Contacts of the strand formed by residues 15 - 23 (chain A) in PDB entry 1G13
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 ALA 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 4.6 1.2 - - - +
13A ASP* 4.1 2.1 - - - +
14A PRO* 1.3 77.2 - - + +
16A VAL* 1.3 66.7 + - - +
40A SER 3.4 6.1 - - - +
41A THR* 4.0 16.8 - - - +
45A LEU* 4.4 13.9 - - + -
143A LEU* 4.5 10.1 - - + -
150A LEU* 3.0 18.8 + - + +
151A GLY* 3.5 19.7 - - - -
152A CYS 4.6 1.6 + - - -
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Residues in contact with VAL 16 (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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7A ASN* 3.5 21.1 - - + +
9A ASP 5.7 0.2 - - - -
10A GLU* 4.0 21.5 - - + +
13A ASP* 3.4 22.0 - - + +
14A PRO 4.7 2.2 - - - +
15A ALA* 1.3 82.2 - - - +
17A ILE* 1.3 68.5 + - - +
18A ARG* 4.5 11.0 - - + +
39A GLY* 3.1 2.8 - - - -
40A SER* 2.8 54.5 + - - +
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Residues in contact with ILE 17 (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 TRP* 3.4 30.0 - - + -
7A ASN* 2.9 31.1 + - - +
16A VAL* 1.3 79.9 - - - +
18A ARG* 1.3 63.2 + - - +
19A SER 3.5 22.0 - - - +
20A LEU* 4.1 10.1 - - + -
37A VAL* 4.2 18.6 - - + -
38A MSE 3.8 2.0 - - - +
39A GLY* 4.5 6.7 - - - -
153A ILE* 3.9 26.2 - - + -
900A EPE 5.7 0.9 - - - -
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Residues in contact with ARG 18 (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 TRP* 3.8 10.8 - - - -
16A VAL* 4.5 9.3 - - + +
17A ILE* 1.3 77.5 - - - +
19A SER* 1.3 59.2 + - - +
38A MSE 2.7 46.7 + - + +
39A GLY* 4.6 1.8 - - - -
40A SER* 3.2 30.8 + - - +
113A THR* 3.3 26.3 + - - +
900A EPE 5.1 5.9 - - - -
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Residues in contact with SER 19 (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 TRP* 3.8 6.1 - - - -
17A ILE* 3.5 5.3 - - - +
18A ARG* 1.3 80.3 - - - +
20A LEU* 1.3 63.5 + - - +
21A THR* 6.0 2.5 - - - -
36A SER* 5.4 1.7 + - - -
37A VAL* 3.3 3.5 - - - -
38A MSE 2.9 50.8 + - - +
86B MSE 4.7 9.4 - - - +
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Residues in contact with LEU 20 (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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3A PHE* 3.7 17.1 - - + -
5A TRP* 3.4 49.5 + - + +
17A ILE* 4.1 5.6 - - + -
19A SER* 1.3 76.9 - - - +
21A THR* 1.3 68.7 + - - +
22A LEU* 5.7 1.1 - - + -
35A LEU* 3.3 34.3 - - + -
36A SER 3.4 9.0 - - - +
37A VAL* 3.8 13.2 - - + -
153A ILE* 3.9 12.1 - - + -
155A ILE* 3.8 28.7 - - + -
900A EPE 5.1 0.3 + - - -
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Residues in contact with THR 21 (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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3A PHE* 4.2 5.2 - - - -
19A SER* 6.0 1.8 - - - -
20A LEU* 1.3 82.9 - - - +
22A LEU* 1.3 61.6 + - - +
23A GLU* 4.5 9.0 + - - -
34A THR 4.1 1.1 - - - -
35A LEU* 3.3 14.3 - - - +
36A SER* 2.8 51.4 + - - +
118A LYS* 4.0 20.7 - - - +
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Residues in contact with LEU 22 (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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3A PHE* 3.7 46.2 - - + +
20A LEU* 5.7 0.9 - - + -
21A THR* 1.3 74.1 - - - +
23A GLU* 1.3 64.9 + - - +
24A PRO 4.0 7.1 - - - +
25A ASP* 4.6 6.4 - - - +
27A ILE* 3.8 22.6 - - + +
33A VAL* 3.2 30.3 - - + -
34A THR 3.4 0.9 - - - -
35A LEU* 3.9 28.5 - - + -
155A ILE* 5.0 6.7 - - + -
157A ALA* 4.3 10.3 - - + -
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Residues in contact with GLU 23 (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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21A THR* 4.5 7.4 + - - -
22A LEU* 1.3 81.5 - - - +
24A PRO* 1.3 70.8 - - + +
25A ASP* 5.5 1.1 - - + +
33A VAL* 3.2 9.1 - - - +
34A THR* 2.6 51.8 + - - +
118A LYS* 3.0 40.5 + - - +
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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