Contacts of the strand formed by residues 195 - 203 (chain A) in PDB entry 2OX0
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 TYR 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.0 10.3 - - + -
35A GLU* 2.5 35.0 + - - -
194A LEU* 1.3 75.6 - - - +
196A SER* 1.3 61.2 + - - +
269A ILE* 4.4 1.8 - - + -
270A THR 3.1 19.1 - - - +
271A PHE* 3.5 16.6 - + - -
272A PRO* 3.5 26.9 - - + -
290A ASN* 3.0 18.2 + - - +
291A PHE* 3.2 63.3 + + + +
292A ALA* 4.0 6.7 - - - -
293A THR* 2.7 39.9 + - + +
295A ARG* 3.6 8.7 + - - +
296A TRP* 4.0 6.3 - - + -
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Residues in contact with SER 196 (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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190A GLU* 3.5 15.9 - - - -
195A TYR* 1.3 77.4 - - - +
197A ILE* 1.3 62.1 + - - +
268A MET 4.6 0.2 - - - -
269A ILE* 3.3 5.9 - - - -
270A THR* 2.6 52.4 + - - +
289A THR 3.4 8.3 - - - -
290A ASN* 3.6 4.5 - - - +
291A PHE* 3.5 10.2 - - - -
500A OGA 2.6 29.3 + - - -
9C MLY 4.2 3.4 - - - -
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Residues in contact with ILE 197 (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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27A PHE* 3.6 28.5 - - + -
148A TRP* 3.9 17.0 - - + +
150A ILE* 4.1 14.1 - - + -
153A LEU* 3.8 31.9 - - + -
196A SER* 1.3 74.1 - - - +
198A ASN* 1.3 60.2 + - - +
199A TYR 4.3 0.2 - - - -
267A PHE* 3.9 22.0 - - + -
268A MET 3.4 3.6 - - - +
269A ILE* 3.9 7.6 - - + -
287A GLU 4.5 0.2 - - - -
288A SER* 2.7 29.9 + - - -
289A THR* 3.0 22.4 + - + +
291A PHE* 4.0 10.3 - - + -
500A OGA 4.6 0.2 - - - -
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Residues in contact with ASN 198 (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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177A TYR* 5.0 1.2 - - - -
197A ILE* 1.3 76.2 - - - +
199A TYR* 1.3 60.8 + - - +
206A LYS* 4.0 0.8 - - - -
208A TRP* 3.8 21.6 - - + -
262A GLN* 3.2 22.2 + - - +
267A PHE* 3.2 5.5 - - - -
268A MET* 2.8 40.0 + - + +
270A THR* 6.3 0.4 - - + -
286A ALA* 3.5 20.0 - - - +
287A GLU 3.4 5.2 - - - -
288A SER* 3.9 10.7 - - - -
500A OGA 3.0 47.9 + - - +
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Residues in contact with TYR 199 (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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49A PRO* 5.3 0.2 - - - +
53A TRP* 3.7 22.0 - + - -
55A PRO* 3.6 26.5 - - + +
59A TYR* 4.3 1.4 + - - -
141A TYR* 4.3 4.5 - - - +
150A ILE* 3.8 14.8 - - + +
198A ASN* 1.3 75.9 - - - +
200A LEU* 1.3 63.2 + - - +
201A HIS* 3.3 50.8 + + - -
265A GLY* 3.5 34.5 + - - -
266A GLU 3.7 5.6 - - - -
267A PHE* 3.4 36.8 - + + -
286A ALA* 3.2 2.1 - - - -
287A GLU* 2.8 36.9 + - + +
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Residues in contact with LEU 200 (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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199A TYR* 1.3 71.7 - - - +
201A HIS* 1.3 61.8 + - - +
202A PHE 4.1 5.6 - - - +
203A GLY 4.8 0.2 - - - +
204A GLU 3.5 20.2 - - - +
205A PRO* 4.0 2.2 - - + -
206A LYS* 4.1 10.5 - - - +
262A GLN* 3.4 29.8 - - + +
263A GLU 3.5 31.4 - - - +
264A ALA* 3.6 7.5 - - + +
265A GLY* 2.8 32.1 + - - -
266A GLU 3.2 8.9 + - - -
284A ASN* 3.9 22.4 - - + +
285A CYS 3.5 22.0 - - - +
286A ALA* 4.0 10.5 - - + -
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Residues in contact with HIS 201 (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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55A PRO* 4.2 4.5 - - + -
59A TYR* 2.7 48.2 + + + +
140A LEU* 3.6 33.7 - - + +
141A TYR* 4.2 9.6 - + - -
176A LEU* 4.6 0.2 - - + -
199A TYR* 3.3 28.1 + + - -
200A LEU* 1.3 72.7 - - - +
202A PHE* 1.3 67.8 + - + +
264A ALA* 4.7 1.4 - - - +
265A GLY* 4.6 4.4 + - - -
285A CYS* 2.9 17.6 + - - +
286A ALA 4.4 2.7 - - - -
287A GLU* 2.8 52.5 + - + +
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Residues in contact with PHE 202 (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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59A TYR* 3.5 40.6 - + + -
62A ILE* 3.6 31.6 - - + -
94A VAL* 5.7 0.9 - - + -
98A ARG* 6.3 0.4 - - - -
178A PHE* 4.4 5.8 - + - -
200A LEU* 3.5 4.1 - - - +
201A HIS* 1.3 81.3 - - + +
203A GLY* 1.3 68.0 + - - +
264A ALA* 4.1 11.7 - - - -
283A PHE* 3.7 32.5 - + - -
284A ASN* 3.4 5.7 - - - +
285A CYS* 3.0 56.2 + - + +
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Residues in contact with GLY 203 (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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202A PHE* 1.3 82.0 - - - +
204A GLU* 1.3 73.2 + - - +
205A PRO* 4.1 0.7 - - - +
264A ALA* 3.7 19.0 + - - +
283A PHE* 3.3 13.5 - - - -
284A ASN* 3.9 1.6 - - - -
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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