Contacts of the strand formed by residues 304 - 310 (chain A) in PDB entry 3PEY
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 ILE 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A SER* 4.4 3.6 - - - +
300A ASN* 5.3 0.3 + - - -
301A VAL* 3.1 31.2 + - + +
302A ASP* 3.7 7.2 - - - +
303A ALA* 1.3 77.2 - - - +
305A LYS* 1.3 60.9 + - - +
306A GLN* 3.4 16.3 + - + -
424A ILE* 3.4 39.0 - - + +
425A GLY* 3.8 10.3 - - - -
427A THR* 3.4 43.3 - - + +
428A GLY* 3.9 14.6 - - - +
434A GLY 3.5 4.5 - - - +
436A ALA* 4.1 15.5 - - + +
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Residues in contact with LYS 305 (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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302A ASP 5.1 1.8 - - - -
303A ALA 3.5 2.2 + - - +
304A ILE* 1.3 70.1 - - - +
306A GLN* 1.3 60.3 + - - +
307A LEU* 3.8 27.1 + - + -
434A GLY 2.8 15.9 + - - +
435A VAL* 3.5 5.3 - - + +
436A ALA 2.9 26.7 + - - +
460A GLU* 3.3 28.0 + - - +
462A THR* 4.2 13.4 + - - +
475A ILE* 5.1 6.3 - - + -
479A VAL* 3.8 32.3 - - + -
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Residues in contact with GLN 306 (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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300A ASN* 2.8 35.4 + - - +
301A VAL 4.6 1.4 + - - -
304A ILE* 3.4 19.7 + - + +
305A LYS* 1.3 75.7 - - - +
307A LEU* 1.3 66.9 + - - +
420A TYR* 2.6 39.4 + - - +
424A ILE* 3.4 21.7 - - + +
436A ALA* 3.6 7.4 - - + -
459A ILE* 3.5 12.8 - - - +
460A GLU* 3.6 20.9 + - - +
461A MET* 3.4 12.1 - - + +
462A THR* 3.0 24.0 + - - -
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Residues in contact with LEU 307 (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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305A LYS* 3.8 26.9 - - + +
306A GLN* 1.3 83.5 - - - +
308A TYR* 1.3 63.6 + - - +
420A TYR* 5.6 0.7 + - - -
435A VAL* 3.8 22.7 - - + -
436A ALA 2.8 12.7 + - - +
437A ILE* 3.3 18.0 - - + -
438A SER* 3.0 24.5 + - - -
461A MET* 5.5 0.9 - - - -
462A THR* 3.2 19.3 - - + +
464A VAL* 3.9 29.6 - - + -
472A VAL* 5.6 1.8 - - + -
475A ILE* 4.1 22.2 - - + -
476A VAL* 4.9 4.9 - - + -
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Residues in contact with TYR 308 (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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307A LEU* 1.3 75.6 - - - +
309A MET* 1.3 72.4 + - - +
310A ASP* 4.5 4.5 - - + -
437A ILE* 4.8 0.2 - - - -
438A SER 3.2 14.4 - - - +
440A VAL* 4.6 11.4 - - + -
446A PHE* 6.6 0.7 - + - -
449A LEU* 3.7 25.4 - - + -
461A MET* 3.9 28.4 + - + -
462A THR 2.9 14.5 + - - -
463A ARG* 3.5 53.9 + - + +
464A VAL* 3.0 27.4 + - - +
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Residues in contact with MET 309 (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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308A TYR* 1.3 78.4 - - - +
310A ASP* 1.3 60.8 + - - +
311A CYS* 3.5 4.9 + - - -
320A VAL* 3.6 23.6 - - - -
324A LEU* 4.3 8.1 - - + -
437A ILE* 3.9 20.9 - - + -
438A SER 2.9 6.1 + - - -
439A PHE* 3.7 19.4 - - + -
440A VAL 2.9 27.4 + - - +
464A VAL* 3.7 29.8 - - + +
465A PRO 3.8 7.2 - - - +
466A THR* 3.6 16.6 - - + -
469A TRP* 3.7 28.9 - - + -
472A VAL* 4.0 12.1 - - + -
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Residues in contact with ASP 310 (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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308A TYR* 4.2 9.5 + - + -
309A MET* 1.3 69.1 - - - +
311A CYS* 1.3 70.1 + - - +
312A LYS* 5.7 1.0 - - - +
316A ASP* 5.0 0.2 - - - +
440A VAL* 3.7 18.9 - - + +
441A HIS* 5.1 0.9 - - - -
463A ARG* 3.0 47.1 + - - +
464A VAL 4.8 2.2 + - - -
466A THR* 4.0 17.1 + - - +
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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