Contacts of the strand formed by residues 49 - 57 (chain E) in PDB entry 1COP
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 SER 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E ILE* 2.9 8.7 - - - +
45E ASN* 2.6 62.9 + - - -
47E ASP* 2.9 11.0 - - - -
48E GLY* 1.3 80.4 - - - +
50E VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 50 (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 TYR* 5.5 4.3 - - + -
22E ASP* 3.1 50.9 + - + +
23E LEU* 3.3 39.9 - - + -
42E LEU* 4.4 14.1 - - + -
43E THR 3.3 4.3 - - - +
44E ILE* 4.2 14.8 - - + +
49E SER* 1.3 84.0 + - - +
51E TYR* 1.3 71.2 + - - +
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Residues in contact with TYR 51 (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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57D PRO* 4.8 11.3 - - + +
64D THR* 6.1 4.0 - - + -
65D THR 4.9 5.6 - - - -
66D ALA* 4.6 31.9 - - + +
23E LEU* 4.8 0.7 - - - -
43E THR* 2.6 46.7 + - + +
45E ASN* 4.1 15.3 - - - +
50E VAL* 1.3 81.6 - - - +
52E ALA* 1.3 64.1 + - - +
53E GLU* 2.7 46.9 + - + +
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Residues in contact with ALA 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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57D PRO* 3.8 2.6 - - - +
58D PHE* 3.2 39.8 + - + +
23E LEU* 3.6 21.1 - - + +
40E ILE* 5.0 1.6 - - + -
41E PHE 3.2 7.9 - - - +
42E LEU* 2.9 32.3 - - + -
50E VAL* 4.4 0.4 - - - +
51E TYR* 1.3 76.9 - - - +
53E GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 53 (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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55D VAL* 5.0 12.8 - - - +
56D LYS 3.5 7.6 - - - +
57D PRO* 4.1 14.8 - - + +
58D PHE* 4.3 2.0 - - - +
40E ILE* 3.5 7.7 - - - +
41E PHE* 3.0 33.9 + - + +
43E THR* 5.7 2.4 + - - +
51E TYR* 2.7 53.2 + - + +
52E ALA* 1.3 79.4 - - - +
54E GLU* 1.3 63.8 + - - +
55E VAL* 4.4 9.2 - - + +
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Residues in contact with GLU 54 (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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38D ARG* 5.0 8.0 + - - -
54D GLU* 4.3 23.7 - - + +
55D VAL* 3.1 24.6 - - - +
56D LYS* 2.6 39.0 + - + +
58D PHE* 6.3 0.7 - - + -
38E ARG* 2.7 48.3 - - - +
39E LYS* 3.4 5.4 - - + -
40E ILE* 3.8 10.9 - - + +
53E GLU* 1.3 74.6 - - - +
55E VAL* 1.3 75.6 + - - +
56E LYS* 4.8 2.7 - - + +
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Residues in contact with VAL 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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53D GLU* 4.3 17.3 - - - +
54D GLU 3.1 14.1 - - - +
55D VAL* 3.6 16.8 - - + -
39E LYS* 3.3 26.6 + - - +
41E PHE* 3.0 33.5 - - + -
53E GLU* 4.4 7.0 - - + +
54E GLU* 1.3 86.3 - - - +
56E LYS* 1.3 60.2 + - - +
57E PRO* 4.5 1.4 - - - +
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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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53D GLU* 4.8 3.6 - - - -
54D GLU* 2.7 58.5 + - + +
38E ARG* 5.6 14.1 - - + +
39E LYS* 3.8 40.2 - - + +
54E GLU* 5.3 4.5 - - + +
55E VAL* 1.3 75.6 - - - +
57E PRO* 1.3 91.3 - - + +
59E PRO 4.9 2.2 - - - +
60E SER 4.2 12.3 + - - +
61E ASN* 5.5 4.0 - - - +
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Residues in contact with PRO 57 (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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51D TYR* 5.0 5.2 - - + +
52D ALA 4.1 5.6 - - - +
53D GLU* 4.2 12.5 - - + +
54D GLU* 5.3 0.5 - - - +
39E LYS* 5.9 0.2 - - + -
55E VAL 4.5 1.3 - - - +
56E LYS* 1.3 118.4 - - + +
58E PHE* 1.3 64.1 + - - +
59E PRO 2.9 13.1 - - - +
60E SER 3.7 13.5 - - - +
61E ASN* 4.1 10.3 - - + -
62E LYS* 4.1 33.9 - - + +
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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