Contacts of the strand formed by residues 15 - 23 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ASN* 4.5 0.7 - - - +
13C ASP* 4.2 1.2 - - - +
14C PRO* 1.3 76.8 - - + +
16C VAL* 1.3 65.2 + - - +
40C SER 3.4 5.2 - - - -
41C THR* 3.8 17.9 - - - +
45C LEU* 4.4 13.7 - - + -
143C LEU* 4.7 8.7 - - + -
150C LEU* 2.9 20.4 + - + +
151C GLY* 3.4 20.8 - - - -
152C CYS 4.5 2.1 + - - -
153C ILE* 5.8 1.2 - - - +
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASN* 3.4 23.6 - - + +
9C ASP 5.0 0.2 - - - +
10C GLU* 4.3 21.1 - - + +
13C ASP* 3.3 27.6 - - + +
14C PRO 5.0 2.0 - - - +
15C ALA* 1.3 76.0 - - - +
17C ILE* 1.3 65.3 + - - +
18C ARG* 3.6 39.0 - - - +
39C GLY* 3.3 2.3 - - - -
40C SER* 3.0 37.2 + - - +
153C ILE* 5.7 0.4 - - - -
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Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TRP* 3.1 28.0 - - + -
7C ASN* 2.8 28.1 + - - +
16C VAL* 1.3 79.0 - - - +
18C ARG* 1.3 66.0 + - - +
19C SER 3.4 25.8 - - - +
20C LEU* 4.0 13.5 - - + -
37C VAL* 4.0 19.1 - - + -
38C MSE 3.7 1.1 - - - +
39C GLY* 4.3 7.4 - - - -
153C ILE* 3.9 30.7 - - + -
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TRP* 3.5 12.7 - - - -
7C ASN* 6.2 0.2 - - - +
10C GLU* 3.7 25.6 + - - +
16C VAL* 3.6 25.9 - - - +
17C ILE* 1.3 80.4 - - - +
19C SER* 1.3 59.4 + - - +
38C MSE 2.7 52.2 + - + +
39C GLY* 4.3 8.3 - - - -
40C SER* 4.0 12.5 + - - +
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Residues in contact with SER 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MSE 4.2 11.1 - - - +
5C TRP* 3.8 5.4 - - - +
17C ILE* 3.4 4.9 - - - +
18C ARG* 1.3 78.6 - - - +
20C LEU* 1.3 63.6 + - - +
21C THR* 5.9 2.9 - - - -
36C SER* 5.2 1.5 + - - -
37C VAL* 3.3 2.5 - - - -
38C MSE 2.9 51.2 + - - +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.9 17.5 - - + -
5C TRP* 3.4 47.3 + - + +
17C ILE* 4.0 13.2 - - + -
19C SER* 1.3 76.5 - - - +
21C THR* 1.3 67.3 + - - +
22C LEU* 5.8 0.4 - - + -
35C LEU* 3.7 20.6 - - + -
36C SER 3.2 17.3 - - - +
37C VAL* 3.7 18.2 - - + -
153C ILE* 5.8 1.8 - - + -
155C ILE* 3.7 30.5 - - + -
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Residues in contact with THR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 4.3 4.3 - - - -
19C SER* 5.9 2.2 - - - -
20C LEU* 1.3 82.8 - - - +
22C LEU* 1.3 62.1 + - - +
23C GLU* 4.5 8.2 + - - -
34C THR 4.2 1.2 + - - -
35C LEU* 3.3 10.4 - - - +
36C SER* 2.6 53.6 + - - +
118C LYS* 3.9 20.6 - - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.6 53.5 - - + +
20C LEU* 5.7 0.4 - - + -
21C THR* 1.3 75.4 - - - +
23C GLU* 1.3 63.4 + - - +
24C PRO 3.8 7.6 - - - +
25C ASP* 4.8 2.8 - - - +
27C ILE* 3.7 26.9 - - + -
33C VAL* 3.1 34.3 - - + -
34C THR 3.4 3.1 - - - +
35C LEU* 4.1 22.4 - - + -
155C ILE* 5.4 2.7 - - + -
157C ALA* 4.6 6.1 - - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR* 4.5 6.1 + - - -
22C LEU* 1.3 83.0 - - - +
24C PRO* 1.3 71.7 - - + +
25C ASP* 5.7 0.7 - - + +
27C ILE* 5.3 0.2 - - - -
33C VAL* 3.2 9.6 - - - +
34C THR* 2.8 51.0 + - - +
118C LYS* 3.1 36.9 + - - +
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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