Contacts of the strand formed by residues 263 - 268 (chain C) in PDB entry 4GUP
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 VAL 263 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 5.4 12.3 - - + +
267A LEU* 4.6 11.7 - - + -
268A GLN 3.4 10.5 - - - +
269A VAL* 5.2 0.7 - - - -
270A PRO* 3.7 24.5 - - + -
181C PRO* 5.7 11.7 - - + -
182C PRO* 5.6 3.1 - - + -
258C VAL 3.7 1.4 - - - +
259C GLU* 3.4 4.7 - - - -
260C HIS* 3.0 35.7 + - + +
261C SER 2.9 9.9 + - - +
262C GLY* 1.4 74.7 - - - +
264C HIS* 1.3 65.3 + - - +
265C MET* 3.9 26.7 - - + +
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Residues in contact with HIS 264 (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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266A VAL 3.7 1.4 - - - +
267A LEU* 3.3 2.6 - - - +
268A GLN* 2.8 57.1 + - + +
258C VAL 3.6 2.0 - - - -
259C GLU* 2.7 49.4 + - + -
262C GLY* 3.5 19.7 + - - -
263C VAL* 1.3 73.5 - - - +
265C MET* 1.4 59.8 + - - +
266C VAL* 5.6 2.2 - - + -
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Residues in contact with MET 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL 4.7 6.7 - - - +
265A MET* 6.1 1.6 - - + +
266A VAL 3.3 4.0 - - - +
267A LEU* 3.7 34.8 - - + -
181C PRO* 5.9 1.3 - - + -
182C PRO* 3.8 36.3 - - + +
184C VAL* 4.0 21.3 - - + -
256C CYS 3.8 0.9 - - - +
257C HIS* 3.5 2.9 - - - +
258C VAL* 2.9 55.9 + - + +
260C HIS* 6.0 0.7 - - + -
263C VAL* 3.9 25.1 - - + +
264C HIS* 1.4 74.6 - - - +
266C VAL* 1.3 64.0 + - - +
267C LEU* 4.3 13.9 - - + +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS 3.7 1.2 - - - +
265A MET* 3.0 26.0 - - - +
266A VAL* 3.1 18.2 + - + +
255C SER* 4.1 13.7 - - - +
256C CYS 3.2 5.2 - - - +
257C HIS* 3.4 45.1 - - + +
264C HIS* 5.6 2.2 - - + -
265C MET* 1.3 76.3 - - - +
267C LEU* 1.4 63.3 + - - +
268C GLN* 5.9 1.1 - - + -
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Residues in contact with LEU 267 (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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181A PRO* 6.4 2.0 - - + -
182A PRO 5.8 0.2 - - - +
263A VAL* 4.9 8.1 - - + -
264A HIS 3.7 3.4 - - - -
265A MET* 4.1 32.3 - - + -
184C VAL* 3.8 46.2 - - + +
185C ARG* 4.6 3.4 - - - +
186C VAL* 4.2 22.4 - - + +
214C TRP* 5.1 0.9 - - - -
255C SER* 3.3 5.3 - - - -
256C CYS* 2.7 51.9 + - + +
258C VAL* 5.2 1.3 - - + -
265C MET* 4.3 20.0 - - + +
266C VAL* 1.4 74.9 - - - +
268C GLN* 1.3 59.2 + - - +
269C VAL* 4.2 1.1 + - - +
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Residues in contact with GLN 268 (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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262A GLY 4.1 2.8 - - - +
263A VAL* 3.2 32.6 - - - +
264A HIS* 2.8 32.1 + - + +
253C LEU* 3.4 39.4 - - - +
254C TYR 4.1 8.7 - - - +
255C SER* 4.4 10.5 - - - +
266C VAL* 5.9 1.3 - - + -
267C LEU* 1.3 73.0 - - - +
269C VAL* 1.3 70.3 + - - +
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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