Contacts of the strand formed by residues 289 - 292 (chain G) in PDB entry 5UWC
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 GLN 289 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211G PRO 5.5 0.3 - - - +
212G GLN* 4.3 12.3 - - - +
213G MET* 3.0 45.6 + - + +
214G THR* 5.0 0.2 - - - +
269G THR* 3.4 4.0 - - - +
270G VAL 3.1 31.8 + - - +
272G ILE* 5.8 0.3 - - - +
286G SER* 4.8 8.5 + - - -
287G THR* 3.7 15.3 - - - +
288G PRO* 1.3 72.8 - - - +
290G ARG* 1.3 63.1 + - - +
291G PHE* 3.6 34.4 - - + -
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Residues in contact with ARG 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G THR* 4.1 18.3 + - - +
268G TYR 3.4 10.5 - - - +
269G THR* 3.9 23.5 + - + +
288G PRO 4.1 1.4 + - - -
289G GLN* 1.3 73.8 - - - +
291G PHE* 1.3 73.5 + - - +
292G GLU* 4.9 3.6 - - + +
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Residues in contact with PHE 291 (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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213G MET* 3.8 26.0 - - + -
214G THR* 4.4 2.2 - - - -
215G ALA* 3.6 36.3 - - + -
217G CYS* 4.0 13.9 - - - -
266G GLY 3.6 2.6 - - - +
267G THR* 3.3 6.8 - - - -
268G TYR* 2.8 68.9 + + + -
270G VAL* 4.9 0.2 - - + -
289G GLN* 3.6 45.5 - - + -
290G ARG* 1.3 77.2 - - - +
292G GLU* 1.3 59.8 + - - +
293G CYS* 4.4 0.2 - - - -
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Residues in contact with GLU 292 (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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217G CYS* 4.5 7.8 - - - +
266G GLY 4.2 1.1 - - - -
267G THR* 4.2 16.4 - - + +
290G ARG* 4.3 3.7 - - + +
291G PHE* 1.3 70.3 - - - +
293G CYS* 1.3 67.2 + - - +
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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