Contacts of the helix formed by residues 39 - 57 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 1.3 78.4 - - - +
40E THR* 1.3 63.8 + - - +
42E ARG* 3.2 30.2 + - - +
43E CYS* 3.3 15.6 + - - -
97E CYS* 4.7 0.3 - - - -
101E ASN* 3.6 30.3 + - + +
104E THR* 4.2 16.0 - - + +
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Residues in contact with THR 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E TYR* 3.5 34.6 + - + -
24E TYR* 3.9 25.8 + - + -
28E CYS* 4.4 1.3 - - - -
38E ASP* 3.2 10.0 + - - -
39E ALA* 1.3 74.4 - - - +
41E ASP* 1.3 66.5 + - - +
43E CYS* 3.1 25.9 + - - +
44E CYS* 3.4 4.7 + - - -
98E PHE* 3.6 16.3 + - + -
101E ASN* 3.5 23.8 + - - +
102E LYS* 5.4 0.3 - - - -
104E THR* 5.1 0.6 - - - -
105E TYR* 4.5 8.7 + - - -
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Residues in contact with ASP 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 3.4 12.8 - - + +
25E GLY* 3.9 4.0 - - - -
26E CYS* 2.8 28.1 + - - +
27E HIS* 2.9 23.0 + - - -
28E CYS* 3.6 8.4 + - - -
36E PRO* 3.1 12.3 - - + +
37E LYS* 2.8 29.6 + - + +
38E ASP* 2.9 19.1 + - - +
40E THR* 1.3 78.3 - - - +
42E ARG* 1.3 63.0 + - - +
44E CYS* 3.0 14.4 + - - +
45E VAL* 3.2 13.2 + - - +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PRO* 3.8 32.0 + - + +
37E LYS 5.0 0.4 + - - -
38E ASP* 3.2 34.6 + - - +
39E ALA* 3.4 21.2 - - - +
40E THR 3.1 0.6 - - - -
41E ASP* 1.3 77.4 - - - +
43E CYS* 1.3 62.4 + - - +
44E CYS 3.2 0.5 + - - -
45E VAL* 3.2 15.2 + - + +
46E THR* 3.2 18.4 + - - -
97E CYS* 5.2 0.2 - - - -
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Residues in contact with CYS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA 3.5 13.0 - - - -
40E THR* 3.1 13.1 + - - +
42E ARG* 1.3 77.4 - - - +
44E CYS* 1.3 58.6 + - - +
46E THR* 3.6 7.9 + - - -
47E HIS* 3.1 26.7 + - - +
94E ALA* 4.7 6.9 - - - +
97E CYS* 2.0 68.4 - - + -
98E PHE* 3.7 19.1 - - + -
101E ASN* 3.6 3.4 - - - -
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Residues in contact with CYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E HIS* 3.6 6.1 - - - +
28E CYS* 2.0 66.2 - - - +
40E THR 3.8 0.2 - - - -
41E ASP 3.0 8.4 + - - +
43E CYS* 1.3 77.7 - - - +
45E VAL* 1.3 65.8 + - - +
46E THR 3.2 0.2 - - - -
47E HIS* 3.2 1.2 + - - +
48E ASP* 2.8 31.7 + - - +
98E PHE* 3.5 23.3 - - - -
190E OAP 3.7 13.0 - - + -
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E HIS* 3.5 37.0 - - + +
36E PRO* 3.6 21.3 - - + -
41E ASP 3.6 6.3 - - - +
42E ARG* 3.2 8.7 + - - +
44E CYS* 1.3 75.2 - - - +
46E THR* 1.3 61.4 + - - +
48E ASP* 3.1 8.8 + - - +
49E CYS* 3.0 37.3 + - - -
122E PRO* 3.3 32.5 - - + +
123E ARG 5.4 1.6 - - - +
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Residues in contact with THR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ARG 3.2 11.3 + - - -
43E CYS* 3.8 10.0 - - - -
45E VAL* 1.3 80.9 - - - +
47E HIS* 1.3 56.2 + - - +
49E CYS* 3.2 10.5 + - + +
50E CYS* 3.0 25.9 + - + +
53E ARG* 5.3 0.3 + - - -
93E ALA* 6.2 3.6 - - + -
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Residues in contact with HIS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.5 24.7 - + - -
43E CYS 3.1 19.7 + - - +
44E CYS 3.2 4.7 + - - +
46E THR* 1.3 73.4 - - - +
48E ASP* 1.3 64.8 + - - +
50E CYS* 3.2 7.2 + - - +
51E TYR* 3.0 47.5 + + - -
90E CYS* 3.5 19.5 - - + -
91E ASP* 2.9 21.8 + - - -
94E ALA* 3.4 28.0 - - + -
190E OAP 3.0 36.0 + - + +
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Residues in contact with ASP 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E HIS* 3.4 9.6 + - - +
31E GLY 3.0 11.6 - - - +
32E GLY* 4.7 1.0 - - - -
44E CYS 2.8 24.1 + - - +
