39F ALA* 1.3 77.2 - - - +
41F ASP* 1.3 64.1 + - - +
43F CYS* 3.2 25.8 + - - +
44F CYS* 3.4 8.3 + - - -
98F PHE* 3.8 14.1 + - + -
101F ASN* 4.0 20.2 + - - +
104F THR* 5.0 0.5 + - - -
105F TYR* 4.3 10.7 + - - -
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Residues in contact with ASP 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 4.1 1.5 - - + -
25F GLY* 3.4 9.5 - - - -
26F CYS* 2.8 24.3 + - - +
27F HIS* 3.1 24.0 + - - +
28F CYS* 3.8 10.9 + - - -
36F PRO* 3.3 11.1 - - + +
37F LYS* 2.7 29.1 + - - +
38F ASP* 2.8 24.4 + - - +
40F THR* 1.3 82.3 - - - +
42F ARG* 1.3 58.0 + - - +
44F CYS* 3.2 3.8 + - - +
45F VAL* 3.2 21.3 + - - +
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F PRO* 3.7 23.3 + - + +
38F ASP* 2.9 16.5 + - - +
39F ALA* 3.1 46.6 + - - +
41F ASP* 1.3 74.3 - - - +
43F CYS* 1.3 65.2 + - - +
45F VAL* 3.1 10.2 + - + +
46F THR* 2.9 27.1 + - - -
97F CYS* 5.2 0.2 - - - -
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Residues in contact with CYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA 3.2 18.5 + - - -
40F THR* 3.2 15.0 + - - +
42F ARG* 1.3 76.0 - - - +
44F CYS* 1.3 58.7 + - - +
46F THR* 3.2 9.6 + - - -
47F HIS* 2.9 27.6 + - - +
94F ALA* 4.8 5.6 - - - +
97F CYS* 2.0 66.6 - - + -
98F PHE* 3.6 17.7 - - + -
101F ASN* 3.9 4.3 - - - -
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Residues in contact with CYS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F HIS* 3.7 3.1 - - - +
28F CYS* 2.0 66.4 - - - +
40F THR 3.4 5.6 + - - -
41F ASP 3.2 8.0 + - - +
43F CYS* 1.3 79.0 - - - +
45F VAL* 1.3 59.4 + - - +
47F HIS* 3.7 0.7 - - - -
48F ASP* 2.7 36.7 + - - +
98F PHE* 3.6 21.3 - - - -
190F OAP 3.9 14.1 - - + -
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F HIS* 3.6 34.1 - - + +
36F PRO* 3.9 11.0 - - + -
41F ASP 3.2 15.0 + - - +
42F ARG* 3.1 9.8 + - + +
44F CYS* 1.3 76.3 - - - +
46F THR* 1.3 64.8 + - - +
48F ASP* 3.5 5.3 + - - +
49F CYS* 3.3 28.7 + - - -
122F PRO* 3.4 44.2 - - + +
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ARG* 2.9 14.4 + - - +
43F CYS* 3.4 10.6 - - - -
45F VAL* 1.3 79.5 - - - +
47F HIS* 1.3 60.7 + - - +
49F CYS* 3.3 8.2 + - + +
50F CYS* 3.1 21.9 + - + +
53F ARG* 4.6 7.1 + - - +
93F ALA* 6.2 4.5 - - + -
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Residues in contact with HIS 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PHE* 3.5 18.8 - + - -
43F CYS 2.9 14.3 + - - +
44F CYS* 3.9 0.7 - - - +
45F VAL 3.3 0.2 - - - -
46F THR* 1.3 73.5 - - - +
48F ASP* 1.3 65.4 + - - +
50F CYS* 3.1 7.8 + - - +
51F TYR* 3.1 55.0 + + - +
90F CYS* 3.3 27.4 - - + -
91F ASP* 2.8 22.4 + - - -
94F ALA* 3.5 17.3 - - + -
190F OAP 2.8 45.4 + - + +
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Residues in contact with ASP 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F HIS* 3.4 13.9 + - - +
31F GLY 3.5 7.4 - - - +
32F GLY* 4.5 0.7 - - - -
44F CYS 2.7 25.0 + - - +
45F VAL* 3.7 6.3 - - - +
46F THR 3.4 0.2 - - - -
47F HIS* 1.3 74.1 - - - +
49F CYS* 1.3 58.6 + - - +
51F TYR* 3.4 2.6 + - - +
52F LYS* 3.0 41.4 + - - +
190F OAP 2.9 32.4 - - + +
191F CA 2.4 30.7 - - - -
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Residues in contact with CYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 3.3 24.1 + - - -
46F THR* 3.6 11.0 - - + +
47F HIS 3.2 0.6 - - - -
48F ASP* 1.3 76.4 - - - +
50F CYS* 1.3 60.6 + - - +
52F LYS* 3.3 4.6 + - - +
