Contacts of the strand formed by residues 260 - 268 (chain B) in PDB entry 1W1J
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 GLY 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PRO* 5.0 0.2 - - - +
202B VAL* 3.6 18.2 - - - -
203B VAL 3.8 4.7 - - - -
204B LEU* 5.0 0.4 - - - -
205B ALA 5.4 0.7 - - - -
254B PHE* 3.5 10.9 - - - +
257B SER* 4.2 5.5 + - - +
258B ASN 3.4 1.6 - - - -
259B MET* 1.3 82.8 + - - +
261B ILE* 1.3 66.3 + - - +
262B VAL* 4.0 2.3 - - - +
541B ILE* 4.2 10.0 - - - +
1561B FAD 3.4 16.6 - - - -
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Residues in contact with ILE 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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83B VAL* 4.4 10.1 - - + -
87B VAL* 3.8 22.0 - - + -
97B LEU* 4.9 3.1 - - + -
99B PRO* 4.2 17.7 - - + -
121B LEU* 4.5 11.7 - - + -
123B MET* 3.9 37.2 - - + -
202B VAL* 3.1 2.5 - - - -
203B VAL* 2.6 48.9 + - + +
260B GLY* 1.3 75.5 - - - +
262B VAL* 1.3 62.7 + - - +
263B THR* 3.7 2.9 + - + +
541B ILE* 3.5 34.1 - - + -
1561B FAD 3.5 8.7 - - - +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 4.1 3.1 - - - +
144B PRO* 3.7 8.8 - - - +
177B LEU* 3.9 17.4 - - + +
181B VAL* 4.0 13.0 - - + -
200B MET* 3.6 31.6 - - + -
201B GLU 3.4 13.0 - - - +
202B VAL* 4.0 6.7 - - + -
254B PHE* 4.3 10.5 - - + +
260B GLY 4.8 2.2 - - - +
261B ILE* 1.3 74.3 - - - +
263B THR* 1.3 62.5 + - - +
264B LYS 3.5 15.5 - - - +
265B ILE* 4.7 2.2 - - + -
1561B FAD 2.5 46.9 + - + +
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Residues in contact with THR 263 (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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80B VAL* 4.5 4.5 - - + -
83B VAL* 4.9 1.1 - - + -
123B MET* 3.8 18.4 - - + -
127B MET* 4.0 14.3 - - + +
143B GLU* 3.8 9.7 - - - +
144B PRO* 3.3 27.2 - - - +
177B LEU* 4.2 0.7 - - - -
201B GLU* 2.7 39.9 + - - +
202B VAL* 4.0 0.3 + - - -
203B VAL* 3.8 28.3 - - + -
209B LEU* 4.6 0.5 - - - +
261B ILE* 3.8 5.6 - - + +
262B VAL* 1.3 78.1 - - - +
264B LYS* 1.3 67.7 + - - +
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Residues in contact with LYS 264 (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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80B VAL* 3.7 14.1 - - - +
129B ARG* 5.0 4.5 - - - +
131B LEU* 3.6 33.3 - - + +
141B VAL* 4.4 3.4 - - + -
142B VAL 3.3 9.0 - - - +
143B GLU* 3.6 22.3 + - + -
177B LEU* 4.1 2.8 - - - +
200B MET* 3.4 2.6 - - - -
201B GLU* 2.7 62.7 + - + +
211B ARG* 4.2 1.3 - - - +
231B GLU 3.4 22.8 + - - -
233B GLN 5.8 0.7 - - - -
235B TRP* 3.8 23.8 - - + +
262B VAL* 3.5 4.6 - - - +
263B THR* 1.3 79.2 + - - +
265B ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 265 (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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141B VAL* 3.3 6.1 - - - +
142B VAL* 2.8 42.1 + - + +
177B LEU* 3.1 37.7 - - + -
180B ALA* 4.6 6.1 - - + -
181B VAL* 4.5 10.1 - - + -
194B TRP* 4.1 11.4 - - + -
197B HIS* 4.0 17.0 - - + +
199B GLY 3.9 6.5 - - - +
200B MET* 4.0 35.2 - - + -
262B VAL* 4.7 0.9 - - + -
264B LYS* 1.3 75.3 - - - +
266B GLY* 1.3 69.7 + - - +
267B ILE* 4.0 15.6 + - + -
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Residues in contact with GLY 266 (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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139B TYR* 5.5 0.4 - - - -
140B CYS 3.2 9.6 - - - -
141B VAL* 4.2 0.7 - - - -
197B HIS* 3.1 17.3 - - - +
198B SER* 3.2 19.4 + - - -
199B GLY 3.4 10.3 + - - -
240B HIS* 4.1 13.2 - - - -
265B ILE* 1.3 77.1 - - - +
267B ILE* 1.3 73.4 + - - +
268B TRP* 5.7 0.9 - - - -
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Residues in contact with ILE 267 (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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139B TYR* 3.5 0.6 - - - -
140B CYS* 2.8 53.5 + - - -
142B VAL* 5.8 0.9 - - + +
176B VAL* 4.0 27.6 - - + +
180B ALA* 4.1 16.6 - - + -
193B HIS* 4.0 15.3 - - + +
196B MET* 3.5 12.8 - - + +
197B HIS* 3.8 19.5 - - + -
265B ILE* 4.0 13.4 + - + -
266B GLY* 1.3 89.3 - - - +
268B TRP* 1.3 76.7 + - - +
269B LEU* 4.5 7.2 - - + -
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Residues in contact with TRP 268 (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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462A MET* 6.0 5.8 - - + -
463A ARG* 3.6 40.9 - - + +
138B ALA 3.7 3.1 - - - -
139B TYR* 3.8 7.6 - - + +
190B TYR* 3.4 20.2 - - + +
195B MET 3.7 15.0 - - - -
196B MET* 2.8 44.1 + - + +
197B HIS 4.3 1.1 - - - -
198B SER* 3.7 14.8 - - - -
240B HIS* 3.0 27.2 + - + -
241B LEU* 3.7 18.4 - - - +
243B PRO* 3.8 31.0 - - + -
266B GLY 5.7 0.7 - - - -
267B ILE* 1.3 85.5 - - - +
269B LEU* 1.3 60.7 + - - +
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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