45E VAL* 3.1 10.5 + - - +
47E HIS* 1.3 75.0 - - - +
49E CYS* 1.3 63.0 + - - +
51E TYR* 3.4 2.1 + - - +
52E LYS* 3.1 24.6 + - - +
124E CYS* 5.3 0.2 - - - -
190E OAP 2.9 34.7 + - + +
191E CA 2.2 31.4 - - - -
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Residues in contact with CYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 3.0 29.7 + - - -
46E THR* 3.2 12.3 + - + +
48E ASP* 1.3 78.1 - - - +
50E CYS* 1.3 62.1 + - - +
52E LYS* 3.5 3.2 + - - +
53E ARG* 3.2 38.8 + - - +
122E PRO 5.6 0.4 - - - -
123E ARG 4.8 0.4 - - - -
124E CYS* 2.0 62.3 - - + +
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Residues in contact with CYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR* 3.0 13.0 + - + +
47E HIS* 3.2 12.5 + - - +
49E CYS* 1.3 77.2 - - - +
51E TYR* 1.3 60.5 + - - +
53E ARG* 3.6 22.5 + - - +
54E LEU* 3.1 30.3 + - - +
86E GLN* 3.6 11.9 - - - -
90E CYS* 2.0 54.1 - - + -
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Residues in contact with TYR 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 5.4 1.2 - - - -
2E LEU* 4.4 10.9 - - - +
5E PHE* 4.7 0.5 - - - -
47E HIS* 3.0 34.3 + + - +
48E ASP 3.9 3.6 - - - +
49E CYS 3.4 0.2 - - - -
50E CYS* 1.3 77.3 - - - +
52E LYS* 1.3 58.8 + - - +
54E LEU* 3.3 5.2 + - + +
55E GLU* 2.8 43.4 + - - +
61E THR* 3.7 29.0 + - + +
62E LYS* 4.2 12.1 - - + -
87E LEU* 3.3 30.0 - - + +
90E CYS* 4.1 9.2 - - + -
91E ASP* 2.9 30.2 + - - -
190E OAP 3.6 42.2 - - + -
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LYS 5.9 2.8 + - - +
48E ASP 3.1 16.7 + - - +
49E CYS* 3.5 5.4 + - - +
51E TYR* 1.3 75.4 - - - +
53E ARG* 1.3 57.0 + - - +
55E GLU* 3.3 12.0 + - - +
56E LYS* 2.9 63.2 + - - +
124E CYS* 5.4 11.2 - - - -
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Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E THR 5.3 0.4 + - - -
49E CYS* 3.2 37.8 + - - +
50E CYS* 3.7 26.1 + - - +
52E LYS* 1.3 81.0 - - - +
54E LEU* 1.3 61.4 + - + +
56E LYS* 3.4 10.0 + - - +
57E ARG* 3.3 21.1 + - - +
86E GLN* 5.5 4.6 + - - +
124E CYS* 4.9 12.9 + - - +
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E CYS* 3.1 24.7 + - - +
51E TYR* 3.7 5.6 - - - +
53E ARG* 1.3 77.3 - - + +
55E GLU* 1.3 65.8 + - - +
57E ARG* 3.3 20.7 + - - +
59E CYS* 3.0 47.6 + - + +
60E GLY 4.5 2.9 - - - +
61E THR* 4.0 9.2 - - + -
83E CYS* 3.7 23.6 - - - +
86E GLN* 3.9 17.7 - - + +
87E LEU* 3.9 18.2 - - + +
90E CYS* 3.3 28.0 - - - -
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Residues in contact with GLU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TYR* 2.8 32.4 + - - +
52E LYS* 3.6 8.3 + - - +
54E LEU* 1.3 74.6 - - - +
56E LYS* 1.3 58.7 + - - +
57E ARG 3.0 1.1 - - - -
58E GLY* 2.9 17.5 + - - -
59E CYS 3.9 9.6 - - - +
61E THR* 4.0 23.3 + - + +
62E LYS* 4.6 11.7 + - - -
190E OAP 5.3 5.2 - - - +
63F PHE 5.0 7.1 - - - +
64F LEU* 3.9 6.7 - - + +
84F ARG* 2.9 16.6 + - - +
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LYS* 2.9 56.9 + - - +
53E ARG* 3.8 8.9 - - - +
54E LEU 3.3 0.6 - - - -
55E GLU* 1.3 76.2 - - - +
57E ARG* 1.3 56.4 + - - +
81F ASP* 4.4 3.5 - - - +
84F ARG* 2.7 21.0 + - - +
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Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ARG 3.3 11.0 + - - +
54E LEU* 3.3 20.6 + - - +
55E GLU 3.0 0.6 - - - -
56E LYS* 1.3 78.2 - - - +
58E GLY* 1.3 59.1 + - - +
59E CYS* 3.6 27.0 - - - -
82E SER* 3.4 33.7 + - - -
83E CYS* 4.5 1.5 - - - +
86E GLN* 4.1 24.4 - - - +
81F ASP* 3.8 14.3 - - - +
83F CYS* 5.1 3.1 - - - -
84F ARG* 3.9 1.8 - - - -
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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