Contacts of the strand formed by residues 51 - 60 (chain E) in PDB entry 3KZ1
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 LYS 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E ILE* 4.5 17.7 - - + -
47E GLU* 3.6 7.9 - - - +
48E VAL 3.0 30.2 + - - +
49E ASP* 3.5 14.4 - - + +
50E GLY* 1.3 84.3 - - - +
52E GLN* 1.3 61.9 + - - +
53E VAL* 3.6 6.3 + - + +
179E LEU* 4.0 24.0 - - + -
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Residues in contact with GLN 52 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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863A HIS* 5.3 15.2 - - + +
864A PRO* 6.2 3.8 - - + -
3E ALA* 4.3 9.8 - - + +
4E ILE* 3.3 34.0 + - + +
45E ASP* 4.6 13.1 - - + +
46E ILE 4.0 17.1 - - - +
47E GLU* 4.6 20.3 + - + +
50E GLY 4.3 0.4 - - - -
51E LYS* 1.3 71.6 - - - +
53E VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 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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864A PRO* 5.8 1.6 - - - -
4E ILE* 3.3 11.4 - - + +
6E LYS* 4.1 18.2 - - + -
44E ALA 3.8 0.2 - - - +
45E ASP* 3.4 8.3 - - - +
46E ILE* 3.1 37.6 + - + +
48E VAL* 5.2 0.2 - - + -
51E LYS* 3.8 11.9 - - + +
52E GLN* 1.3 82.3 - - - +
54E GLU* 1.3 65.2 + - - +
55E LEU* 3.3 27.8 + - + -
175E THR* 3.6 27.4 - - + -
179E LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 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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864A PRO* 3.2 47.1 - - + +
867A ARG* 3.2 13.5 + - - -
1038B THR* 3.6 20.3 - - + +
4E ILE 2.9 9.1 + - - -
5E ARG* 3.1 38.5 + - + +
6E LYS 3.0 24.9 + - - +
43E VAL* 3.5 25.4 - - + -
44E ALA 3.6 2.7 - - - -
45E ASP* 3.8 9.0 - - - +
53E VAL* 1.3 73.6 - - - +
55E LEU* 1.3 59.4 + - - +
56E ALA* 3.4 1.9 + - - +
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Residues in contact with LEU 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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6E LYS* 3.3 11.2 - - + +
8E LEU* 4.2 15.5 - - + -
25E PHE* 3.8 15.9 - - + -
43E VAL* 3.4 7.9 - - - +
44E ALA 2.8 41.5 + - - +
46E ILE* 4.0 11.7 - - + -
53E VAL* 3.3 30.5 - - + -
54E GLU* 1.3 70.7 - - - +
56E ALA* 1.3 59.8 + - - +
57E LEU* 3.5 14.7 + - + +
79E VAL* 6.3 0.2 - - + -
171E PHE* 3.8 29.6 - - + -
175E THR* 3.8 24.7 - - + +
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Residues in contact with ALA 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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1038B THR* 3.9 24.2 - - + +
6E LYS 3.0 13.4 + - - +
7E LYS* 4.1 7.0 - - + -
8E LEU 2.9 30.5 + - - +
41E ASN* 5.4 1.3 - - - +
42E TYR 3.6 6.5 - - - +
54E GLU 3.4 2.3 + - - +
55E LEU* 1.3 71.2 - - - +
57E LEU* 1.3 60.1 + - - +
58E TRP* 3.2 22.0 - - - +
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Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.7 22.7 - - + -
22E LEU* 4.1 29.4 - - + +
25E PHE* 4.5 6.1 - - + -
26E SER* 4.0 17.5 - - - -
41E ASN* 3.5 4.3 - - - -
42E TYR* 2.7 54.3 + - + +
44E ALA* 3.9 22.0 - - + +
55E LEU* 3.8 30.1 - - + +
56E ALA* 1.3 69.1 - - - +
58E TRP* 1.3 62.7 + - - +
59E ASP 3.7 1.4 + - - -
171E PHE* 4.0 17.3 - - + -
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Residues in contact with TRP 58 (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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1036B VAL* 6.4 0.9 - - + -
1044B PHE* 3.7 28.7 - + - -
1056B ILE* 4.5 9.2 - - + -
7E LYS* 3.6 39.4 - - + +
8E LEU* 2.8 17.7 + - - +
9E VAL* 3.6 15.1 - - + +
10E ILE* 3.0 30.7 + - - +
22E LEU* 4.4 1.1 - - - +
39E PHE* 3.7 28.3 - + - -
40E GLU 3.8 3.6 - - - -
41E ASN* 4.0 14.2 + - - -
56E ALA* 3.2 34.2 - - - +
57E LEU* 1.3 73.7 - - - +
59E ASP* 1.3 60.6 + - - +
60E THR* 3.9 1.2 + - - -
72E LEU 4.6 1.1 - - - -
73E SER* 3.8 30.5 - - - +
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Residues in contact with ASP 59 (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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10E ILE* 3.5 14.7 - - - +
18E LYS* 4.1 2.3 - - - +
19E THR* 2.9 45.0 + - - +
22E LEU* 3.7 15.7 - - + +
37E THR* 3.5 11.2 + - - +
39E PHE* 4.0 4.9 - - - -
40E GLU* 2.9 45.8 + - + +
42E TYR* 4.0 5.8 + - + -
57E LEU 3.7 1.6 + - - -
58E TRP* 1.3 73.0 - - - +
60E THR* 1.3 75.4 + - - +
73E SER* 4.6 4.3 + - - -
550E MG 3.7 4.5 - - - -
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Residues in contact with THR 60 (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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9E VAL* 4.0 12.3 - - + -
10E ILE 2.3 35.2 + - - +
11E VAL* 3.7 9.8 - - + +
18E LYS* 3.6 10.6 - - - -
37E THR* 3.9 6.1 - - - -
38E VAL 4.7 2.7 - - - -
39E PHE* 6.1 0.7 - - + -
58E TRP 4.5 0.7 - - - +
59E ASP* 1.3 89.1 + - - +
61E ALA* 1.3 63.0 + - - +
70E ARG* 3.5 32.3 - - + -
73E SER* 3.7 26.7 - - - +
550E MG 3.8 8.3 - - - -
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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
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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