53F ARG* 2.9 43.6 + - - +
122F PRO 4.9 0.7 - - - -
123F ARG 4.7 1.6 - - - -
124F CYS* 2.0 61.5 - - + +
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Residues in contact with CYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F THR* 3.1 13.4 + - - +
47F HIS* 3.1 13.4 + - - +
49F CYS* 1.3 78.4 - - - +
51F TYR* 1.3 60.3 + - - +
53F ARG* 3.3 27.8 - - - +
54F LEU* 3.1 25.5 + - - +
86F GLN* 4.9 1.3 + - - -
90F CYS* 2.0 57.2 - - + -
93F ALA* 6.0 1.8 - - - -
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Residues in contact with TYR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ASN* 5.4 1.7 + - - -
2F LEU* 4.5 6.8 - - - +
5F PHE* 4.4 6.4 - - - +
47F HIS* 3.1 34.8 + + - +
48F ASP 3.8 7.0 - - - +
50F CYS* 1.3 77.2 - - - +
52F LYS* 1.3 61.0 + - - +
54F LEU* 3.0 16.4 + - + +
55F GLU* 2.8 37.5 + - - +
61F THR* 3.9 26.1 + - + +
62F LYS* 4.3 10.1 - - + -
87F LEU* 3.5 22.0 - - + +
90F CYS* 4.2 7.0 - - + -
91F ASP* 2.9 25.2 + - - -
190F OAP 3.4 45.8 - - + -
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Residues in contact with LYS 52 (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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33B ARG* 4.7 16.2 - - - +
115B LYS* 4.0 34.7 + - + -
48F ASP* 3.0 24.7 + - - +
49F CYS* 3.4 9.2 - - - +
51F TYR* 1.3 75.8 - - - +
53F ARG* 1.3 63.1 + - - +
55F GLU* 3.3 16.8 + - - +
56F LYS* 3.1 41.4 + - - +
124F CYS* 4.3 23.5 - - - -
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F THR* 4.6 7.7 + - - +
49F CYS* 2.9 23.4 + - - +
50F CYS* 3.3 45.4 - - - +
52F LYS* 1.3 77.1 - - - +
54F LEU* 1.3 65.0 + - - +
56F LYS* 3.3 26.5 + - + +
57F ARG* 3.4 15.4 + - - +
86F GLN* 4.3 17.6 - - - +
124F CYS* 5.1 8.9 + - - +
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Residues in contact with LEU 54 (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 3.1 15.5 + - - +
51F TYR* 3.0 10.8 + - + +
53F ARG* 1.3 78.7 - - - +
55F GLU* 1.3 64.6 + - - +
57F ARG* 3.0 15.9 + - - +
59F CYS* 3.2 38.1 + - + +
60F GLY 4.9 0.4 - - - +
61F THR* 3.8 16.4 - - + -
83F CYS 3.9 11.2 - - - +
86F GLN* 3.5 41.5 - - + +
87F LEU* 3.6 37.5 - - + -
90F CYS* 3.8 9.4 - - - -
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Residues in contact with GLU 55 (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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115B LYS* 3.2 36.0 + - - +
63E PHE 4.5 10.7 - - - +
64E LEU* 4.0 6.9 - - + +
84E ARG* 2.7 29.5 + - - +
51F TYR* 2.8 19.7 + - - +
52F LYS* 3.5 20.3 + - - +
53F ARG 3.3 0.2 - - - -
54F LEU* 1.3 76.3 - - - +
56F LYS* 1.3 51.2 + - + +
58F GLY* 2.9 13.5 + - - -
59F CYS 4.0 10.7 + - - +
61F THR* 4.4 16.6 - - + +
190F OAP 6.1 1.4 - - - +
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ASP* 4.1 7.6 - - - +
84E ARG* 3.0 19.8 + - - +
52F LYS* 3.1 32.7 + - - +
53F ARG* 3.6 22.2 - - + +
54F LEU 3.2 0.2 - - - -
55F GLU* 1.3 74.5 - - - +
57F ARG* 1.3 59.9 + - + +
58F GLY 3.1 1.9 + - - -
124F CYS* 5.9 4.6 - - - +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ASP* 3.9 13.8 - - - +
83E CYS* 4.7 5.5 - - - -
53F ARG 3.4 12.3 + - - +
54F LEU* 3.0 8.5 + - - +
56F LYS* 1.3 76.0 - - + +
58F GLY* 1.3 58.7 + - - +
59F CYS* 3.6 28.5 + - - -
82F SER* 2.6 40.6 + - - -
83F CYS* 3.9 5.1 - - - +
86F GLN* 2.4 41.4 + - - +
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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