Contacts of the strand formed by residues 223 - 229 (chain A) in PDB entry 2WSK
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 PRO 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ALA* 4.7 12.6 - - + +
203A GLN 3.6 11.2 - - - +
204A PHE* 3.8 3.3 - - + -
220A GLY 4.5 2.0 - - - +
221A TYR 3.6 1.3 - - - +
222A ASN* 1.3 88.8 - - - +
224A VAL* 1.3 59.0 + - - +
225A ALA 4.8 0.2 - - - +
226A MET* 4.1 24.0 - - + +
263A VAL* 3.2 42.0 - - + +
266A HIS* 3.5 14.8 - - - +
267A SER* 3.7 5.5 - - - -
268A ALA 2.9 25.5 + - - -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.8 11.0 - - + +
95A PRO* 5.9 1.7 - - - +
104A PHE* 3.6 32.3 - - + -
203A GLN 3.0 4.6 + - - +
204A PHE* 3.5 5.6 - - - -
205A ALA* 3.2 43.1 - - + +
222A ASN 3.7 1.3 - - - +
223A PRO* 1.3 75.6 - - - +
225A ALA* 1.3 63.0 + - + +
226A MET* 4.2 1.3 - - - -
267A SER* 6.0 0.2 - - - -
268A ALA* 3.8 4.7 - - + +
277A PHE* 3.5 37.5 - - + +
278A SER* 4.6 10.6 + - - -
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 5.2 3.8 - - + -
94A ASP 5.5 0.7 - - - +
95A PRO* 5.1 7.0 - - - +
97A ALA* 4.6 5.8 - - + +
100A ILE* 3.9 25.4 - - + -
104A PHE* 5.8 0.2 - - + -
203A GLN* 3.4 15.6 + - + -
224A VAL* 1.3 81.6 - - + +
226A MET* 1.3 57.8 + - - +
227A PHE 3.1 4.7 - - - -
228A ALA* 3.0 43.1 + - + +
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Residues in contact with MET 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PRO 4.6 4.2 + - - -
202A ALA* 4.2 13.9 - - + +
223A PRO* 4.1 20.6 - - + +
224A VAL 4.2 0.6 - - - -
225A ALA* 1.3 70.1 - - - +
227A PHE* 1.3 60.4 + - + +
228A ALA 3.4 0.4 - - - -
262A ILE* 5.8 2.4 - - + +
263A VAL 4.0 19.3 - - - +
264A LEU* 4.3 16.4 - - - -
266A HIS 3.8 22.4 - - - +
267A SER* 4.9 7.2 - - - -
279A LEU* 5.2 3.8 - - + -
306A LEU* 4.2 23.3 - - + -
316A TYR* 3.7 33.3 + - + +
320A CYS* 3.4 17.1 - - - -
324A TRP* 3.0 27.2 + - - -
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Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 5.5 2.7 - - + -
95A PRO 3.5 15.0 + - - -
96A CYS* 3.5 30.7 - - + +
97A ALA 3.3 17.7 + - - +
98A ARG* 3.7 13.0 - - + +
225A ALA 3.1 1.6 + - - -
226A MET* 1.3 81.3 - - + +
228A ALA* 1.3 59.5 + - - +
229A LEU 4.2 0.3 + - - -
316A TYR* 3.8 29.4 - + - -
319A ALA* 3.9 15.0 - - + -
320A CYS* 3.4 42.4 - - + -
323A TYR* 3.3 49.1 + + + -
324A TRP* 4.1 5.3 - - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.7 2.6 + - - +
98A ARG 3.6 22.4 - - - +
99A GLN* 4.2 5.4 - - - +
100A ILE* 4.6 0.9 - - + -
202A ALA* 3.4 6.2 - - - -
203A GLN* 2.7 51.3 + - - +
225A ALA* 3.0 20.8 + - + +
227A PHE* 1.3 81.0 - - - +
229A LEU* 1.3 56.9 + - - +
324A TRP* 3.9 4.1 - - - -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG 4.5 3.0 + - - -
176A TYR* 3.0 48.7 - - + +
201A VAL* 3.1 30.3 - - + +
203A GLN* 4.1 2.6 - - - +
227A PHE 4.2 0.4 + - - -
228A ALA* 1.3 74.0 - - - +
230A HIS* 1.3 65.8 + - - +
231A PRO* 2.9 12.7 - - - +
240A ALA* 3.8 22.5 - - + +
241A LEU* 4.0 18.8 - - + +
244A PHE* 3.8 29.8 - - + -
324A TRP* 3.9 18.4 - - + -
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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