Contacts of the strand formed by residues 156 - 165 (chain B) 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 LYS 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ASP* 4.3 2.5 - - - -
153B PHE 3.0 24.5 + - - +
154B GLU 3.3 3.7 + - - +
155B GLY* 1.3 79.6 - - - +
157B PRO* 1.3 79.0 - - + +
158B THR* 3.0 7.9 + - - +
217B PRO* 5.1 7.6 - - + -
218B ILE 4.2 12.3 - - - +
219B ASP* 5.8 3.4 - - + -
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Residues in contact with PRO 157 (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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150B ILE* 4.5 15.3 - - + -
151B SER 3.6 7.4 - - - +
152B ASP* 3.8 19.2 - - - +
155B GLY 4.9 0.2 - - - +
156B LYS* 1.3 86.4 - - + +
158B THR* 1.3 59.5 + - - +
218B ILE* 2.8 47.6 + - + +
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Residues in contact with THR 158 (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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149B VAL 3.4 3.1 - - - +
150B ILE* 4.3 2.7 - - - -
151B SER 2.6 36.1 + - - +
153B PHE* 3.9 15.5 + - - +
156B LYS* 3.0 14.0 + - - +
157B PRO* 1.3 75.0 + - - +
159B LEU* 1.3 69.8 + - - +
160B MET* 3.6 15.4 + - - +
201B THR* 5.1 0.7 - - + -
215B MET* 3.4 26.0 - - + -
216B HIS 3.3 26.9 - - - +
217B PRO* 3.4 10.3 - - + +
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Residues in contact with LEU 159 (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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148B MET* 3.7 41.5 - - + -
149B VAL 3.4 9.6 - - - +
150B ILE* 3.4 29.8 - - + -
158B THR* 1.3 74.1 - - - +
160B MET* 1.3 59.0 + - - +
178B LEU* 4.3 7.3 - - + +
198B LEU* 4.2 9.9 - - + -
216B HIS* 2.7 45.9 + - + +
218B ILE* 4.1 4.9 - - + +
224B ILE* 3.9 17.5 - - + -
239B PHE* 3.9 28.5 - - + -
265B ILE* 4.4 7.9 - - + -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.2 9.4 - - - +
149B VAL* 2.9 44.3 + - + -
151B SER* 3.3 31.6 - - - +
153B PHE* 3.9 21.8 - - + -
158B THR* 3.7 16.8 - - - +
159B LEU* 1.3 75.3 - - - +
161B MET* 1.3 61.3 + - - +
178B LEU* 5.7 1.1 - - - -
213B THR* 4.2 14.4 - - + -
214B VAL 2.9 20.4 - - - +
215B MET* 3.7 24.9 - - + +
270B HIS* 5.6 1.8 - - + -
271B PHE* 3.7 7.1 - - + -
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Residues in contact with MET 161 (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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144B PHE* 4.0 19.1 - - + -
145B SER* 3.3 11.2 - - - +
147B ARG 3.9 5.2 - - - +
148B MET* 3.5 24.7 - - + -
160B MET* 1.3 73.9 - - - +
162B ARG* 1.3 91.1 + - - +
163B LEU* 4.4 3.8 - - + +
176B VAL* 5.6 0.2 - - - -
178B LEU* 4.6 6.5 - - + -
213B THR* 3.6 2.8 - - - +
214B VAL* 2.8 46.7 + - - +
241B VAL* 4.0 22.4 - - + -
260B TYR* 3.5 27.1 - - + +
271B PHE* 3.6 9.2 - - - -
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Residues in contact with ARG 162 (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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143B LEU 3.7 0.2 - - - +
145B SER* 2.9 46.8 + - - -
161B MET* 1.3 86.8 - - - +
163B LEU* 1.3 60.3 + - - +
211B SER* 4.5 5.1 + - - +
212B TRP 3.1 14.4 - - - +
213B THR* 3.6 21.8 + - - +
214B VAL* 4.9 0.2 - - - -
271B PHE* 3.3 31.2 - - + +
272B VAL 2.9 30.1 + - - -
273B ASP* 4.6 2.2 + - - +
274B VAL* 3.9 18.7 - - - +
289B LYS 3.3 15.6 + - - -
290B PHE* 2.9 54.3 + - + +
292B GLU 4.0 1.8 + - - -
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Residues in contact with LEU 163 (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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142B VAL* 3.7 21.1 - - + -
143B LEU 3.3 5.4 - - - -
144B PHE* 3.4 40.4 - - + -
161B MET* 4.4 7.0 - - + -
162B ARG* 1.3 75.1 - - - +
164B ALA* 1.3 59.7 + - - +
176B VAL* 4.5 7.0 - - + -
208B PHE* 3.8 7.6 - - + -
211B SER* 3.2 4.9 + - - -
212B TRP* 2.8 61.8 + - + +
214B VAL* 4.2 14.8 - - + -
241B VAL* 4.9 3.1 - - + -
243B PHE* 3.8 28.5 - - + -
290B PHE* 3.6 2.0 - - - -
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Residues in contact with ALA 164 (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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142B VAL* 3.5 2.6 - - - -
143B LEU* 2.8 39.6 + - + +
163B LEU* 1.3 74.6 - - - +
165B ASN* 1.3 63.0 + - - +
166B LEU* 3.6 0.9 + - + +
208B PHE* 3.9 2.7 - - - -
210B LEU 3.3 7.6 - - - +
211B SER* 4.7 2.5 - - - -
287B LEU* 3.8 27.8 - - + -
290B PHE* 3.5 25.7 - - + -
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Residues in contact with ASN 165 (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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25A ARG* 2.9 19.8 + - - -
141B GLY* 3.9 8.0 - - - +
142B VAL* 4.7 1.1 - - - +
164B ALA* 1.3 72.0 - - - +
166B LEU* 1.3 62.6 + - - +
167B ARG* 2.7 39.2 + - - +
169B GLU 2.8 26.3 + - - +
170B GLN* 4.2 1.0 - - - +
171B ILE* 4.4 12.2 - - - +
208B PHE* 3.4 28.7 + - + -
209B SER* 3.4 30.1 + - - +
210B LEU 2.8 14.2 + - - +
247B HIS* 4.8 2.6 + - - -
285B LEU* 5.0 0.7 - - - +
287B LEU* 4.5 4.9 - - - +
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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