Contacts of the strand formed by residues 49 - 57 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D THR 4.6 0.2 - - - -
44D ILE* 2.8 25.5 - - - +
45D ASN* 2.9 32.6 + - - -
47D ASP* 2.9 14.4 + - - +
48D GLY* 1.3 80.0 - - - +
50D VAL* 1.3 62.1 + - - +
51D TYR* 4.1 1.6 - - - -
66E ALA* 5.0 16.0 - - - +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D TYR* 5.3 2.5 - - + -
22D ASP* 3.2 46.2 - - + +
23D LEU* 3.1 44.3 - - + +
42D LEU* 4.2 11.4 - - + -
43D THR 4.2 0.7 - - - -
44D ILE* 4.1 20.2 - - + +
48D GLY 4.2 6.1 - - - +
49D SER* 1.3 80.0 - - - +
51D TYR* 1.3 62.5 + - - +
52D ALA 3.8 1.5 + - - -
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D THR* 2.9 60.5 + - + +
45D ASN* 5.5 2.7 - - - +
49D SER* 5.7 1.1 - - - -
50D VAL* 1.3 76.3 - - - +
52D ALA* 1.3 65.6 + - - +
53D GLU* 2.4 50.2 + - + +
57E PRO* 5.0 5.4 - - + +
58E PHE 5.6 2.5 - - - -
62E LYS* 4.3 33.8 + - + +
65E THR* 6.1 0.7 - - - -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 5.3 0.2 - - + -
23D LEU* 4.2 15.0 - - + +
40D ILE* 4.8 4.7 - - + -
41D PHE 3.2 7.9 - - - +
42D LEU* 3.1 30.7 - - + +
50D VAL 3.8 3.0 + - - -
51D TYR* 1.3 79.3 - - - +
53D GLU* 1.3 62.9 + - - +
58E PHE* 3.3 46.8 + - + +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 3.5 8.0 - - - +
41D PHE* 3.0 35.4 + - + +
43D THR* 5.7 2.5 - - - +
51D TYR* 2.4 49.4 + - + +
52D ALA* 1.3 74.2 - - - +
54D GLU* 1.3 61.4 + - - +
55D VAL* 4.4 11.8 - - + +
55E VAL* 4.3 20.8 - - - +
56E LYS 3.6 5.3 - - - +
57E PRO* 4.2 13.0 - - + +
58E PHE* 4.7 2.2 - - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.3 37.2 - - - +
39D LYS* 3.1 9.4 - - + +
40D ILE* 3.4 19.1 - - + +
53D GLU* 1.3 74.4 - - - +
55D VAL* 1.3 70.4 + - - +
56D LYS* 5.1 2.7 - - + +
38E ARG* 5.8 1.6 - - - +
54E GLU* 4.2 23.6 - - + +
55E VAL* 3.1 24.3 - - - +
56E LYS* 2.7 36.4 + - + +
57E PRO 5.3 0.7 - - - +
58E PHE* 6.1 4.8 - - + -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 2.6 34.1 + - - +
41D PHE* 3.0 39.3 - - + -
53D GLU* 4.4 12.6 - - + +
54D GLU* 1.3 81.5 - - - +
56D LYS* 1.3 57.5 + - - +
57D PRO* 4.4 1.0 - - - +
53E GLU* 5.0 13.9 - - - +
54E GLU 3.1 14.1 - - - +
55E VAL* 3.6 18.4 - - + -
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLY 4.8 2.6 + - - -
38D ARG* 3.7 34.9 - - - +
39D LYS* 3.4 30.9 - - + +
54D GLU* 5.4 2.9 - - + -
55D VAL* 1.3 75.5 - - - +
57D PRO* 1.3 80.7 - - + +
58D PHE 3.8 0.2 + - - -
59D PRO 5.0 0.2 - - - +
60D SER* 3.8 27.5 + - - +
53E GLU* 3.5 3.1 - - - +
54E GLU* 2.6 59.9 + - + +
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Residues in contact with PRO 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 4.2 17.3 - - - +
55D VAL 4.4 1.1 - - - +
56D LYS* 1.3 101.8 - - + +
58D PHE* 1.3 55.2 - - - +
59D PRO 2.5 23.6 - - - +
64D THR* 5.4 11.7 - - + -
51E TYR* 4.8 10.5 - - + +
52E ALA 3.8 11.0 - - - +
53E GLU* 4.1 16.3 - - + +
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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