Contacts of the strand formed by residues 265 - 272 (chain A) in PDB entry 4C02
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 PHE 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.4 1.4 - - - +
194A SER* 3.9 8.1 - - - +
195A GLY* 3.5 32.9 - - - -
201A GLN* 3.8 11.7 - - - -
249A THR* 5.1 2.2 - - - -
252A TYR* 3.3 57.3 - + + -
253A ASN* 3.6 24.0 - - - -
263A LEU 3.4 3.6 + - - -
264A GLY* 1.3 73.3 - - - -
266A ILE* 1.3 64.3 + - - +
267A ALA* 3.4 40.6 - - - -
268A SER* 3.5 8.3 - - - -
281A LEU* 3.7 23.6 - - + -
282A ILE 4.1 5.6 - - - -
283A THR* 4.5 3.8 - - - +
1513A EDO 3.7 10.4 + - - -
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.9 31.4 - - + -
184A LEU* 4.6 8.1 - - + -
195A GLY* 3.6 1.8 - - - -
196A LEU* 2.9 53.7 + - + +
201A GLN* 4.1 0.2 - - - +
204A VAL* 4.8 3.6 - - + -
232A VAL* 3.9 10.3 - - + -
265A PHE* 1.3 82.3 - - - +
267A ALA* 1.3 62.0 + - + +
282A ILE* 2.9 25.1 + - + +
283A THR* 3.6 28.3 - - - +
284A HIS* 3.8 3.8 - - - +
1513A EDO 4.0 21.8 - - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.5 2.9 - - + -
201A GLN* 3.5 37.0 - - + +
204A VAL* 5.5 1.1 - - + -
205A ALA 5.5 0.7 - - - +
265A PHE* 3.4 17.6 - - - -
266A ILE* 1.3 88.3 - - + +
268A SER* 1.3 57.4 + - - +
281A LEU 3.6 0.2 - - - -
282A ILE* 2.7 48.8 + - + +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLN* 3.0 17.4 + - - +
202A ARG 5.0 0.2 + - - -
245A TRP* 2.9 24.3 + - - -
249A THR* 2.8 41.9 + - - +
265A PHE* 3.5 9.4 - - - -
267A ALA* 1.3 74.0 - - - +
269A ASP* 1.3 63.5 + - - +
280A TRP 3.3 7.9 - - - -
281A LEU* 4.5 2.2 - - - -
282A ILE* 5.1 0.4 - - - -
88B HIS* 3.3 19.8 - - - -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN 4.8 0.4 - - - +
202A ARG* 2.7 37.9 + - - +
205A ALA* 3.5 29.9 - - + +
206A ARG* 2.9 26.9 + - - -
245A TRP* 4.1 5.1 + - - -
268A SER* 1.3 77.2 + - - +
270A MET* 1.3 72.1 + - - +
271A THR* 4.0 4.3 + - - +
278A GLN 3.8 1.4 - - - +
279A LEU* 3.8 1.7 - - - -
280A TRP* 2.9 43.8 + - + +
282A ILE* 5.0 0.4 - - + +
83B TYR* 5.6 1.2 - - - -
88B HIS* 4.9 2.6 - - - -
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Residues in contact with MET 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ARG* 3.7 11.9 + - - +
206A ARG* 3.1 17.7 + - - -
245A TRP* 3.7 21.3 - - + -
269A ASP* 1.3 76.7 + - - +
271A THR* 1.3 61.4 + - - +
277A THR* 5.3 6.5 - - - -
278A GLN 3.4 6.1 - - - +
279A LEU* 3.8 14.8 - - + -
1514A EDO 4.9 1.2 + - - -
83B TYR* 3.9 18.2 - - + +
86B THR* 3.6 31.6 - - - -
87B GLY 3.5 20.2 - - - +
88B HIS* 5.9 2.6 + - - +
1108B FLC 3.2 40.2 - - + +
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 3.8 31.1 + - - +
269A ASP* 4.0 3.6 - - - +
270A MET* 1.3 76.5 - - - +
272A SER* 1.3 60.0 + - - +
273A ARG* 3.1 11.9 + - + +
277A THR* 4.2 2.3 - - - -
278A GLN* 2.8 52.6 + - + +
280A TRP* 3.9 30.5 - - + +
1514A EDO 5.3 0.8 + - - -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 5.1 0.4 - - - +
271A THR* 1.3 69.9 + - - +
273A ARG* 1.3 59.6 + - - +
276A SER 4.0 4.3 - - - -
277A THR* 4.0 18.0 - - - +
1514A EDO 5.0 13.0 + - - -
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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