Contacts of the strand formed by residues 357 - 365 (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 TYR 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B CYS* 3.7 16.4 - - - -
322B SER* 2.6 36.2 + - - -
327B ASN* 3.3 45.1 - - + +
330B LYS* 3.9 32.1 + - + +
331B ASN* 2.5 30.7 + - - -
338B CYS* 3.7 9.3 - - - -
343B ARG* 3.8 13.5 - - - +
346B LEU* 3.7 9.4 - - - +
355B THR* 3.2 5.6 + - - +
356B ASP* 1.3 82.1 - - - +
358B ILE* 1.3 73.1 + - - +
359B ASN* 3.4 25.3 + - + +
385B ASP* 4.2 5.0 - - - +
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Residues in contact with ILE 358 (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* 5.8 1.3 - - - -
338B CYS* 4.3 1.0 - - - -
343B ARG* 4.9 1.9 - - - +
344B VAL 3.3 23.1 + - - +
346B LEU* 4.0 17.9 - - + -
356B ASP 4.0 0.4 + - - -
357B TYR* 1.3 90.0 - - - +
359B ASN* 1.3 63.6 + - - +
360B ALA* 2.9 28.0 + - + +
375B THR* 4.5 5.2 - - - +
376B GLN* 6.0 2.2 - - + +
382B THR* 5.2 7.9 - - + +
385B ASP* 3.8 13.0 - - + +
386B PHE* 3.7 34.8 - - + +
389B MET* 3.9 26.2 - - + -
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Residues in contact with ASN 359 (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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322B SER* 4.1 2.0 + - - -
330B LYS 4.6 3.2 + - - +
331B ASN* 2.9 22.9 + - - +
333B TYR 6.1 0.2 - - - +
336B VAL* 2.8 28.5 + - - +
337B PRO 4.3 0.6 - - - -
338B CYS* 3.5 8.1 - - - +
357B TYR* 3.4 20.3 + - + +
358B ILE* 1.3 71.3 - - - +
360B ALA* 1.3 52.1 + - - +
375B THR* 2.6 26.7 + - - -
376B GLN* 3.6 35.5 + - - +
517B ALA 5.4 0.2 - - - -
554B ARG* 2.9 29.5 + - - +
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Residues in contact with ALA 360 (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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338B CYS* 4.0 2.3 - - - -
343B ARG* 3.3 9.4 - - - +
344B VAL* 3.0 25.4 + - + -
358B ILE* 2.9 14.8 + - + +
359B ASN* 1.3 76.8 + - - +
361B SER* 1.3 62.0 + - - +
373B ILE* 3.7 4.9 - - + -
374B GLY 3.3 7.4 - - - -
375B THR* 3.4 15.9 - - - +
389B MET* 3.6 30.1 - - + -
554B ARG* 3.7 1.3 - - - +
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Residues in contact with SER 361 (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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338B CYS* 3.8 10.7 - - - +
339B LEU 4.7 1.7 + - - -
342B THR* 3.5 10.6 + - - -
343B ARG* 5.0 0.5 - - - -
344B VAL* 4.2 5.2 - - - -
360B ALA* 1.3 75.6 + - - +
362B PHE* 1.3 65.3 + - - +
363B MET* 3.6 1.6 + - - +
373B ILE* 3.3 2.6 - - - -
374B GLY 2.9 30.7 + - - -
553B GLN 3.5 24.5 + - - -
554B ARG* 2.9 36.2 + - - -
555B ALA 5.2 0.2 + - - -
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Residues in contact with PHE 362 (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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342B THR* 2.8 41.4 + - + +
343B ARG 4.0 5.4 - - - -
344B VAL* 3.8 26.2 - - + +
345B LYS 5.1 0.9 - - - -
361B SER* 1.3 75.7 - - - +
363B MET* 1.3 60.8 + - - +
370B ASN* 3.3 39.5 - - + +
372B TYR 3.6 3.8 - - - -
373B ILE* 3.9 22.4 - - + -
393B GLN* 3.4 35.7 - - - -
510B PRO* 4.8 6.1 - - + -
553B GLN* 3.7 14.9 - - - +
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Residues in contact with MET 363 (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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361B SER 3.6 4.3 - - - +
362B PHE* 1.3 80.3 - - - +
364B ASP* 1.3 66.1 + - - +
370B ASN* 3.5 2.1 + - - -
371B ALA 3.0 21.4 + - - -
372B TYR* 2.9 30.9 + - + +
374B GLY* 3.5 32.8 - - - -
522B THR* 4.8 5.8 - - + +
523B GLY* 5.2 0.4 - - - -
526B CYS* 4.0 21.3 - - + -
550B MET* 3.6 40.2 - - + -
553B GLN* 3.7 8.1 - - + +
554B ARG* 3.8 29.8 - - + +
557B SER* 4.4 1.3 - - - +
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Residues in contact with ASP 364 (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* 3.2 21.4 - - - +
278B VAL* 3.0 26.0 + - + +
279B HIS* 3.2 15.6 + - + -
363B MET* 1.3 77.7 - - - +
365B GLY* 1.3 59.2 + - - +
368B GLN 3.6 3.6 - - - +
369B LYS* 3.3 15.1 - - - +
370B ASN* 3.0 23.3 + - - +
372B TYR* 3.6 10.9 - - - -
530B ILE* 3.8 1.7 - - - +
550B MET* 5.4 0.9 - - - +
553B GLN* 2.8 35.5 + - - +
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Residues in contact with GLY 365 (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* 2.7 23.7 + - - -
279B HIS* 3.5 7.6 - - - +
364B ASP* 1.3 74.1 - - - +
366B TYR* 1.3 63.1 + - - -
367B LYS 3.1 0.2 + - - -
368B GLN 2.8 12.7 + - - +
371B ALA* 3.5 17.9 - - - +
372B TYR* 3.8 5.6 - - - -
530B ILE* 4.0 3.6 - - - -
702B EDO 3.4 11.4 - - - -
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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