Contacts of the strand formed by residues 284 - 289 (chain C) in PDB entry 3GUT
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 MET 284 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ILE* 4.2 26.2 - - + +
197C CYS 6.0 1.3 - - - +
198C ARG* 5.0 2.7 - - - +
199C VAL* 3.8 35.4 - - + +
202C ASN* 5.4 9.0 - - + +
269C SER* 5.2 0.9 - - - -
270C MET* 2.7 50.1 + - + +
282C GLU* 3.9 2.4 + - - +
283C PRO* 1.3 77.6 - - - +
285C GLU* 1.3 76.5 + - - +
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Residues in contact with GLU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN* 3.4 22.7 - - - +
267C ARG* 5.6 14.4 - - + -
268C VAL 3.9 6.5 - - - +
269C SER* 5.4 0.7 - - - +
270C MET* 4.6 1.6 - - - +
283C PRO* 4.6 11.5 - - - +
284C MET* 1.3 82.4 - - + +
286C PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ARG 4.1 7.0 - - - -
202C ASN* 3.3 20.0 - - - -
203C SER 3.5 11.9 - - - -
204C GLY* 3.3 30.5 - - - -
210C ASP* 5.7 0.2 - - + -
212C ILE* 4.8 6.5 - - + -
228C PHE* 4.4 10.3 - + + -
254C THR* 3.6 30.1 - - + -
267C ARG* 4.6 2.9 - - - -
268C VAL* 2.6 47.0 + - + +
270C MET* 3.9 29.4 - - + -
284C MET 3.4 5.4 + - - +
285C GLU* 1.3 75.9 - - - +
287C GLN* 1.3 66.1 + - - +
288C TYR* 4.0 28.5 - + - -
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN 2.9 14.1 + - - +
203C SER* 3.3 24.7 - - - -
204C GLY 3.3 4.0 + - - -
265C PRO* 3.2 27.2 - - + +
266C VAL 3.6 11.2 - - - +
267C ARG* 3.4 36.0 + - - +
286C PHE* 1.3 73.4 - - - +
288C TYR* 1.3 67.2 + - - +
289C LEU* 3.5 20.5 - - + +
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Residues in contact with TYR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLY 3.9 1.8 - - - -
205C SER 3.2 28.7 - - - -
206C CYS* 3.3 9.4 - - + -
208C GLY* 4.6 2.0 - - - -
228C PHE* 3.6 18.1 - + - -
233C TRP* 3.2 34.4 - + - -
254C THR* 4.4 3.3 - - - -
255C PRO* 2.3 42.5 + - - +
257C TYR* 3.7 20.2 - + + -
262C LEU* 3.8 8.3 - - + +
265C PRO* 3.4 4.9 - - - +
266C VAL* 3.1 43.8 + - + -
268C VAL* 3.7 21.5 - - + -
286C PHE* 3.9 15.7 + + - -
287C GLN* 1.3 72.3 - - - +
289C LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C SER* 3.0 24.0 - - - +
204C GLY* 2.9 25.2 + - - +
205C SER* 3.6 1.1 - - - -
206C CYS* 2.8 33.1 + - - +
262C LEU* 4.6 2.0 - - - -
265C PRO* 3.8 29.6 - - + -
287C GLN* 3.5 19.3 - - + +
288C TYR* 1.3 75.1 - - - +
290C PRO* 1.3 81.8 - - + +
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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