Contacts of the strand formed by residues 360 - 365 (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 PHE 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY* 5.6 6.7 - - - -
358A THR* 5.3 5.2 - - + -
359A THR* 1.4 82.1 - - - +
361A TYR* 1.3 80.6 + - - +
362A GLU* 4.2 23.6 - - + -
499A LEU* 3.6 22.7 - - + -
500A LEU 3.4 5.8 - - - +
501A ARG* 4.1 8.3 - - + -
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Residues in contact with TYR 361 (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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359A THR* 3.8 23.5 - - - +
360A PHE* 1.3 94.2 - - - +
362A GLU* 1.3 69.9 - - - +
363A GLY 3.9 0.3 + - - -
387A PHE* 3.9 33.9 - + + -
498A PHE* 3.8 2.1 - - - +
499A LEU* 3.3 3.8 - - - -
500A LEU* 2.8 40.8 + - + +
502A PHE* 3.8 22.4 - + - -
510A THR* 2.5 44.1 + - - -
511A GLN* 3.5 31.4 - - - -
512A GLU* 4.3 7.6 - - + -
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Residues in contact with GLU 362 (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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14A ALA* 5.5 6.8 - - - +
146A PHE 4.8 3.1 - - - +
147A GLY 5.9 4.5 - - - -
360A PHE* 4.2 25.3 - - + -
361A TYR* 1.3 82.3 - - - +
363A GLY* 1.3 56.4 + - - +
387A PHE* 5.1 3.8 - - - -
416A LYS* 3.7 27.9 + - - +
498A PHE* 3.5 7.4 - - - +
499A LEU* 4.2 9.0 - - + +
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Residues in contact with GLY 363 (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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361A TYR 3.9 0.6 + - - -
362A GLU* 1.3 74.3 - - - +
364A THR* 1.3 70.8 + - - +
385A PRO* 5.9 0.7 - - - -
387A PHE* 5.2 3.4 - - - -
416A LYS* 5.5 1.1 + - - +
497A ASP* 3.2 2.8 - - - +
498A PHE* 2.7 59.9 + - - -
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Residues in contact with THR 364 (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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363A GLY* 1.3 78.3 - - - +
365A TRP* 1.4 76.0 + - - +
366A ARG* 3.6 16.9 - - - +
370A THR* 4.0 2.1 + - - +
385A PRO* 3.8 15.2 - - - +
496A GLY 3.3 6.5 - - - +
497A ASP* 2.6 31.9 - - + +
498A PHE* 3.4 3.8 - - - -
643A GLN* 5.3 1.7 + - - -
646A GLN* 3.1 31.4 + - - -
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Residues in contact with TRP 365 (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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364A THR* 1.4 80.6 - - - +
366A ARG* 1.3 61.1 + - - +
370A THR* 3.6 10.3 - - - -
371A ALA* 4.1 7.9 - - + +
384A ASN* 3.4 24.5 + - - -
385A PRO* 3.9 6.8 - - + +
413A LEU* 4.6 5.6 - - + -
415A GLN* 5.3 5.4 - - + -
429A GLU* 6.3 0.9 - - + -
431A ILE* 4.2 18.2 - - + -
487A PRO* 3.5 10.8 + - + -
488A SER* 2.9 39.3 - - - -
489A THR* 3.4 25.6 - - + -
494A LYS 3.7 12.6 - - - +
495A GLU* 2.7 34.0 - - - +
496A GLY* 2.9 26.2 + - - +
497A ASP 5.1 1.8 - - - -
498A PHE* 3.6 43.2 - + + -
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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