Contacts of the strand formed by residues 195 - 201 (chain Q) in PDB entry 2JA7
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 195 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154Q ILE 3.7 0.2 - - - +
155Q ARG* 3.9 1.2 - - - +
156Q LEU* 3.2 55.1 + - + +
161Q LYS* 3.5 36.0 - - + +
164Q LEU* 4.2 17.9 - - + -
165Q LEU* 6.0 0.2 - - + -
175Q LEU* 4.8 8.5 - - + -
193Q GLY 3.6 4.0 - - - +
194Q GLU* 1.3 78.0 - - - +
196Q VAL* 1.3 70.3 + - - +
211Q TYR* 4.5 1.1 - - + -
212Q ARG 3.5 16.8 - - - +
213Q ILE* 3.8 15.0 - - + +
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Residues in contact with VAL 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Q HIS* 3.2 46.0 - - + -
154Q ILE 3.0 15.7 - - - +
155Q ARG* 5.1 1.3 - - + -
156Q LEU* 4.1 2.5 - - - -
178Q ILE* 4.9 3.1 - - + -
188Q LEU* 4.8 2.7 - - + -
190Q LEU* 3.3 45.5 - - + -
194Q GLU 5.0 0.2 - - - +
195Q VAL* 1.3 79.5 - - - +
197Q LYS* 1.3 65.9 + - - +
198Q ILE* 3.8 1.1 + - + -
211Q TYR* 3.5 2.4 - - - -
212Q ARG* 2.7 43.8 + - + +
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Residues in contact with LYS 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009M ASN* 6.0 5.3 - - - +
1013M ASP* 5.6 2.8 + - - -
152Q LYS 4.0 0.5 - - - +
153Q HIS* 3.5 3.6 - - - -
154Q ILE* 2.8 40.6 + - + +
156Q LEU* 4.1 19.8 - - + +
196Q VAL* 1.3 71.9 - - - +
198Q ILE* 1.3 61.1 + - - +
199Q ILE* 3.4 36.5 + - + +
209Q ALA* 4.0 14.0 - - - +
210Q SER 3.4 7.2 - - - +
211Q TYR* 3.6 41.9 + - + -
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Residues in contact with ILE 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342M GLU* 3.2 48.0 - - + +
151Q PRO* 3.8 19.1 - - + -
152Q LYS 4.0 4.0 - - - +
153Q HIS* 3.9 22.7 - - + +
178Q ILE* 5.8 0.4 - - + -
196Q VAL* 4.2 6.1 - - + +
197Q LYS* 1.3 73.2 - - - +
199Q ILE* 1.3 62.0 + - - +
200Q ARG* 4.0 5.4 + - - +
208Q TYR 3.4 3.1 - - - +
210Q SER* 2.6 48.6 + - - +
211Q TYR 4.8 1.6 - - - -
212Q ARG* 3.1 38.6 - - + +
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Residues in contact with ILE 199 (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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151Q PRO* 3.9 7.4 - - - +
152Q LYS* 3.4 36.6 + - + +
154Q ILE* 4.4 19.7 - - + -
197Q LYS* 3.4 43.7 - - + +
198Q ILE* 1.3 77.8 - - - +
200Q ARG* 1.3 66.0 + - - +
201Q LYS* 6.1 0.4 - - - -
207Q ARG* 4.5 27.1 - - + +
208Q TYR 3.6 7.9 - - - +
209Q ALA* 4.8 3.6 - - + -
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Residues in contact with ARG 200 (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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870M GLU* 3.5 20.4 + - - -
1342M GLU* 3.0 30.3 + - - -
1345M ARG* 3.1 52.7 - - - +
1365M TYR* 4.1 0.2 + - - -
1373M ASP* 4.3 2.6 + - - -
151Q PRO* 3.6 24.5 - - + -
198Q ILE* 4.6 4.5 - - - +
199Q ILE* 1.3 75.5 - - - +
201Q LYS* 1.3 75.9 + - - +
207Q ARG* 3.3 6.4 - - - +
208Q TYR* 2.9 59.6 + - + +
210Q SER* 4.9 6.7 + - - -
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Residues in contact with LYS 201 (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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870M GLU* 4.5 3.1 - - - +
942M PHE* 5.0 4.6 - - + -
945M GLU* 3.3 45.9 + - - +
946M VAL* 3.9 31.6 - - + +
1365M TYR* 5.6 0.2 + - - -
199Q ILE* 6.1 0.7 - - - -
200Q ARG* 1.3 96.2 + - - +
202Q SER* 1.3 62.0 + - - +
206Q GLY 3.2 7.0 - - - +
207Q ARG* 4.4 19.5 - - + +
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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