Contacts of the strand formed by residues 195 - 200 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191E LEU* 3.4 6.2 - - - +
192E ARG 2.8 33.1 + - - +
193E HIS* 3.8 10.8 - - + +
194E GLY* 1.3 88.8 + - - +
196E LEU* 1.3 64.1 + - - +
197E CYS* 4.3 1.0 - - - +
260E VAL* 3.7 26.3 - - + +
261E ILE 4.1 5.9 + - - +
262E ASP* 4.1 28.4 - - - +
263E SER 4.8 1.6 - - - +
268E TYR* 5.8 1.2 - - - -
349E LEU* 5.3 8.2 - - - +
350E ASP* 4.6 21.2 + - - +
353E ARG* 5.7 8.3 - - - +
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Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ILE* 4.5 13.7 - - + -
190E THR 3.4 14.1 - - - +
191E LEU* 3.8 18.8 - - + +
195E ARG* 1.3 75.7 - - - +
197E CYS* 1.3 57.7 + - - +
260E VAL* 3.4 19.8 - - - +
261E ILE* 3.5 29.5 + - + +
311E TRP* 4.2 24.5 - - + -
341E THR* 5.6 1.8 - - - +
342E PRO* 5.5 5.4 - - + +
344E CYS 4.6 1.6 - - - +
346E ALA* 4.1 30.7 - - + -
349E LEU* 4.2 27.6 - - + +
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Residues in contact with CYS 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ILE* 3.2 9.5 - - - +
190E THR 2.9 35.3 + - - +
192E ARG* 4.4 7.0 - - + -
195E ARG 4.3 4.3 - - - +
196E LEU* 1.3 77.1 - - - +
198E PHE* 1.3 61.7 + - - +
199E MET* 4.1 5.6 + - + -
258E TYR* 4.0 27.4 - - + +
259E HIS 3.3 12.3 - - - +
260E VAL* 4.0 7.6 - - + +
261E ILE* 4.9 4.0 - - - +
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Residues in contact with PHE 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ALA* 3.4 33.7 - - + -
188E VAL 3.8 5.6 - - - -
189E ILE* 4.6 7.4 - - + +
197E CYS* 1.3 72.9 - - - +
199E MET* 1.3 71.0 + - - +
200E LEU* 3.5 24.5 - - + -
217E MET* 5.5 9.4 - - - -
238E ILE* 5.0 12.6 - - + -
257E ILE* 3.1 20.3 - - + +
258E TYR* 3.9 1.4 - - - -
259E HIS* 2.9 35.3 + - + +
261E ILE* 5.6 4.7 - - + +
267E LEU* 5.5 12.1 - - + -
283E ILE* 4.3 28.9 - - + -
285E VAL* 6.1 0.7 - - + -
304E TYR* 5.5 3.8 - + + -
309E ILE* 4.2 19.7 - - + -
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Residues in contact with MET 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C GLU* 3.5 33.4 - - - +
187E ALA* 3.7 1.6 - - - +
188E VAL* 2.9 51.2 + - + +
190E THR* 3.2 30.5 - - - +
192E ARG* 4.5 11.2 - - + -
197E CYS* 4.1 3.5 + - + +
198E PHE* 1.3 79.1 - - - +
200E LEU* 1.3 63.6 + - - +
256E ILE* 4.5 22.0 - - + -
257E ILE 3.9 3.4 - - - +
258E TYR* 4.3 25.4 - - + -
313E GLN 5.6 0.2 - - - +
314E ARG* 5.9 4.3 - - - -
315E PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E PHE* 4.7 5.2 - - + -
184E SER* 3.1 23.6 - - - +
187E ALA* 3.9 8.5 - - + -
198E PHE* 3.5 24.7 - - + -
199E MET* 1.3 75.6 - - - +
201E ARG* 1.3 73.9 + - - +
202E VAL* 3.9 1.5 + - + -
217E MET* 5.8 0.7 - - - -
256E ILE* 3.2 3.4 - - - +
257E ILE* 2.9 46.0 + - + +
285E VAL* 4.1 22.2 - - + -
304E TYR* 3.2 46.0 - - + +
315E PHE* 4.2 4.1 - - - -
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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