Contacts of the strand formed by residues 156 - 165 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ASP* 4.3 3.1 - - - +
153D PHE 3.0 25.0 + - - +
154D GLU 3.3 3.1 + - - +
155D GLY* 1.3 79.8 - - - +
157D PRO* 1.3 81.4 - - + +
158D THR* 3.1 7.8 + - - +
217D PRO* 5.1 7.4 - - + -
218D ILE 4.3 11.4 - - - +
219D ASP* 5.8 3.1 - - + -
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Residues in contact with PRO 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 4.5 15.0 - - + -
151D SER* 3.5 7.6 - - - +
152D ASP* 3.8 19.7 - - - +
155D GLY 4.8 0.2 - - - +
156D LYS* 1.3 85.3 - - + +
158D THR* 1.3 59.7 + - - +
218D ILE* 2.8 48.1 + - + +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL 3.4 3.5 - - - +
150D ILE* 4.3 3.1 - - - -
151D SER 2.6 37.6 + - - +
153D PHE* 3.9 15.8 + - + +
156D LYS* 3.1 13.9 + - - +
157D PRO* 1.3 74.1 + - - +
159D LEU* 1.3 69.1 + - - +
160D MET* 3.6 14.8 + - - +
201D THR* 5.1 0.7 - - + -
215D MET* 3.4 25.8 - - + -
216D HIS 3.3 26.7 - - - +
217D PRO* 3.4 9.8 - - + +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D MET* 3.7 40.6 - - + -
149D VAL 3.4 8.5 - - - +
150D ILE* 3.4 31.4 - - + -
158D THR* 1.3 74.2 - - - +
160D MET* 1.3 60.6 + - - +
178D LEU* 4.3 7.9 - - + +
198D LEU* 4.2 10.1 - - + -
215D MET* 3.4 0.2 - - - -
216D HIS* 2.7 45.2 + - + +
218D ILE* 4.1 4.4 - - + +
224D ILE* 3.9 18.4 - - + -
239D PHE* 3.9 28.5 - - + -
265D ILE* 4.4 8.3 - - + -
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Residues in contact with MET 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D MET* 3.3 9.5 - - - +
149D VAL* 2.9 44.6 + - + -
151D SER* 3.3 31.6 - - - +
153D PHE* 3.9 21.8 - - + -
158D THR* 3.7 16.8 - - - +
159D LEU* 1.3 74.5 - - - +
161D MET* 1.3 61.1 + - - +
178D LEU* 5.7 1.3 - - - -
213D THR* 4.2 15.3 - - + -
214D VAL 2.9 20.2 - - - +
215D MET* 3.7 26.5 - - + +
270D HIS* 5.6 1.8 - - + -
271D PHE* 3.7 7.7 - - + -
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Residues in contact with MET 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 4.0 19.1 - - + -
145D SER* 3.3 10.8 - - - +
147D ARG 3.9 5.6 - - - +
148D MET* 3.5 24.7 - - + -
160D MET* 1.3 74.3 - - - +
162D ARG* 1.3 91.7 + - - +
163D LEU* 4.3 3.8 - - + -
176D VAL* 5.6 0.2 - - - -
178D LEU* 4.6 6.5 - - + -
213D THR* 3.5 2.3 - - - +
214D VAL* 2.8 46.3 + - - +
241D VAL* 3.9 23.1 - - + -
260D TYR* 3.5 26.9 - - + +
271D PHE* 3.6 9.6 - - - -
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Residues in contact with ARG 162 (chain D).
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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145D SER* 2.9 47.4 + - - -
161D MET* 1.3 86.0 - - - +
163D LEU* 1.3 60.7 + - - +
211D SER* 4.5 5.1 + - - +
212D TRP 3.1 14.1 - - - +
213D THR* 3.6 21.3 + - - +
214D VAL 4.5 0.2 - - - +
271D PHE* 3.3 30.4 - - + +
272D VAL 3.0 29.8 + - - -
273D ASP* 4.6 2.0 + - - +
274D VAL* 4.2 17.9 - - - +
275D PHE* 5.8 1.8 - - - -
289D LYS 3.3 17.0 + - - -
290D PHE* 2.9 55.1 + - + +
292D GLU 4.0 1.4 + - - -
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL* 3.7 20.9 - - + -
143D LEU 3.3 5.4 - - - -
144D PHE* 3.4 40.8 - - + -
161D MET* 4.3 7.0 - - + -
162D ARG* 1.3 74.8 - - - +
164D ALA* 1.3 59.4 + - - +
176D VAL* 4.5 6.3 - - + -
208D PHE* 3.8 8.5 - - + -
211D SER* 3.2 5.2 + - - -
212D TRP* 2.7 62.1 + - + +
214D VAL* 4.2 15.0 - - + -
241D VAL* 4.9 2.7 - - + -
243D PHE* 3.8 28.7 - - + -
290D PHE* 3.6 2.2 - - - -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLY 3.7 0.2 - - - +
142D VAL* 3.5 1.5 - - - -
143D LEU* 2.9 40.2 + - + +
163D LEU* 1.3 74.2 - - - +
165D ASN* 1.3 64.3 + - - +
166D LEU* 3.5 0.9 + - + +
208D PHE* 3.9 2.7 - - - -
210D LEU 3.3 9.0 - - - +
211D SER* 4.7 1.6 - - - -
287D LEU* 3.8 28.9 - - + -
290D PHE* 3.4 25.1 - - + -
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Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLY* 3.9 8.1 - - - +
142D VAL* 4.7 1.1 - - - +
164D ALA* 1.3 72.6 - - - +
166D LEU* 1.3 81.6 + - - +
167D ARG* 2.7 26.2 + - - +
169D GLU 2.8 26.9 + - - -
170D GLN* 4.2 0.6 - - - +
171D ILE* 4.4 11.6 - - - +
208D PHE* 3.4 27.8 + - + -
209D SER* 3.4 33.0 + - - +
210D LEU* 2.8 13.6 + - - +
247D HIS* 4.9 3.0 + - - -
285D LEU* 5.5 2.4 - - - +
287D LEU* 4.6 6.4 - - - +
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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
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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