Contacts of the strand formed by residues 52 - 58 (chain T) in PDB entry 1GTN
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 THR 52 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23T GLY* 3.7 17.3 - - - -
24T LEU 3.4 3.8 - - - +
26T ARG* 3.8 0.7 + - - -
33T HIS* 2.4 27.4 + - - -
47T GLN 4.6 1.3 - - - +
48T PHE* 3.5 7.0 - - + -
49T THR* 3.0 35.8 + - - +
51T HIS* 1.3 74.7 - - - +
53T SER* 1.3 58.4 + - - +
54T ALA 3.3 24.5 - - - +
55T ILE* 3.9 15.0 - - + -
81T TRP* 2.9 26.0 + - + -
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Residues in contact with SER 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S GLN* 3.1 37.5 + - - +
49S THR* 3.9 5.4 - - - -
81S TRP* 2.8 42.4 + - - +
24T LEU 3.4 4.0 + - - -
25T THR 3.9 1.0 + - - -
26T ARG* 3.6 33.9 - - - +
48T PHE* 3.7 7.3 - - - -
52T THR* 1.3 71.9 - - - +
54T ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S LEU* 4.4 2.0 - - + -
45S ILE 3.2 12.8 - - - +
46S ALA* 4.1 9.2 - - + -
81S TRP* 4.0 18.2 - - + -
24T LEU* 2.8 53.0 + - + -
48T PHE* 3.7 2.7 - - - -
52T THR* 3.3 8.5 - - - +
53T SER* 1.3 82.8 + - - +
55T ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S VAL 3.8 0.9 - - - +
44S LEU* 3.4 5.5 - - - +
45S ILE* 2.7 58.6 + - + +
10T VAL* 4.2 21.3 - - + -
12T ILE* 5.0 2.5 - - + -
21T VAL* 3.7 23.8 - - + -
22T ILE 3.1 9.9 - - - +
24T LEU* 4.8 0.2 - - - -
46T ALA* 4.6 4.7 - - + +
47T GLN 4.4 11.2 - - - +
48T PHE* 4.4 17.7 - - + -
52T THR* 3.9 4.3 - - + -
54T ALA* 1.3 81.6 - - - +
56T LYS* 1.3 66.3 + - - +
57T VAL* 4.2 2.9 - - + -
81T TRP* 3.7 29.4 - - + -
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Residues in contact with LYS 56 (chain T).
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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36S GLU* 3.0 27.8 + - + +
37S LYS 3.7 16.8 + - - -
38S LEU* 3.5 24.3 - - + +
42S GLU* 4.2 10.0 + - + +
43S VAL 3.4 8.3 - - - +
44S LEU* 4.3 5.8 - - + -
20T ASN 3.5 1.9 - - - +
21T VAL* 3.5 1.6 - - - -
22T ILE* 2.6 45.8 + - + +
24T LEU* 4.1 15.1 - - + +
32T PHE* 4.2 11.0 - - - -
55T ILE* 1.3 74.7 - - - +
57T VAL* 1.3 70.0 + - - +
58T ARG* 3.5 39.0 - - + +
142W A 3.8 1.6 - - - +
143W G 3.5 7.7 + - - -
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Residues in contact with VAL 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S GLU* 3.8 8.7 - - - +
43S VAL* 2.9 34.0 + - + +
45S ILE* 4.5 15.5 - - + -
12T ILE* 4.4 11.2 - - + -
19T VAL* 4.1 17.7 - - + -
20T ASN 3.4 7.6 - - - +
21T VAL* 4.3 7.2 - - + -
55T ILE* 4.5 7.0 - - + -
56T LYS* 1.3 78.6 - - - +
58T ARG* 1.3 64.1 + - - +
59T GLY 4.2 1.1 + - - -
61T ALA* 4.2 7.4 - - + -
63T ILE* 3.8 25.8 - - + -
72T SER* 3.9 20.6 - - - +
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Residues in contact with ARG 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S GLU* 3.0 33.0 + - + +
18T GLY 4.4 1.3 - - - +
19T VAL* 3.4 9.1 - - - +
20T ASN* 2.9 50.9 + - + +
22T ILE* 3.7 22.0 - - + +
32T PHE* 3.9 6.7 - - - -
56T LYS* 3.5 33.7 - - + +
57T VAL* 1.3 72.9 - - - +
59T GLY* 1.3 62.1 + - - +
142W A 5.3 1.0 - - - +
143W G 3.8 13.7 + - - -
144W C 4.0 18.6 + - - -
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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