Contacts of the strand formed by residues 185 - 191 (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 VAL 185 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24q ALA 3.6 9.6 - - - +
25q ASP* 5.1 0.7 - - - -
26q ARG* 3.8 4.0 - - - +
171q MET* 4.1 29.8 - - + -
172q LEU* 3.6 31.0 - - + -
175q VAL* 5.1 10.8 - - + -
182q GLY* 5.9 0.2 - - - -
184q GLY* 1.3 79.6 - - - +
186q ILE* 1.3 67.3 + - - +
187q VAL* 4.1 10.8 - - + -
199q THR* 3.4 6.2 - - - -
200q LEU* 2.9 56.1 + - + +
202q ALA* 4.2 5.6 - - + -
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Residues in contact with ILE 186 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22q ILE 4.0 0.6 - - - +
23q ALA* 3.2 5.0 - - - +
24q ALA* 3.0 43.5 + - + +
25q ASP 4.9 1.8 - - - +
26q ARG* 4.1 32.1 - - + +
42q ILE* 4.9 4.1 - - + +
185q VAL* 1.3 77.0 - - - +
187q VAL* 1.3 65.4 + - - +
188q HIS* 4.0 22.4 - - + +
197q THR* 4.0 21.8 - - + -
198q ARG 3.3 12.8 - - - +
199q THR* 4.2 14.6 - - + -
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Residues in contact with VAL 187 (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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21q ALA* 4.9 0.4 - - + -
22q ILE 3.6 5.8 - - - +
23q ALA* 4.1 8.3 - - + -
164q PHE* 4.2 20.4 - - + -
167q ILE* 3.8 26.7 - - + -
168q SER* 4.1 8.7 - - - +
185q VAL* 4.1 6.1 - - + -
186q ILE* 1.3 80.5 - - - +
188q HIS* 1.3 70.1 + - - +
189q ILE* 4.4 9.1 - - + +
196q THR 3.7 1.4 - - - +
197q THR* 3.4 2.9 - - - -
198q ARG* 2.9 36.9 + - + +
200q LEU* 4.0 33.4 - - + -
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Residues in contact with HIS 188 (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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20q VAL 4.1 0.3 - - - +
21q ALA* 3.3 2.0 - - - -
22q ILE* 2.9 45.8 + - + +
42q ILE* 3.8 36.5 + - + +
50q TYR* 3.6 28.3 - + + -
186q ILE* 4.0 20.4 - - + +
187q VAL* 1.3 76.0 - - - +
189q ILE* 1.3 60.7 + - - +
190q ILE* 4.0 7.0 + - + +
195q ILE* 5.3 0.6 - - + +
196q THR 3.4 4.3 - - - +
197q THR* 2.7 40.9 + - + -
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Residues in contact with ILE 189 (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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19q CYS* 3.9 19.1 - - + -
20q VAL 3.3 17.7 - - - +
21q ALA* 4.1 7.9 - - + +
160q PRO* 4.6 20.4 - - + +
163q LEU* 3.6 26.0 - - + -
164q PHE* 4.9 5.8 - - + +
187q VAL* 4.4 14.1 - - + +
188q HIS* 1.3 74.5 - - - +
190q ILE* 1.3 62.7 + - - +
191q GLU* 4.2 4.2 + - + +
196q THR* 2.9 54.2 + - - +
198q ARG* 4.0 17.7 - - + +
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Residues in contact with ILE 190 (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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19q CYS* 3.3 3.0 - - - +
20q VAL* 2.8 57.1 + - + +
22q ILE* 6.4 0.2 - - + -
48q ARG* 3.6 37.2 - - - +
49q LEU* 4.1 1.3 - - - +
50q TYR* 4.5 15.5 - - + -
110q ALA 4.4 3.4 - - - +
111q GLY* 4.0 7.0 - - - -
112q LEU* 3.9 10.2 - - + +
188q HIS* 4.6 5.8 - - + +
189q ILE* 1.3 84.3 - - - +
191q GLU* 1.3 63.4 + - - +
194q LYS 4.1 2.5 - - - -
195q ILE* 3.7 33.7 - - + +
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Residues in contact with GLU 191 (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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219p LEU* 5.2 3.8 - - - +
18q ASN 4.1 6.1 - - - +
19q CYS* 4.2 11.4 - - + -
48q ARG* 5.2 2.9 - - - +
112q LEU* 3.5 13.8 - - - +
160q PRO* 3.3 35.9 - - + +
189q ILE* 4.8 7.8 - - + +
190q ILE* 1.3 80.5 - - - +
192q LYS* 1.3 67.7 + - - +
193q ASP* 3.2 9.0 - - - +
194q LYS* 2.6 59.6 + - + +
195q ILE* 5.0 1.7 - - - +
196q THR* 4.2 7.4 + - - +
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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