Contacts of the strand formed by residues 26 - 34 (chain A) in PDB entry 1GPN
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 HIS 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 4.7 4.0 + - - -
19A ARG* 4.2 20.6 - - + +
20A VAL 3.1 16.8 - - - +
21A PRO* 4.5 1.3 - - + -
22A VAL* 4.0 2.4 - - - +
25A SER* 1.3 93.3 + - - +
27A ILE* 1.3 74.5 + - - +
103A SER* 3.3 39.2 + - - +
137A TYR* 4.7 1.6 - - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.5 5.4 - - - +
20A VAL* 2.8 41.9 + - + +
22A VAL* 4.0 4.3 - - + -
26A HIS* 1.3 81.8 - - - +
28A SER* 1.3 63.6 + - - +
100A TRP* 3.9 15.5 - - + -
101A VAL 3.4 13.0 - - - +
102A PRO* 4.2 12.8 - - + -
103A SER* 4.0 9.4 - - - +
133A LYS* 3.4 45.8 - - + +
136A ALA* 4.4 5.2 - - + -
137A TYR* 3.8 27.4 - - + -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.9 26.9 + - - +
6A LEU* 3.7 23.8 - - - +
18A THR 3.6 5.2 - - - -
19A ARG* 5.5 0.5 - - - +
27A ILE* 1.3 78.9 - - - +
29A ALA* 1.3 62.0 + - - +
30A PHE* 3.9 19.5 - - - -
99A ILE 4.5 0.2 - - - -
100A TRP* 3.5 3.5 - - - -
101A VAL* 2.8 42.9 + - - +
102A PRO 4.7 0.7 + - - -
103A SER* 4.5 1.0 - - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY* 3.3 2.1 - - - -
18A THR* 2.9 40.3 + - + +
20A VAL* 4.0 18.6 - - + -
28A SER* 1.3 75.8 - - - +
30A PHE* 1.3 63.9 + - - +
31A LEU* 3.7 23.3 - - + -
60A ALA 3.5 0.9 - - - +
99A ILE 3.3 5.4 - - - +
100A TRP* 4.0 18.2 - - + +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 3.8 17.7 - - - -
6A LEU* 3.4 11.7 - - - -
8A VAL* 3.5 27.8 - - + -
15A VAL* 3.7 19.3 - - + -
16A MET 4.1 0.9 - - - -
17A GLY* 3.4 29.8 - - - -
28A SER* 3.9 21.5 - - - -
29A ALA* 1.3 72.1 - - - +
31A LEU* 1.3 63.1 + - - +
33A ILE* 3.5 24.0 - - + +
60A ALA* 3.4 7.2 - - + -
97A LEU 4.0 0.2 - - - +
98A ASN* 3.5 3.8 - - - -
99A ILE* 2.9 39.5 + - + +
101A VAL* 4.0 11.4 - - + -
105A ARG* 5.6 1.3 - - - -
187A PHE* 3.6 23.1 - + + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 4.7 4.0 - - + -
29A ALA* 3.9 25.4 - - + +
30A PHE* 1.3 81.0 - - - +
32A GLY* 1.3 63.5 + - - +
59A ASN 4.4 0.7 - - - +
60A ALA* 2.9 33.2 + - - +
61A SER 3.8 18.4 - - - +
62A THR* 3.4 21.5 - - - +
63A TYR* 3.8 39.7 - - + +
98A ASN* 3.6 15.7 - - + +
99A ILE 4.9 0.7 - - - +
100A TRP* 4.2 11.0 - - + -
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Residues in contact with GLY 32 (chain A).
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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31A LEU* 1.3 74.3 - - - +
33A ILE* 1.3 62.0 + - - +
58A TRP* 3.2 21.1 + - - -
59A ASN 5.1 0.3 - - - +
62A THR 4.1 3.6 - - - -
64A PRO* 3.7 30.4 - - - +
96A TYR* 3.3 16.1 - - - -
97A LEU 3.4 2.7 + - - -
98A ASN* 3.0 13.9 + - - -
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.3 18.2 - - + -
30A PHE* 3.5 32.3 - - + +
32A GLY* 1.3 73.3 - - - +
34A PRO* 1.3 78.5 - - + +
54A TRP* 4.8 2.5 - - + -
58A TRP* 4.6 0.9 - - + +
60A ALA* 4.1 16.8 - - + -
96A TYR* 3.1 1.2 - - - -
97A LEU* 2.7 48.6 + - + +
99A ILE* 3.9 23.1 - - + -
179A TRP* 3.9 25.1 - - + -
187A PHE* 4.0 13.5 - - + -
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Residues in contact with PRO 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 5.5 0.2 + - - -
32A GLY 3.5 7.6 - - - +
33A ILE* 1.3 96.8 - - + +
35A PHE* 1.3 60.2 + - - +
36A ALA 4.5 3.1 - - - +
51A LYS* 4.1 26.9 - - + +
54A TRP* 3.9 22.7 - - + -
58A TRP* 3.6 33.7 - - + +
95A LEU 3.5 4.9 - - - +
96A TYR* 3.4 25.1 - - + -
179A TRP* 4.4 6.9 + - - -
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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