Contacts of the strand formed by residues 168 - 171 (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 LEU 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.8 40.4 - - + +
87B ASP* 4.2 10.3 - - - +
88B HIS 5.9 0.7 - - - +
151B ARG* 3.0 26.2 + - - -
163B ALA 3.8 6.1 - - - +
164B ILE* 3.7 14.1 - - + -
165B THR* 3.1 34.5 + - - +
167B ARG* 1.3 83.5 - - + +
169B MET* 1.3 60.9 + - - +
198B THR* 4.7 0.9 - - + -
212B ILE* 3.8 21.1 - - + -
213B TYR 3.5 11.2 - - - +
214B THR* 3.9 22.2 - - + +
215B ARG* 3.8 4.4 - - - +
219B TYR* 6.0 0.7 - - - +
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.9 26.0 - - + -
148B VAL* 3.7 39.7 - - + -
164B ILE* 4.3 2.9 - - - -
168B LEU* 1.3 75.3 - - - +
170B CYS* 1.3 69.7 + - - +
187B LEU* 3.8 22.4 - - + -
189B CYS* 5.1 1.6 - - - -
194B GLU* 4.6 12.8 - - - +
195B GLY* 4.7 1.6 - - - -
212B ILE* 3.6 7.1 - - - +
213B TYR* 2.9 49.0 + - + +
215B ARG* 3.9 21.1 - - + +
1230B GOL 3.1 22.0 - - - +
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Residues in contact with CYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.4 7.1 - - - +
149B LEU* 2.9 33.2 + - + +
151B ARG* 5.3 0.7 - - - -
154B CYS* 2.0 52.3 - - + -
160B HIS* 5.0 0.7 - - - -
164B ILE* 3.7 23.1 - - - -
169B MET* 1.3 82.9 - - - +
171B ALA* 1.3 61.5 + - - +
210B PRO* 4.3 1.8 - - + -
211B GLY 3.3 9.4 - - - +
212B ILE* 5.0 0.9 - - - -
213B TYR* 4.7 2.2 - - - -
1230B GOL 2.7 16.2 + - - +
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Residues in contact with ALA 171 (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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146B LEU* 4.1 22.2 - - + +
147B PRO 3.4 12.3 - - - +
148B VAL* 4.7 2.5 - - + -
149B LEU* 4.0 5.2 - - - +
170B CYS* 1.3 75.4 - - - +
172B GLU* 1.3 67.8 + - - +
187B LEU* 4.9 10.3 - - + -
210B PRO* 3.5 6.9 - - - +
211B GLY* 3.1 24.7 + - - -
213B TYR* 3.7 22.9 - - + -
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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
------------------------------------------------------------
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