Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 2XWA
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 GLY 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B CYS* 3.3 7.1 - - - +
171B ALA 3.1 31.1 + - - -
173B SER* 3.7 7.4 - - - -
177B ASP* 3.8 18.8 - - - -
178B SER* 5.3 1.6 - - - -
210B PRO* 1.3 71.9 - - - +
212B ILE* 1.3 60.2 + - - -
213B TYR* 3.3 17.1 - - - -
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 4.2 22.2 - - + -
160B HIS* 3.7 28.9 - - + +
163B ALA* 6.4 0.2 - - + -
164B ILE* 3.8 22.7 - - + -
168B LEU* 3.8 29.8 - - + -
169B MET 3.6 6.5 - - - +
170B CYS* 5.0 0.7 - - - -
197B VAL* 4.1 1.0 - - - +
198B THR* 3.0 47.9 + - + +
199B SER* 6.2 0.7 - - - +
210B PRO 3.6 8.3 + - - +
211B GLY* 1.3 73.8 - - - +
213B TYR* 1.3 71.0 + - - +
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.1 4.9 - - + +
146B LEU* 3.6 22.7 - - - +
168B LEU* 3.5 5.0 - - - -
169B MET* 2.9 47.1 + - + +
170B CYS 4.7 0.9 - - - -
171B ALA* 3.7 20.0 - - + -
177B ASP* 4.3 4.9 + - - -
178B SER* 3.2 21.1 + - - -
187B LEU* 3.8 34.5 - - + -
195B GLY* 4.2 4.3 - - - -
196B VAL 3.3 13.7 - - - +
197B VAL* 3.5 40.8 - - + -
198B THR* 4.3 0.4 - - - -
211B GLY* 3.3 27.1 - - - -
212B ILE* 1.3 76.0 - - - +
214B THR* 1.3 62.8 + - - +
215B ARG 3.5 0.2 + - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE 4.6 0.2 + - - -
88B HIS 5.1 0.4 - - - +
89B ASP* 4.2 19.5 + - - +
90B LEU* 3.9 28.9 - - + -
167B ARG 4.2 1.8 - - - +
168B LEU* 3.9 16.3 - - + +
195B GLY* 3.4 5.5 - - - -
196B VAL* 2.8 37.2 + - - +
198B THR* 4.0 15.0 - - - +
213B TYR* 1.3 70.7 - - - +
215B ARG* 1.3 64.6 + - - +
216B VAL* 3.5 2.1 + - - +
219B TYR* 3.5 32.5 - - + +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 2.4 32.7 + - - -
115B ARG 3.3 24.0 + - - -
116B ASP* 3.6 23.1 + - - +
117B VAL* 5.4 3.4 - - - +
151B ARG* 4.1 0.9 - - - +
166B GLU* 2.9 31.5 + - - +
167B ARG 2.9 19.0 + - - +
168B LEU 3.8 18.8 - - - +
169B MET* 3.9 24.7 - - + -
194B GLU* 3.7 7.7 + - - +
213B TYR 3.5 0.2 + - - -
214B THR* 1.3 70.6 - - - +
216B VAL* 1.3 64.9 + - - +
217B ALA* 3.8 16.7 - - - +
218B SER* 3.1 18.7 + - - -
219B TYR* 3.1 22.4 - - - -
1230B GOL 5.5 0.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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