Contacts of the strand formed by residues 195 - 200 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G LEU* 3.4 6.2 - - - +
192G ARG 2.8 33.4 + - - +
193G HIS* 3.8 11.2 - - + +
194G GLY* 1.3 88.9 + - - +
196G LEU* 1.3 64.9 + - - +
197G CYS* 3.6 1.0 + - - +
260G VAL* 3.7 26.0 - - + +
261G ILE 4.1 6.2 + - - +
262G ASP* 4.1 29.6 - - - +
263G SER 4.8 1.6 - - - +
268G TYR* 5.8 1.6 - - - -
349G LEU* 5.3 7.9 - - - +
350G ASP* 4.6 21.0 + - - +
353G ARG* 5.7 8.1 - - - +
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Residues in contact with LEU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G ILE* 4.5 12.8 - - + -
190G THR 3.4 13.2 - - - +
191G LEU* 3.8 19.2 - - + +
195G ARG* 1.3 74.7 - - - +
197G CYS* 1.3 57.9 + - - +
260G VAL* 3.4 19.8 - - - +
261G ILE* 3.5 29.6 + - + +
311G TRP* 4.2 25.4 - - + -
341G THR* 5.6 1.8 - - - +
342G PRO* 5.5 5.6 - - + +
344G CYS 4.6 1.8 - - - +
346G ALA* 4.1 30.7 - - + -
349G LEU* 4.2 26.0 - - + +
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Residues in contact with CYS 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G ILE* 3.2 9.8 - - - +
190G THR 2.9 35.5 + - - +
192G ARG* 4.4 6.1 - - + -
195G ARG 4.3 4.5 - - - +
196G LEU* 1.3 77.3 - - - +
198G PHE* 1.3 60.7 + - - +
199G MET* 5.0 5.4 - - + -
258G TYR* 4.0 26.9 - - + +
259G HIS 3.3 13.9 - - - +
260G VAL* 4.0 7.0 - - + +
261G ILE* 4.9 3.8 - - - +
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Residues in contact with PHE 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G ALA* 3.4 33.7 - - + -
188G VAL 3.8 6.1 - - - -
189G ILE* 4.6 6.1 - - + +
197G CYS* 1.3 73.0 - - - +
199G MET* 1.3 69.8 + - - +
200G LEU* 3.5 23.3 - - + -
217G MET* 5.5 10.1 - - - -
238G ILE* 5.0 12.8 - - + -
257G ILE* 3.1 19.7 - - + +
258G TYR* 3.9 1.4 - - - -
259G HIS* 2.9 36.1 + - + +
261G ILE* 5.6 4.4 - - + +
267G LEU* 5.5 12.3 - - + -
283G ILE* 4.3 28.7 - - + -
285G VAL* 6.1 0.7 - - + -
304G TYR* 5.5 4.3 - + + -
309G ILE* 4.2 20.0 - - + -
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Residues in contact with MET 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLU* 3.5 33.7 - - - +
187G ALA* 3.7 1.4 - - - +
188G VAL* 2.9 51.2 + - + +
190G THR* 3.2 29.4 - - - +
192G ARG* 4.5 11.4 - - + -
197G CYS* 4.1 4.0 + - + +
198G PHE* 1.3 80.7 - - - +
200G LEU* 1.3 63.5 + - - +
256G ILE* 4.5 20.6 - - + -
257G ILE 3.9 2.5 - - - -
258G TYR* 4.3 25.4 - - + -
314G ARG* 5.9 4.5 - - - -
315G PHE* 4.0 13.8 - - + -
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Residues in contact with LEU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G PHE* 4.7 4.5 - - + -
184G SER* 3.1 23.1 - - - +
187G ALA* 3.9 7.9 - - + -
198G PHE* 3.5 24.5 - - + -
199G MET* 1.3 75.6 - - - +
201G ARG* 1.3 73.7 + - - +
202G VAL* 3.9 1.2 + - + -
217G MET* 5.8 0.4 - - - -
256G ILE* 3.2 3.5 - - - +
257G ILE* 2.9 45.6 + - + +
285G VAL* 4.1 23.3 - - + -
304G TYR* 3.2 46.2 - - + +
315G PHE* 4.2 5.0 - - - -
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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