Contacts of the strand formed by residues 19 - 25 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14P ALA* 3.7 16.8 - - + -
16P GLU* 3.8 7.6 - - + +
17P ASP 3.3 1.0 + - - -
18P GLY* 1.3 76.0 - - - +
20P ASN* 1.3 72.0 + - - +
21P VAL* 4.2 10.8 - - + -
36P GLU 3.5 0.3 - - - +
37P LYS* 3.3 5.9 - - - -
38P LEU* 2.7 49.9 + - + +
57P VAL* 4.1 13.5 - - + -
58P ARG 3.5 12.1 - - - +
59P GLY* 4.5 1.6 - - - -
60P LYS 3.2 38.8 - - - +
61P ALA* 4.2 4.7 - - + -
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Residues in contact with ASN 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLY 3.4 14.8 + - - -
19P VAL* 1.3 73.9 + - - +
21P VAL* 1.3 62.0 + - - +
22P ILE* 3.8 17.3 - - + +
35P SER* 2.8 22.0 + - - +
36P GLU 3.4 3.1 - - - -
37P LYS* 3.1 26.8 + - - +
56P LYS 3.7 1.4 - - - +
57P VAL* 3.5 5.5 - - - +
58P ARG* 2.9 47.2 + - + +
124W C 5.8 1.0 - - - -
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Residues in contact with VAL 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ILE* 3.8 28.9 - - + -
19P VAL* 4.2 3.4 - - + -
20P ASN* 1.3 74.7 - - - +
22P ILE* 1.3 62.1 + - - +
23P GLY 3.9 0.5 + - - -
34P HIS 3.8 1.2 - - - +
35P SER* 3.7 1.0 - - - -
36P GLU* 2.9 33.3 + - + +
38P LEU* 3.8 28.9 - - + -
44P LEU* 3.8 23.6 - - + -
46P ALA* 5.4 0.9 - - + -
55P ILE* 3.8 23.3 - - + -
56P LYS 3.7 2.9 - - - +
57P VAL* 4.6 4.0 - - + +
81P TRP* 4.2 13.5 - - + -
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Residues in contact with ILE 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ASN* 4.1 13.9 - - + +
21P VAL* 1.3 75.6 - - - +
23P GLY* 1.3 64.7 + - - +
24P LEU* 3.8 7.2 - - + +
32P PHE* 3.5 48.9 - - + -
34P HIS 3.4 8.3 - - - +
35P SER* 4.0 18.2 - - - +
55P ILE* 3.1 7.4 - - - +
56P LYS* 2.8 52.0 + - + +
58P ARG* 3.6 39.9 - - - +
81P TRP* 4.2 2.2 - - - -
124W C 5.6 0.2 - - - +
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Residues in contact with GLY 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P ILE* 1.3 72.6 - - - +
24P LEU* 1.3 62.6 + - - -
32P PHE* 3.8 4.0 - - - -
33P HIS* 3.2 33.6 + - - -
34P HIS 2.8 12.4 + - - +
52P THR* 3.9 6.3 - - - -
54P ALA 3.6 4.7 - - - -
81P TRP* 3.6 26.0 - - - -
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Residues in contact with LEU 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O HIS* 5.6 0.2 - - + -
36O GLU* 4.1 18.6 - - + +
44O LEU* 4.0 22.9 - - + -
81O TRP* 5.2 2.0 - - + -
22P ILE* 3.8 26.9 - - + +
23P GLY* 1.3 79.2 - - - -
25P THR* 1.3 65.6 + - - +
30P THR* 3.9 26.9 - - + -
31P ARG 3.5 8.1 - - - +
32P PHE* 4.3 7.2 - - + -
33P HIS* 4.1 1.8 - - - -
52P THR* 3.5 6.1 - - - -
53P SER 3.4 18.9 + - - -
54P ALA* 2.6 29.6 + - + +
56P LYS* 3.9 15.7 - - + +
123W G 4.6 5.6 - - - +
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Residues in contact with THR 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O TRP* 2.8 33.4 + - - +
23P GLY 4.0 0.2 + - - -
24P LEU* 1.3 73.8 - - - +
26P ARG* 1.3 56.0 + - - +
29P ASP 3.1 12.6 + - - +
30P THR* 4.2 0.7 - - - -
31P ARG* 2.8 74.7 + - + +
33P HIS* 3.4 29.8 - - + -
51P HIS 3.4 7.2 - - - +
53P SER* 4.2 0.7 - - - -
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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