Contacts of the strand formed by residues 252 - 261 (chain B) in PDB entry 2WLJ
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 GLN 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 5.4 0.3 + - - -
135B PHE 3.8 3.1 - - - +
136B THR* 2.6 56.9 + - - +
138B PRO* 3.0 18.1 - - + +
246B HIS* 3.7 6.2 - - - -
247B HIS* 3.2 19.7 + - - +
250B PHE* 2.9 33.2 - - + +
251B ALA* 1.3 78.3 - - - +
253B ASN* 1.3 69.8 + - - +
254B VAL* 3.7 6.6 + - - +
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 5.3 2.3 - - - +
244B THR* 4.8 7.6 - - + +
245B GLY 3.1 10.7 - - - +
246B HIS* 3.4 27.0 + - - +
252B GLN* 1.3 82.1 + - - +
254B VAL* 1.3 62.9 + - - +
255B HIS* 4.2 20.1 + - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 4.1 17.9 - - + +
139B THR 4.2 4.7 - - - +
140B ALA* 3.7 27.6 - - + +
171B ILE* 4.4 9.9 - - + -
243B PHE* 4.4 7.2 - - + -
244B THR* 3.4 7.3 - - - +
245B GLY 2.7 35.6 + - - +
247B HIS* 3.9 26.7 - - + -
250B PHE* 4.1 13.7 - - + -
252B GLN 3.8 9.2 - - - +
253B ASN* 1.3 79.2 - - - +
255B HIS* 1.3 69.1 + - - +
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Residues in contact with HIS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B THR* 5.8 0.2 - - - -
140B ALA* 3.7 10.8 + - - +
243B PHE* 3.3 8.1 - - - +
244B THR* 4.1 22.6 + - + -
253B ASN* 4.2 16.2 + - + +
254B VAL* 1.3 88.3 + - - +
256B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 256 (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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140B ALA* 3.8 17.7 - - + -
142B VAL* 4.3 9.6 - - + +
144B PHE* 3.8 22.4 - - + -
242B LEU* 3.6 0.7 - - - +
243B PHE* 2.8 38.9 + - + +
255B HIS* 1.3 77.5 - - - +
257B ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 257 (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* 3.7 11.4 - - - -
240B LEU* 6.2 0.7 - - + -
241B VAL 3.1 16.2 - - - +
242B LEU* 3.8 25.6 - - + -
256B ALA* 1.3 76.8 - - - +
258B HIS* 1.3 68.5 + - - +
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Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.7 41.1 - - + +
145B SER 4.4 3.6 + - - -
146B SER* 5.1 5.7 + - - -
239B PHE 3.7 0.7 - - - +
240B LEU* 3.4 4.0 - - - +
241B VAL* 2.9 29.4 + - + +
257B ARG* 1.3 81.2 + - - +
259B ALA* 1.3 86.2 + - - +
260B TYR* 3.4 38.8 - + + -
264B GLU* 5.7 1.2 + - - -
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Residues in contact with ALA 259 (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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238B GLU* 4.9 9.4 - - - +
239B PHE 3.3 4.7 - - - +
240B LEU* 3.9 20.6 - - + -
258B HIS* 1.3 90.9 + - - +
260B TYR* 1.3 62.7 + - - +
261B SER 4.3 0.3 + - - -
264B GLU* 4.1 4.7 - - - +
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Residues in contact with TYR 260 (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* 3.9 1.9 - - - +
145B SER* 2.7 34.8 + - - -
146B SER 3.8 7.4 - - - -
147B ARG* 3.7 20.0 - - - -
148B MET* 3.5 42.2 - - + -
161B MET* 3.4 24.5 - - + +
238B GLU* 3.5 6.3 - - - +
239B PHE* 2.6 47.8 + - + +
241B VAL* 3.6 26.5 - - + -
258B HIS* 3.4 28.0 - + - -
259B ALA* 1.3 75.6 - - - +
261B SER* 1.3 65.7 + - - +
264B GLU* 3.3 13.5 - - + +
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Residues in contact with SER 261 (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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237B SER 5.2 0.2 - - - -
238B GLU* 4.3 15.7 - - - +
239B PHE* 5.4 0.9 - - - -
259B ALA 4.2 0.8 + - - -
260B TYR* 1.3 76.3 - - - +
262B CYS* 1.3 55.3 + - - +
263B ASP* 3.4 25.4 + - - +
264B GLU* 2.7 49.8 + - - +
265B ILE* 3.9 5.8 + - - +
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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