Contacts of the strand formed by residues 19 - 25 (chain S) 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 VAL 19 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14S ALA* 3.8 13.0 - - + -
16S GLU* 3.4 27.8 - - + +
18S GLY* 1.3 76.6 - - - +
20S ASN* 1.3 71.4 + - - +
21S VAL* 3.9 8.2 + - + -
36S GLU 3.2 2.3 - - - +
37S LYS* 3.2 4.5 - - - -
38S LEU* 2.7 42.8 + - + +
57S VAL* 4.1 15.5 - - + -
58S ARG 3.4 15.5 - - - +
59S GLY* 4.5 0.7 - - - -
60S LYS 3.4 25.1 - - - +
61S ALA* 4.3 8.5 - - + -
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Residues in contact with ASN 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S GLY 3.8 10.1 + - - -
19S VAL* 1.3 75.6 - - - +
21S VAL* 1.3 61.4 + - - +
22S ILE* 3.9 21.1 - - + +
35S SER* 3.0 20.1 + - - +
36S GLU 3.3 3.6 - - - -
37S LYS* 3.3 32.0 + - - +
56S LYS 3.7 0.9 - - - +
57S VAL* 3.5 3.5 - - - +
58S ARG* 2.8 49.2 + - + +
139W C 4.7 2.6 + - - +
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Residues in contact with VAL 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ILE* 3.7 35.9 - - + -
19S VAL* 3.9 4.2 + - + -
20S ASN* 1.3 73.3 - - - +
22S ILE* 1.3 60.3 + - - +
23S GLY 4.1 1.0 + - - -
35S SER* 3.9 0.3 - - - -
36S GLU* 2.9 32.7 + - - +
38S LEU* 3.8 27.1 - - + -
44S LEU* 3.9 19.5 - - + -
46S ALA* 5.7 0.4 - - + -
55S ILE* 3.7 23.3 - - + -
56S LYS 3.5 3.8 - - - -
57S VAL* 4.6 5.2 - - + +
81S TRP* 4.3 12.6 - - + -
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Residues in contact with ILE 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S ASN* 3.9 20.2 - - + +
21S VAL* 1.3 74.3 - - - +
23S GLY* 1.3 63.4 + - - +
24S LEU* 3.6 9.2 + - + +
32S PHE* 3.3 50.7 - - + -
34S HIS 3.4 9.4 - - - +
35S SER* 3.2 23.8 - - - +
55S ILE* 3.4 4.8 - - - -
56S LYS* 2.7 47.4 + - + +
58S ARG* 3.5 36.3 - - + +
81S TRP* 4.3 2.5 - - - -
139W C 5.5 0.7 - - - +
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Residues in contact with GLY 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S ILE* 1.3 70.5 - - - +
24S LEU* 1.3 62.8 + - - -
32S PHE* 3.7 3.8 - - - -
33S HIS* 3.0 33.7 + - - -
34S HIS 3.0 11.2 + - - -
52S THR* 3.7 6.5 - - - -
54S ALA 3.7 5.6 - - - -
81S TRP* 3.6 27.6 - - - -
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Residues in contact with LEU 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R GLU* 3.8 29.6 - - + +
44R LEU* 4.1 21.8 - - + -
81R TRP* 5.2 2.7 - - + -
22S ILE* 3.7 28.7 - - + +
23S GLY* 1.3 76.2 - - - -
25S THR* 1.3 64.1 + - - +
30S THR* 4.1 19.3 - - + -
31S ARG 3.4 9.2 - - - +
32S PHE* 4.1 11.0 - - + -
33S HIS* 4.0 0.9 - - - -
52S THR* 3.4 20.1 - - - +
53S SER 3.5 5.4 + - - -
54S ALA* 2.7 27.5 + - + +
56S LYS* 4.1 13.0 - - + +
138W G 4.6 4.0 - - - +
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Residues in contact with THR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R TRP* 2.7 34.1 + - - +
24S LEU* 1.3 72.1 - - - +
26S ARG* 1.3 59.0 + - - +
29S ASP 2.8 23.5 + - - +
30S THR* 4.3 0.5 - - - -
31S ARG* 2.8 60.8 + - + +
33S HIS* 3.4 29.2 - - + -
51S HIS* 3.4 7.2 - - + +
53S SER* 4.2 1.1 - - - -
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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