Contacts of the strand formed by residues 280 - 285 (chain A) in PDB entry 1QXP
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 ASN 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TYR* 3.5 40.1 - - + +
270A LYS 3.9 4.0 - - - -
271A GLN* 3.4 22.9 + - - +
278A ARG* 4.8 20.4 - - - +
279A VAL* 1.4 72.8 - - - +
281A LEU* 1.4 54.6 + - - +
327A SER* 3.4 5.4 - - - -
328A PHE* 2.7 40.7 + - + +
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Residues in contact with LEU 281 (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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225A TYR* 2.9 20.9 + - - -
270A LYS* 2.7 19.6 + - + +
272A VAL* 3.4 35.4 - - + -
279A VAL* 3.5 14.1 - - + -
280A ASN* 1.4 76.2 - - - +
282A ILE* 1.3 61.9 + - - +
297A TRP* 3.2 58.1 - - + +
316A ARG* 5.3 7.6 - - + -
325A TRP* 3.4 31.6 - - + +
326A MET 3.4 7.0 - - - +
327A SER* 4.4 2.7 - - - -
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 4.6 6.5 - - + -
228A ILE* 4.1 28.7 - - + -
266A VAL* 3.5 35.4 - - + -
268A ASP 3.6 5.6 - - - +
269A ALA* 4.4 2.0 - - + +
281A LEU* 1.3 75.3 - - - +
283A ARG* 1.4 63.5 + - - +
284A MET* 3.6 20.8 + - + -
325A TRP* 3.2 16.7 - - - -
326A MET* 2.8 36.2 + - + +
327A SER 4.6 2.5 - - - -
328A PHE* 4.4 7.4 - - + -
330A ASP* 3.8 28.3 - - + +
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Residues in contact with ARG 283 (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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266A VAL* 3.4 3.8 - - - +
267A THR* 2.9 29.3 + - - -
268A ASP* 2.6 51.1 + - + +
270A LYS* 5.8 0.2 - - - +
282A ILE* 1.4 72.1 - - - +
284A MET* 1.4 57.1 + - - +
316A ARG 4.6 1.8 + - - -
318A LYS* 3.5 32.6 + - - +
319A MET* 3.0 61.3 - - - +
323A GLU* 3.4 7.2 - - - +
324A PHE 3.1 17.3 - - - +
325A TRP* 3.3 40.8 - - + +
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Residues in contact with MET 284 (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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240A CYS* 5.7 4.0 - - + -
256A LYS* 5.7 0.4 - - - +
264A TYR* 4.8 11.4 - - + -
265A SER 3.2 10.5 - - - +
266A VAL* 3.8 22.2 - - + -
267A THR* 4.4 1.7 + - - -
282A ILE* 3.6 9.4 - - + -
283A ARG* 1.4 79.8 - - - +
285A ARG* 1.4 65.0 + - - +
319A MET* 4.1 1.2 - - - +
322A GLY 3.3 1.7 - - - +
323A GLU 2.4 27.3 - - - +
324A PHE* 3.1 37.5 + - + -
326A MET* 3.1 33.7 - - + -
330A ASP* 3.1 28.5 - - - +
334A GLU* 4.2 14.1 - - + +
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Residues in contact with ARG 285 (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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93A THR* 3.8 18.9 + - - +
115A THR 5.1 0.6 + - - -
116A LEU* 3.2 46.6 + - + +
264A TYR* 4.0 3.7 - - - +
265A SER* 2.7 29.2 + - - +
267A THR* 3.8 14.6 - - + -
284A MET* 1.4 78.8 - - - +
286A ASN* 1.3 70.6 + - - +
287A PRO* 3.0 14.6 - - - +
319A MET* 3.9 30.2 - - - +
320A GLU 3.8 22.6 + - - +
321A ASP* 4.1 5.3 + - - +
322A GLY* 3.5 9.9 - - - +
324A PHE* 5.4 2.0 - - - -
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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