Contacts of the strand formed by residues 368 - 376 (chain B) 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 GLN 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B SER* 3.5 5.7 - - - -
364B ASP* 3.6 1.6 - - - +
365B GLY 2.8 31.5 + - - +
366B TYR 3.1 2.1 + - - +
367B LYS* 1.3 82.0 - - - +
369B LYS* 1.3 69.0 + - - +
371B ALA* 3.5 21.8 + - + +
491B GLN* 5.4 0.4 - - - +
508B GLU* 3.5 48.4 + - + +
509B PRO 4.6 1.8 + - - -
702B EDO 2.6 39.9 + - - +
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Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B SER* 4.1 12.1 - - - +
364B ASP* 3.3 14.4 - - - +
368B GLN* 1.3 78.4 + - - +
370B ASN* 1.3 94.3 + - - +
371B ALA 3.3 0.7 + - - -
508B GLU 5.2 2.3 - - - +
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Residues in contact with ASN 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PHE* 3.3 44.3 - - + +
363B MET 3.5 8.1 - - - +
364B ASP* 3.0 15.8 + - - +
368B GLN* 3.6 0.8 + - - -
369B LYS* 1.3 90.0 - - + +
371B ALA* 1.3 64.7 + - - +
372B TYR 3.2 5.6 - - - -
508B GLU 4.5 5.4 - - - +
510B PRO* 3.4 21.6 - - + +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B MET 3.0 3.8 + - - -
365B GLY* 3.5 24.9 - - - +
368B GLN* 3.5 35.1 + - - +
369B LYS 3.3 1.4 + - - -
370B ASN* 1.3 78.9 - - - +
372B TYR* 1.3 72.2 + - + +
509B PRO 4.5 0.9 - - - +
510B PRO* 3.4 2.6 - - - +
511B ILE* 3.0 23.9 + - - +
702B EDO 3.6 11.0 - - - +
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PHE* 3.6 4.0 - - - -
363B MET* 2.9 41.0 + - + +
364B ASP 3.6 25.4 - - - -
365B GLY* 3.8 8.3 - - - -
370B ASN* 3.2 2.5 - - - -
371B ALA* 1.3 90.9 - - + +
373B ILE* 1.3 63.1 + - - +
374B GLY 4.1 0.2 - - - -
510B PRO* 3.7 7.3 - - - +
511B ILE* 3.2 23.6 - - + +
513B VAL* 4.2 10.8 - - + -
525B PHE* 5.1 4.9 - + - -
526B CYS* 3.7 41.5 - - + -
529B ASP* 2.5 40.5 + - + +
530B ILE* 3.6 8.4 - - + +
702B EDO 2.7 20.2 + - - -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 3.9 14.1 - - + -
360B ALA* 3.7 28.3 - - + -
361B SER 3.3 4.7 - - - +
362B PHE* 3.9 14.8 - - + -
372B TYR* 1.3 76.5 - - - +
374B GLY* 1.3 63.2 + - - +
375B THR* 3.8 1.5 + - - -
389B MET* 3.8 22.0 - - + -
393B GLN* 3.9 27.8 - - + -
510B PRO* 3.6 28.5 - - + +
511B ILE 2.9 6.1 + - - +
512B VAL* 3.4 17.1 - - + +
513B VAL* 2.8 29.8 + - - +
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ALA* 3.3 2.1 - - - -
361B SER 2.9 33.3 + - - -
363B MET* 3.5 22.3 - - - -
373B ILE* 1.3 70.9 - - - +
375B THR* 1.3 60.8 + - - -
513B VAL* 3.4 7.2 - - - -
518B GLY 4.7 0.2 - - - -
522B THR* 4.0 10.8 - - - -
554B ARG* 3.5 15.5 + - - -
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Residues in contact with THR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ILE* 4.5 7.4 - - - +
359B ASN 2.6 22.7 + - - -
360B ALA* 3.4 15.6 - - - +
373B ILE* 4.4 1.1 - - - +
374B GLY* 1.3 75.7 - - - -
376B GLN* 1.3 69.6 + - - +
386B PHE* 4.2 13.3 - - + -
389B MET* 4.3 5.1 - - + +
512B VAL* 3.8 24.2 - - + -
513B VAL 3.0 7.7 + - - -
514B HIS* 3.0 34.5 - - + +
518B GLY* 3.1 21.6 + - - -
554B ARG* 4.1 2.2 - - - +
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LYS 2.9 24.9 + - - -
331B ASN* 3.7 1.0 - - - -
332B ARG* 2.9 31.6 + - + +
333B TYR* 4.6 1.2 + - - -
358B ILE* 6.0 2.5 - - + +
359B ASN* 3.6 33.6 + - + +
375B THR* 1.3 90.0 + - - +
377B GLY* 1.3 69.2 + - - +
378B PRO* 3.3 11.1 - - + +
379B LEU* 3.7 13.9 - - - +
382B THR* 4.4 8.9 + - - +
386B PHE* 5.3 0.2 - - - -
514B HIS* 3.8 5.2 - - - +
515B CYS 3.4 2.5 - - - -
516B SER 3.4 14.6 - - - +
517B ALA* 3.8 15.0 - - - +
554B ARG* 4.1 3.4 - - - +
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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