Contacts of the strand formed by residues 15 - 23 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 4.7 0.3 - - - +
13B ASP* 4.0 2.1 - - - +
14B PRO* 1.3 71.4 - - - +
16B VAL* 1.3 68.0 + - - +
40B SER 3.5 5.6 - - - +
41B THR* 3.7 18.6 - - - +
45B LEU* 4.4 18.4 - - + -
143B LEU* 4.6 5.6 - - + -
150B LEU* 2.8 23.4 + - + +
151B GLY* 3.4 19.9 - - - -
152B CYS 4.5 2.3 + - - -
153B ILE* 5.8 0.7 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 3.5 22.0 - - - +
10B GLU* 3.6 20.2 - - + +
13B ASP* 3.5 20.6 - - + +
14B PRO 4.7 2.7 - - - +
15B ALA* 1.3 80.4 - - - +
17B ILE* 1.3 64.9 + - - +
18B ARG* 3.5 34.5 + - - +
39B GLY* 3.3 2.1 - - - -
40B SER* 2.9 42.1 + - - +
153B ILE* 5.5 1.6 - - - -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 3.4 26.4 - - + -
7B ASN* 3.0 25.7 + - - -
16B VAL* 1.3 81.2 - - - +
18B ARG* 1.3 64.7 + - - +
19B SER 3.4 28.7 - - - +
20B LEU* 4.1 10.1 - - + -
37B VAL* 4.0 18.6 - - + -
38B MSE 3.5 4.3 - - - +
39B GLY* 4.6 4.9 - - - -
153B ILE* 3.6 35.2 - - + -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 3.5 12.4 - - - -
16B VAL* 3.5 21.6 - - + +
17B ILE* 1.3 76.0 - - - +
19B SER* 1.3 60.4 + - - +
38B MSE 2.7 37.0 + - + +
39B GLY* 4.6 3.8 - - - -
40B SER* 2.9 33.8 + - - +
113B THR* 4.7 6.2 + - + +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 3.6 7.4 - - - -
17B ILE* 3.4 5.8 - - - +
18B ARG* 1.3 81.0 - - - +
20B LEU* 1.3 65.1 + - - +
21B THR* 6.0 2.9 - - - -
36B SER* 5.5 2.5 + - - -
37B VAL* 3.4 2.5 - - - -
38B MSE 2.8 51.2 + - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.6 26.6 - - + -
5B TRP* 3.4 38.1 + - + +
17B ILE* 4.1 9.2 - - + -
19B SER* 1.3 77.1 - - - +
21B THR* 1.3 72.9 + - - +
22B LEU* 5.7 1.1 - - + -
35B LEU* 4.3 14.4 - - + -
36B SER* 3.3 18.2 - - - +
37B VAL* 3.9 17.3 - - + -
153B ILE* 5.7 2.5 - - + -
155B ILE* 3.7 35.0 - - + -
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.0 5.6 - - - -
19B SER* 6.0 2.5 - - - -
20B LEU* 1.3 83.2 - - - +
22B LEU* 1.3 62.2 + - - +
23B GLU* 4.7 8.5 + - - -
34B THR 4.3 1.5 + - - -
35B LEU* 3.4 9.4 - - - +
36B SER* 2.5 51.5 + - - +
118B LYS* 4.2 18.5 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.5 51.6 - - + +
20B LEU* 5.6 1.1 - - + -
21B THR* 1.3 76.3 - - - +
23B GLU* 1.3 64.4 + - - +
24B PRO 3.8 7.0 - - - +
25B ASP* 4.5 3.6 - - - +
27B ILE* 3.5 31.4 - - + -
33B VAL* 4.4 16.6 - - + -
34B THR 3.4 4.5 - - - +
35B LEU* 3.7 35.2 - - + -
155B ILE* 5.3 2.9 - - + -
157B ALA* 4.2 8.5 - - + -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 4.7 6.3 + - - -
22B LEU* 1.3 83.3 - - - +
24B PRO* 1.4 73.2 - - + +
25B ASP* 4.8 0.9 - - + +
33B VAL* 3.1 8.1 - - - +
34B THR* 2.6 53.7 + - - +
118B LYS* 3.3 39.2 + - - +
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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