Contacts of the strand formed by residues 211 - 217 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ARG* 4.5 10.4 + - - -
163A LEU 3.2 11.3 + - - -
164A ALA* 4.6 6.1 - - - -
208A PHE* 3.8 4.8 - - - -
210A LEU* 1.3 82.6 + - - +
212A TRP* 1.3 67.3 + - - +
213A THR* 4.3 2.2 + - - -
274A VAL* 5.0 7.6 - - - +
275A PHE* 4.5 22.4 - - - -
285A LEU* 5.1 4.9 - - - -
287A LEU* 5.7 0.2 - - - -
290A PHE* 3.9 14.1 - - - -
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Residues in contact with TRP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ARG* 3.1 3.0 - - - -
163A LEU* 2.8 57.6 + - + +
174A ALA* 4.1 13.5 - - + -
175A ASP* 4.1 9.0 - - - -
176A VAL* 4.0 15.7 - - + -
202A ARG* 3.2 46.5 + - + +
203A SER 3.5 22.0 - - - -
204A ARG 4.1 2.5 - - - -
205A SER* 3.6 36.8 - - - -
208A PHE* 3.6 24.9 - + + -
211A SER* 1.3 76.9 + - - +
213A THR* 1.3 80.5 + - - +
214A VAL* 3.7 9.9 + - + +
243A PHE* 4.7 2.0 - + - -
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Residues in contact with THR 213 (chain A).
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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160A MET* 4.2 17.5 - - + -
161A MET 3.6 12.3 - - - +
162A ARG* 3.5 26.8 + - + +
211A SER* 4.3 3.0 + - - -
212A TRP* 1.3 80.5 + - - +
214A VAL* 1.3 67.0 + - - +
215A MET* 3.7 26.9 + - + +
271A PHE* 4.8 8.1 - - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A MET* 2.9 28.1 - - - +
161A MET* 2.8 32.7 + - + +
163A LEU* 4.2 12.8 - - + -
176A VAL* 3.5 22.2 - - + -
178A LEU* 5.4 4.9 - - + +
200A LEU* 3.2 37.9 - - + -
202A ARG 4.0 9.2 - - - +
212A TRP* 4.1 18.6 - - - +
213A THR* 1.3 73.2 - - - +
215A MET* 1.3 63.1 + - - +
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Residues in contact with MET 215 (chain A).
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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153A PHE* 4.1 41.5 - - + -
158A THR* 3.4 12.3 - - + -
159A LEU 3.4 3.4 - - - -
160A MET* 3.7 23.1 - - + +
178A LEU* 5.7 0.2 - - - -
200A LEU* 3.1 12.7 - - - +
201A THR* 2.9 48.9 + - + +
202A ARG 5.4 1.4 + - - +
213A THR* 3.7 28.2 + - + +
214A VAL* 1.3 83.1 - - - +
216A HIS* 1.3 59.8 + - - +
217A PRO* 3.7 0.7 - - - -
192D PHE* 6.5 1.8 - - + -
194D ARG* 5.7 1.6 - - - +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.3 2.5 - - - -
159A LEU* 2.7 35.1 + - + +
178A LEU* 4.6 6.0 - - + +
198A LEU* 3.3 33.1 - - + +
199A THR* 2.7 32.8 + - - +
200A LEU* 3.9 11.0 - - + -
215A MET* 1.3 73.2 - - - +
217A PRO* 1.3 75.8 + - - +
218A ILE* 3.4 3.2 + - + +
222A SER* 2.4 41.4 + - - -
223A PRO* 4.5 1.1 - - + -
224A ILE* 3.8 21.4 - - + +
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Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS* 5.1 9.2 - - + -
157A PRO 3.9 0.4 - - - +
158A THR* 3.4 17.5 - - + +
199A THR* 3.9 13.5 - - + +
200A LEU 5.2 0.4 - - - -
201A THR* 3.0 36.8 - - + +
215A MET 3.5 1.1 - - - +
216A HIS* 1.3 101.9 + - - +
218A ILE* 1.3 61.5 + - - +
219A ASP* 3.9 10.1 + - + +
222A 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