Contacts of the strand formed by residues 357 - 365 (chain A) in PDB entry 2PA5
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 TYR 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A CYS* 3.9 18.4 - - - -
322A SER* 2.7 37.6 + - - -
327A ASN* 3.2 48.5 - - + +
330A LYS* 3.6 28.4 - - + +
331A ASN* 2.6 30.2 + - - -
338A CYS* 3.6 16.2 - - - -
343A ARG* 3.9 10.1 - - - +
346A LEU* 3.9 8.8 - - - +
355A THR* 3.2 6.8 + - - +
356A ASP* 1.3 82.7 - - - +
358A ILE* 1.3 67.5 + - - +
359A ASN* 3.5 24.9 + - + +
385A ASP* 4.1 4.5 - - - +
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Residues in contact with ILE 358 (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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330A LYS* 5.7 1.8 - - - -
338A CYS* 4.1 1.9 - - - -
343A ARG* 4.9 1.6 + - - +
344A VAL 3.3 22.7 + - - +
346A LEU* 4.2 17.9 - - + -
356A ASP 3.9 0.6 + - - -
357A TYR* 1.3 89.6 - - - +
359A ASN* 1.3 64.8 + - - +
360A ALA* 2.9 28.0 + - + +
375A THR* 4.5 4.5 - - - +
376A GLN* 6.0 2.5 - - + +
382A THR* 5.2 7.0 - - - +
385A ASP* 4.0 9.4 - - + +
386A PHE* 3.8 36.3 - - + +
389A MET* 4.0 26.7 - - + -
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Residues in contact with ASN 359 (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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330A LYS 4.4 3.0 + - - +
331A ASN* 3.0 21.9 + - - +
336A VAL* 2.9 28.3 + - - +
337A PRO* 4.0 3.7 - - - +
338A CYS* 3.5 8.0 - - - +
357A TYR* 3.5 21.4 + - + +
358A ILE* 1.3 71.4 - - - +
360A ALA* 1.3 52.4 + - - +
375A THR* 2.6 25.2 + - - -
376A GLN* 3.5 38.3 + - - +
517A ALA 5.6 0.2 + - - -
554A ARG* 3.0 28.2 + - - +
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Residues in contact with ALA 360 (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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338A CYS* 4.1 1.8 - - - -
343A ARG* 3.4 9.0 - - - +
344A VAL* 2.9 25.5 + - + -
358A ILE* 2.9 15.3 + - + +
359A ASN* 1.3 78.3 + - - +
361A SER* 1.3 63.6 + - - +
373A ILE* 3.8 4.9 - - + -
374A GLY 3.3 7.4 - - - -
375A THR* 3.4 15.3 - - - +
389A MET* 3.7 28.9 - - - -
554A ARG* 3.7 1.1 - - - +
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Residues in contact with SER 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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338A CYS* 3.7 11.4 - - - +
339A LEU 4.6 1.6 + - - -
342A THR* 3.5 10.9 + - - -
343A ARG* 4.9 0.9 - - - -
344A VAL* 4.1 5.2 - - - -
360A ALA* 1.3 75.4 + - - +
362A PHE* 1.3 63.4 + - - +
363A MET* 3.5 1.4 - - - +
373A ILE* 3.3 2.5 - - - -
374A GLY 2.9 30.6 + - - -
553A GLN 3.3 25.9 + - - -
554A ARG* 2.9 35.6 + - - -
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Residues in contact with PHE 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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342A THR* 3.0 35.4 + - + +
343A ARG 4.0 5.6 - - - -
344A VAL* 3.9 23.5 - - + +
345A LYS 5.0 1.6 - - - -
361A SER* 1.3 73.2 - - - +
363A MET* 1.3 62.9 + - - +
370A ASN* 3.4 43.3 - - + +
372A TYR 3.6 3.1 - - - -
373A ILE* 3.9 24.2 - - + -
393A GLN* 3.5 32.5 - - - -
510A PRO* 4.7 6.7 - - + -
553A GLN* 3.7 17.2 - - - +
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Residues in contact with MET 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 SER 3.5 6.7 - - - +
362A PHE* 1.3 80.9 - - - +
364A ASP* 1.3 67.1 + - - +
370A ASN* 3.4 2.3 + - - -
371A ALA 2.9 21.9 + - - -
372A TYR* 2.8 35.1 + - + +
373A ILE 4.4 0.9 - - - -
374A GLY* 3.5 32.1 - - - -
522A THR* 4.7 6.1 - - + -
523A GLY* 5.1 0.2 - - - -
526A CYS* 4.0 19.5 - - + -
550A MET* 3.6 39.7 - - + -
553A GLN* 3.7 6.5 - - + +
554A ARG* 3.8 28.9 - - + +
557A SER* 4.3 1.8 - - - +
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Residues in contact with ASP 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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277A SER* 3.3 26.0 - - - +
278A VAL* 3.0 22.5 + - + +
279A HIS* 3.3 21.0 + - + -
363A MET* 1.3 79.2 - - - +
365A GLY* 1.3 59.0 + - - +
368A GLN 3.5 4.0 - - - +
369A LYS* 3.4 16.7 + - - +
370A ASN* 3.0 24.2 + - - +
372A TYR* 3.5 11.6 - - - -
530A ILE* 3.8 1.7 - - - +
550A MET* 5.4 0.5 - - - +
553A GLN* 2.8 33.0 + - - +
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Residues in contact with GLY 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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277A SER* 2.8 23.4 + - - -
279A HIS* 3.4 8.6 - - - +
364A ASP* 1.3 73.4 - - - +
366A TYR* 1.3 64.5 + - - -
367A LYS 3.0 0.2 + - - -
368A GLN* 2.8 13.8 + - - -
371A ALA* 3.5 20.5 - - - +
372A TYR* 3.8 12.1 - - - -
530A ILE* 4.0 5.4 - - - -
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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