Contacts of the strand formed by residues 264 - 269 (chain A) in PDB entry 3PE7
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A VAL* 3.8 21.1 - - + -
256A SER 3.7 2.5 - - - -
257A TYR* 3.8 48.9 + - + +
261A SER 4.5 1.6 + - - -
262A PRO* 3.1 34.7 + - - +
263A ASP* 1.3 74.0 - - - +
265A PHE* 1.3 64.4 + - - +
281A SER* 3.4 7.1 - - - -
282A MET* 2.9 52.2 + - + +
283A PRO 4.6 2.5 - - - +
284A ALA* 4.4 25.5 - - - +
285A CYS 5.5 1.8 + - - +
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Residues in contact with PHE 265 (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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255A VAL* 3.3 7.8 - - - -
256A SER* 2.8 40.2 + - - +
257A TYR* 5.4 1.3 - - - -
258A LEU* 6.5 0.9 - - + -
263A ASP* 3.8 34.3 - - + -
264A ARG* 1.3 74.7 - - - +
266A ILE* 1.3 63.1 + - - +
267A TYR* 3.7 22.4 + + + -
278A GLN* 3.5 35.9 - - + -
280A THR 3.3 6.7 - - - +
281A SER* 3.6 29.6 - - - +
282A MET* 4.6 1.6 - - - +
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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
----------------------------------------------------------
253A VAL* 3.7 26.2 - - + -
254A TYR 3.6 3.8 - - - +
255A VAL* 4.8 0.4 - - - +
265A PHE* 1.3 70.8 - - - +
267A TYR* 1.3 59.7 + - - +
278A GLN* 3.7 1.2 - - - +
279A LEU* 2.7 43.1 + - + +
280A THR* 2.8 38.3 + - + +
282A MET* 3.7 24.5 - - + -
288A LEU* 3.9 17.5 - - + -
297A MET* 4.0 16.6 - - - -
325A PHE* 4.2 28.5 - - + -
327A MET* 4.7 1.8 - - + -
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Residues in contact with TYR 267 (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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232A LYS* 4.1 12.3 - - - -
238A GLU* 5.1 0.4 + - - -
253A VAL* 3.4 9.5 - - - +
254A TYR* 2.9 65.6 + + + +
256A SER* 3.5 32.3 + - - -
265A PHE* 3.7 19.9 - + + -
266A ILE* 1.3 80.3 - - - +
268A SER* 1.3 59.2 + - - +
276A ASN* 4.5 4.5 - - + -
277A ARG* 3.2 26.0 - - - -
278A GLN* 3.1 36.5 + - + +
279A LEU* 4.3 4.0 - - - -
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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
----------------------------------------------------------
251A ALA* 3.3 27.0 - - - +
252A LEU 3.5 4.9 + - - -
253A VAL* 4.1 6.4 - - - +
254A TYR* 4.5 2.7 - - - -
267A TYR* 1.3 75.6 - - - +
269A ALA* 1.3 58.3 + - - +
275A GLU 3.7 0.9 - - - +
276A ASN* 3.3 3.8 - - - +
277A ARG* 2.8 35.0 + - - +
279A LEU* 3.8 27.2 - - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 3.7 21.3 - - + +
251A ALA* 3.6 7.1 - - - -
252A LEU* 2.8 42.1 + - + +
254A TYR* 4.4 1.8 - - + -
268A SER* 1.3 74.0 - - - +
270A ASP* 1.3 64.9 + - - +
271A PRO* 3.6 1.0 - - - +
274A LEU* 5.4 2.7 - - + -
275A GLU 3.3 4.9 - - - +
276A ASN* 3.7 26.7 - - - +
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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