Contacts of the strand formed by residues 241 - 249 (chain O) in PDB entry 4WNC
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 241 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178O VAL 3.3 13.9 - - - -
179O HIS* 3.4 11.5 - - - -
180O ALA 3.0 18.9 + - - -
240O VAL* 1.3 71.3 - - - +
242O VAL* 1.3 63.9 + - - +
313O TRP* 3.6 9.3 - - - -
314O TYR* 2.9 57.8 + - - +
316O ASN* 3.0 16.9 + - - -
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Residues in contact with VAL 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O THR 4.0 0.3 - - - +
177O THR* 3.2 4.9 + - - -
178O VAL* 2.9 59.6 + - + +
241O SER* 1.3 78.3 - - - +
243O VAL* 1.3 64.0 + - - +
244O ASP* 5.5 0.8 - - + +
311O ILE* 3.6 28.0 - - + -
312O SER 3.4 13.0 - - - +
313O TRP* 3.6 33.9 - - + -
314O TYR* 3.9 4.9 - - - -
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Residues in contact with VAL 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O THR* 4.1 23.3 - - + +
156O CYS* 3.8 16.4 - - + -
157O LEU* 4.2 20.0 - - + +
160O LEU* 5.4 2.7 - - + -
175O MET* 4.0 15.9 - - + -
176O THR 3.6 2.5 - - - -
177O THR* 4.3 4.9 - - - -
242O VAL* 1.3 78.0 - - - +
244O ASP* 1.3 63.8 + - - +
245O LEU* 4.0 12.3 - - + +
310O LEU 4.8 0.9 - - - +
311O ILE* 3.3 6.8 - - - +
312O SER* 2.8 42.8 + - - +
314O TYR* 3.8 20.2 - - + -
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Residues in contact with ASP 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O LEU 3.9 0.5 - - - +
175O MET* 3.4 2.9 - - - -
176O THR* 2.8 51.9 + - + +
178O VAL* 6.1 4.0 - - + -
242O VAL* 5.5 1.1 - - + +
243O VAL* 1.3 75.3 - - - +
245O LEU* 1.3 57.2 + - - +
246O THR* 3.5 4.5 + - - -
309O LYS* 3.0 50.6 + - - +
310O LEU 3.5 4.5 - - - -
311O ILE* 3.9 10.8 - - + +
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Residues in contact with LEU 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157O LEU* 3.8 34.1 - - + -
160O LEU* 4.7 13.2 - - + -
161O ALA* 5.0 7.6 - - + -
164O ILE* 5.5 1.6 - - + -
170O ILE* 4.7 13.0 - - + -
174O LEU 4.0 12.3 - - - +
175O MET* 4.5 5.4 - - + +
228O LEU* 4.3 22.2 - - + -
243O VAL* 4.0 4.2 - - + -
244O ASP* 1.3 71.8 + - - +
246O THR* 1.3 69.0 + - - +
247O CYS* 3.8 22.1 + - + -
308O VAL 3.5 2.4 - - - +
309O LYS* 3.3 1.7 - - - -
310O LEU* 2.8 52.0 + - + +
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Residues in contact with THR 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O GLY* 3.3 1.6 - - - -
174O LEU* 2.8 48.3 + - + +
244O ASP* 3.5 4.5 + - - -
245O LEU* 1.3 70.7 - - - +
247O CYS* 1.3 60.6 + - - +
307O PHE* 3.7 32.0 - - + -
308O VAL 3.4 10.1 - - - +
309O LYS* 2.9 35.1 + - + +
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Residues in contact with CYS 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O ILE* 4.6 9.4 - - - -
170O ILE* 4.2 14.1 - - + -
172O GLU 3.3 11.9 - - - +
173O GLY* 4.0 6.1 - - - -
245O LEU* 4.2 24.7 - - + -
246O THR* 1.3 75.2 - - - +
248O ARG* 1.3 62.9 + - - +
249O LEU* 4.0 14.5 + - - -
306O HIS 3.6 0.9 - - - +
307O PHE* 3.5 10.2 - - - -
308O VAL* 3.0 52.8 + - - +
310O LEU* 4.7 3.8 - - - -
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Residues in contact with ARG 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O ILE* 3.6 4.3 - - - +
171O VAL* 2.7 49.4 + - + +
172O GLU* 2.8 40.1 + - + +
247O CYS* 1.3 72.7 - - - +
249O LEU* 1.3 70.6 + - - +
250O GLU* 4.9 1.4 - - - +
306O HIS* 3.1 39.1 + - - +
307O PHE* 4.3 13.6 - - + +
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Residues in contact with LEU 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O ILE* 3.6 29.6 - - + -
168O PHE* 4.3 8.5 - - + -
169O GLY 3.2 9.9 - - - +
170O ILE* 4.7 0.9 - - + -
171O VAL* 3.9 1.8 - - - -
247O CYS* 4.0 17.9 - - - -
248O ARG* 1.3 82.6 + - - +
250O GLU* 1.3 59.2 + - - +
251O LYS 3.4 14.4 - - - +
253O ALA* 4.0 22.2 - - + -
258O ILE* 4.3 15.0 - - + -
305O ASP 3.9 17.3 - - - +
306O HIS* 2.7 41.9 + - - +
308O VAL* 4.4 12.1 - - + -
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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