Contacts of the strand formed by residues 19 - 25 (chain q) in PDB entry 5GJQ
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 CYS 19 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16q GLY* 3.0 27.8 + - - -
17q LYS 3.4 19.0 - - - -
18q ASN* 1.3 79.2 - - - +
20q VAL* 1.3 64.1 + - - +
112q LEU* 4.2 4.7 - - - +
119q PRO* 3.5 9.6 - - - +
158q MET 4.1 2.5 - - - -
159q ASP 4.6 0.2 - - - -
160q PRO* 4.0 28.3 - - + -
163q LEU* 3.7 12.8 - - - -
189q ILE* 3.9 10.3 - - + -
190q ILE 3.3 14.4 - - - +
191q GLU* 4.2 12.1 - - + -
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Residues in contact with VAL 20 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14q MET 3.3 15.7 - - - +
15q LYS* 4.2 3.8 - - + -
19q CYS* 1.3 78.5 - - - +
21q ALA* 1.3 61.6 + - - +
110q ALA* 4.1 7.9 - - + -
111q GLY* 3.7 21.3 - - - +
112q LEU* 4.2 9.4 - - + -
119q PRO* 4.2 6.3 - - + -
120q PHE 4.0 6.7 - - - +
121q ILE* 3.5 26.5 - - + -
163q LEU* 3.8 4.3 - - - -
188q HIS 4.1 0.2 - - - +
189q ILE* 3.3 2.3 - - - +
190q ILE* 2.8 56.7 + - + +
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Residues in contact with ALA 21 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13q ALA* 3.3 4.2 - - - +
14q MET 2.9 32.8 + - - +
20q VAL* 1.3 74.8 - - - +
22q ILE* 1.3 63.0 + - - +
110q ALA* 4.2 3.6 - - - +
163q LEU* 3.7 24.7 - - + +
167q ILE* 3.6 24.7 - - + -
187q VAL* 4.9 1.1 - - + -
188q HIS 3.3 9.6 - - - +
189q ILE* 4.2 9.4 - - + -
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Residues in contact with ILE 22 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11q VAL* 4.3 1.3 - - + -
12q MET 3.2 12.3 - - - +
13q ALA* 4.0 5.8 - - + -
21q ALA* 1.3 77.9 - - - +
23q ALA* 1.3 65.3 + - - +
42q ILE* 3.8 21.5 - - + +
50q TYR* 4.2 14.6 - - + +
51q ILE 4.3 3.1 - - - -
52q GLY* 3.8 34.1 - - - +
108q VAL* 4.0 16.2 - - + +
110q ALA* 3.6 22.0 - - + +
167q ILE* 4.1 2.0 - - - -
187q VAL* 3.6 0.3 - - - -
188q HIS* 2.9 48.6 + - + +
190q ILE* 6.4 0.4 - - + -
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Residues in contact with ALA 23 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11q VAL* 3.3 1.9 - - - +
12q MET* 2.9 32.2 + - - +
22q ILE* 1.3 76.0 - - - +
24q ALA* 1.3 65.4 + - - +
42q ILE* 3.6 5.6 - - - +
167q ILE* 3.9 13.4 - - + +
171q MET* 3.6 29.8 - - + +
185q VAL* 4.5 1.1 - - + -
186q ILE 3.2 13.7 - - - +
187q VAL* 4.1 13.9 - - + -
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Residues in contact with ALA 24 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10q ALA 3.1 14.6 - - - +
11q VAL* 3.9 11.9 - - + -
23q ALA* 1.3 77.7 - - - +
25q ASP* 1.3 71.8 + - - +
41q LYS* 4.4 7.6 - - + -
42q ILE* 3.5 22.1 - - + +
171q MET* 3.9 7.9 - - - -
186q ILE* 3.0 36.8 + - + +
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Residues in contact with ASP 25 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9q GLY* 3.8 2.3 - - - -
10q ALA 2.9 25.3 + - - +
24q ALA* 1.3 80.5 - - - +
26q ARG* 1.3 60.4 + - - +
27q ARG* 3.7 6.4 + - - +
39q PHE 4.6 0.7 - - - +
41q LYS* 2.8 43.6 + - - +
171q MET* 3.7 5.1 - - + +
175q VAL* 4.4 13.0 - - + -
180q VAL 4.4 0.3 - - - +
181q SER* 3.4 9.3 - - - -
182q GLY* 2.9 37.5 + - - +
184q GLY 3.1 14.4 - - - +
185q VAL* 4.4 0.9 - - + +
186q ILE* 4.9 1.6 - - - +
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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