Contacts of the strand formed by residues 197 - 202 (chain R) in PDB entry 2X1X
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 MET 197 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R CYS 4.4 0.2 - - - +
163R ALA* 3.7 0.2 - - - -
164R ARG* 3.1 70.9 + - + +
165R TYR* 5.9 1.1 - - + -
195R ALA* 3.5 0.7 - - - +
196R GLY* 1.3 81.2 - - - +
198R VAL* 1.3 68.9 + - - +
199R PHE* 4.9 2.0 - - + -
213R MET* 3.7 43.1 - - + -
214R TYR 3.4 16.6 - - - +
215R ILE* 4.3 7.4 - - + -
216R VAL* 4.1 3.1 - - - +
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Residues in contact with VAL 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R VAL* 4.8 1.3 - - + -
148R ILE* 3.8 30.7 - - + -
161R LEU* 3.8 7.9 - - + -
162R CYS 3.3 7.9 - - - +
163R ALA* 3.7 20.0 - - + -
192R ILE* 4.1 19.1 - - + -
195R ALA* 4.3 1.8 - - + -
197R MET* 1.3 79.4 - - - +
199R PHE* 1.3 68.8 + - - +
213R MET* 3.7 2.6 - - - +
214R TYR* 2.9 48.0 + - + +
216R VAL* 3.7 22.7 - - + -
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Residues in contact with PHE 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161R LEU* 3.9 5.8 - - - -
162R CYS* 2.8 64.2 + - + +
164R ARG* 3.8 39.3 - - + -
197R MET* 4.9 4.0 - - + -
198R VAL* 1.3 79.4 - - - +
200R CYS* 1.3 70.1 + - - +
201R GLU* 4.2 9.9 - - + -
210R GLN* 3.8 24.9 - - + -
211R SER* 3.5 12.3 - - - +
212R ILE 3.6 12.1 - - - +
213R MET* 3.5 30.1 - - + -
214R TYR* 4.6 4.3 - - - -
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Residues in contact with CYS 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125R PHE* 3.6 15.0 - - + -
148R ILE* 3.9 6.1 - - - -
150R CYS* 2.0 47.8 - - - -
159R VAL* 3.7 5.8 - - + -
160R SER 3.2 10.8 - - - +
161R LEU* 4.2 6.5 - - - +
185R PHE* 3.7 26.5 - - - -
199R PHE* 1.3 74.2 - - - +
201R GLU* 1.3 59.6 + - - +
210R GLN* 3.6 4.0 - - - +
211R SER* 2.8 32.2 + - - -
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Residues in contact with GLU 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R PHE* 4.2 0.9 - - - -
158R ASN 4.1 1.2 - - - +
159R VAL* 3.6 1.8 - - - -
160R SER* 2.8 37.7 + - - +
162R CYS* 3.8 20.6 - - - -
169R ARG* 2.7 39.1 + - - -
199R PHE* 4.2 12.5 - - + -
200R CYS* 1.3 75.6 - - - +
202R ALA* 1.3 61.0 + - - +
203R LYS* 5.2 8.5 + - + +
208R SER* 4.6 16.5 + - - -
209R TYR 3.4 16.4 - - - +
210R GLN* 4.0 15.8 - - + +
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Residues in contact with ALA 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124R PRO* 5.5 2.2 - - + -
125R PHE* 3.6 22.0 - - + -
157R LEU* 4.1 24.0 - - + -
158R ASN 4.0 5.2 - - - +
159R VAL* 3.8 19.5 - - + -
201R GLU* 1.3 74.8 - - - +
203R LYS* 1.3 61.1 + - - +
209R TYR* 2.7 40.7 + - + +
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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