Contacts of the strand formed by residues 211 - 217 (chain C) in PDB entry 2WLM
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 SER 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ARG* 4.5 8.1 + - - -
163C LEU 3.2 10.9 + - - -
164C ALA* 4.6 5.8 - - - -
208C PHE* 3.8 4.4 - - - -
210C LEU* 1.3 83.2 + - - +
212C TRP* 1.3 68.0 + - - +
213C THR* 4.3 2.4 + - - -
274C VAL* 4.9 10.1 - - - +
275C PHE* 4.1 25.2 - - - -
285C LEU* 5.0 4.0 - - - -
290C PHE* 3.9 14.5 - - - -
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Residues in contact with TRP 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 3.1 3.0 - - - -
163C LEU* 2.8 57.5 + - + +
174C ALA* 4.1 13.5 - - + -
175C ASP* 4.1 9.2 - - - -
176C VAL* 4.0 15.7 - - + -
202C ARG* 3.2 45.6 + - + +
203C SER 3.5 21.8 - - - -
204C ARG 4.1 2.7 - - - -
205C SER* 3.6 37.0 - - - -
208C PHE* 3.6 24.7 - + + -
211C SER* 1.3 75.8 + - - +
213C THR* 1.3 80.6 + - - +
214C VAL* 3.7 10.3 + - + +
243C PHE* 4.7 2.0 - + - -
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Residues in contact with THR 213 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C MET* 4.2 16.4 - - + -
161C MET 3.6 12.1 - - - +
162C ARG* 3.6 24.0 + - + +
211C SER* 4.3 2.6 + - - -
212C TRP* 1.3 81.5 + - - +
214C VAL* 1.3 67.7 + - - +
215C MET* 3.7 29.0 + - + +
271C PHE* 4.8 9.8 - - + +
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 2.9 28.8 - - - +
161C MET* 2.8 32.6 + - + +
163C LEU* 4.2 13.2 - - + -
176C VAL* 3.5 21.5 - - + -
178C LEU* 5.4 5.3 - - + +
200C LEU* 3.2 38.8 - - + -
202C ARG 4.0 8.7 - - - +
212C TRP* 4.1 18.6 - - - +
213C THR* 1.3 73.0 - - - +
215C MET* 1.3 62.3 + - - +
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Residues in contact with MET 215 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B PHE* 6.4 2.2 - - + -
153C PHE* 4.1 41.7 - - + -
158C THR* 3.4 12.1 - - + -
159C LEU 3.4 3.4 - - - -
160C MET* 3.7 22.2 - - - +
178C LEU* 5.7 0.2 - - - -
200C LEU* 3.0 11.5 - - - +
201C THR* 2.9 48.1 + - + +
202C ARG* 5.4 1.4 + - - +
213C THR* 3.7 28.2 + - + +
214C VAL* 1.3 83.5 - - - +
216C HIS* 1.3 60.4 + - - +
217C PRO* 3.7 0.9 - - - -
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Residues in contact with HIS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C THR* 3.3 2.2 - - - -
159C LEU* 2.7 35.6 + - + +
178C LEU* 4.7 6.9 - - + +
198C LEU* 3.3 32.9 - - + +
199C THR* 2.7 32.4 + - - +
200C LEU* 3.9 11.4 - - + +
215C MET* 1.3 73.8 - - - +
217C PRO* 1.3 75.8 + - - +
218C ILE* 3.4 2.5 + - + +
222C SER* 2.4 42.1 + - - -
223C PRO* 4.5 0.9 - - + -
224C ILE* 3.8 21.4 - - + +
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Residues in contact with PRO 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C LYS* 5.1 9.6 - - + -
157C PRO 3.9 0.2 - - - +
158C THR* 3.4 17.0 - - + +
199C THR* 3.9 12.6 - - + +
200C LEU 5.2 0.2 - - - -
201C THR* 3.0 37.7 - - + +
215C MET 3.5 1.1 - - - +
216C HIS* 1.3 102.1 + - - +
218C ILE* 1.3 62.4 + - - +
219C ASP* 3.9 10.9 + - + +
222C SER* 4.0 0.9 - - - -
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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
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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