Contacts of the strand formed by residues 195 - 200 (chain A) in PDB entry 5YWB
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 ARG 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A LEU* 3.4 6.2 - - - +
192A ARG* 2.8 33.2 + - - +
193A HIS* 3.8 11.0 - - + +
194A GLY* 1.3 90.1 + - - +
196A LEU* 1.3 64.1 + - - +
197A CYS* 4.3 1.0 - - - +
260A VAL* 3.7 25.1 - - + +
261A ILE 4.1 6.3 + - - +
262A ASP* 4.1 28.8 - - - +
263A SER 4.8 1.6 - - - +
268A TYR* 5.8 1.4 - - - -
349A LEU* 5.3 8.5 - - - +
350A ASP* 4.6 20.6 + - - +
353A ARG* 5.7 8.1 - - - +
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Residues in contact with LEU 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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189A ILE* 4.5 12.8 - - + -
190A THR 3.4 13.5 - - - +
191A LEU* 3.8 17.9 - - + +
195A ARG* 1.3 77.1 - - - +
197A CYS* 1.3 59.2 + - - +
260A VAL* 3.4 19.8 - - - +
261A ILE* 3.5 29.3 + - + +
311A TRP* 4.2 24.7 - - + -
341A THR* 5.6 2.0 - - - +
342A PRO* 5.5 5.8 - - + +
344A CYS 4.6 1.3 - - - +
346A ALA* 4.1 30.5 - - + -
349A LEU* 4.2 26.7 - - + +
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Residues in contact with CYS 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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189A ILE* 3.2 10.3 - - - +
190A THR 2.9 36.2 + - - +
192A ARG* 4.4 6.7 - - + -
195A ARG 4.3 4.5 - - - +
196A LEU* 1.3 76.0 - - - +
198A PHE* 1.3 61.3 - - - +
199A MET* 5.0 5.2 - - + -
258A TYR* 4.0 26.7 - - + +
259A HIS 3.3 13.7 - - - +
260A VAL* 4.0 7.0 - - + +
261A ILE* 4.9 3.6 - - - +
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Residues in contact with PHE 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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187A ALA* 3.4 33.7 - - + -
188A VAL 3.8 4.9 - - - -
189A ILE* 4.6 7.4 - - + +
197A CYS* 1.3 73.6 - - - +
199A MET* 1.3 69.1 + - - +
200A LEU* 3.5 24.7 - - + -
217A MET* 5.5 9.9 - - - -
238A ILE* 5.0 13.0 - - + -
257A ILE* 3.1 20.9 - - + +
258A TYR* 3.9 1.6 - - - -
259A HIS* 2.9 35.9 + - + +
261A ILE* 5.6 4.7 - - + +
267A LEU* 5.5 12.3 - - + -
283A ILE* 4.3 28.7 - - + -
285A VAL* 6.1 0.7 - - + -
304A TYR* 5.5 4.0 - + + -
309A ILE* 4.2 19.3 - - + -
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Residues in contact with MET 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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187A ALA* 3.7 1.4 - - - +
188A VAL* 2.9 50.8 + - + +
190A THR* 3.2 30.7 - - - +
192A ARG* 4.5 10.8 - - + -
197A CYS* 4.1 2.9 + - + +
198A PHE* 1.3 78.9 - - - +
200A LEU* 1.3 62.5 + - - +
256A ILE* 4.5 21.3 - - + -
257A ILE 3.9 2.7 - - - +
258A TYR* 4.3 25.1 - - + -
313A GLN 5.6 0.2 - - - +
314A ARG* 5.9 4.3 - - - -
315A PHE* 4.0 14.1 - - + -
229G GLU* 3.5 32.8 - - - +
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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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183A PHE* 4.7 4.5 - - + -
184A SER* 3.1 23.6 - - - +
187A ALA* 3.9 7.9 - - + -
198A PHE* 3.5 24.7 - - + -
199A MET* 1.3 76.0 - - - +
201A ARG* 1.3 73.2 + - - +
202A VAL* 4.7 0.8 - - + +
217A MET* 5.8 0.4 - - - -
256A ILE* 3.2 3.4 - - - +
257A ILE* 2.9 46.3 + - + +
285A VAL* 4.1 23.6 - - + -
304A TYR* 3.2 46.0 - - + +
315A PHE* 4.2 5.1 - - - -
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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