Contacts of the strand formed by residues 456 - 465 (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 456 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B TRP* 3.6 21.9 - - + -
450B HIS* 3.4 3.2 + - - -
451B ASN 2.9 30.4 + - - +
454B GLU* 3.6 31.8 + - - +
455B ARG* 1.3 82.6 - - - +
457B LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 457 (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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391B TRP* 4.6 2.4 - - - -
448B GLU* 3.6 30.7 - - + +
449B ILE 3.4 3.6 - - - -
450B HIS* 3.5 40.8 - - + +
456B GLN* 1.3 74.0 - - - +
458B ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 458 (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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390B VAL* 2.9 30.9 + - - +
391B TRP* 2.9 62.6 + - + +
394B LYS* 3.5 18.8 - - - +
395B VAL 3.2 26.0 + - - +
396B LEU* 4.2 16.6 - - + -
448B GLU* 3.4 5.4 - - - -
449B ILE* 2.9 35.9 + - + +
457B LYS* 1.3 76.2 - - - +
459B GLN* 1.3 69.3 + - - +
460B VAL* 3.9 8.5 + - + -
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Residues in contact with GLN 459 (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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396B LEU* 4.1 13.7 - - - +
434B LEU* 3.9 13.5 - - + +
446B THR* 3.6 33.6 + - + +
447B LEU 3.3 5.8 - - - +
448B GLU* 4.6 1.8 - - + +
458B ARG* 1.3 83.3 - - - +
460B VAL* 1.3 63.2 + - - +
461B THR* 5.4 4.4 + - - +
494B ALA* 5.9 0.7 - - - +
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Residues in contact with VAL 460 (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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387B TRP* 5.0 1.1 - - + -
390B VAL* 4.4 3.6 - - + -
395B VAL* 3.6 21.1 - - + +
396B LEU 3.4 15.3 - - - +
398B ILE* 3.9 30.1 - - + -
446B THR* 3.7 2.3 - - - +
447B LEU* 2.7 49.4 + - + +
449B ILE* 3.7 31.4 - - + -
458B ARG* 4.0 8.7 - - + -
459B GLN* 1.3 78.8 - - - +
461B THR* 1.3 70.9 + - - +
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Residues in contact with THR 461 (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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396B LEU 2.9 11.0 + - - -
397B VAL* 3.3 5.2 - - - +
398B ILE 2.9 26.2 + - - +
444B LYS* 3.7 27.3 - - + -
445B THR 3.6 5.6 - - - +
446B THR* 4.7 8.3 + - - +
459B GLN* 5.4 4.7 + - - +
460B VAL* 1.3 76.8 - - - +
462B HIS* 1.3 61.4 + - - +
463B PHE* 3.4 31.4 - - + -
490B GLN* 3.6 29.7 + - + +
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Residues in contact with HIS 462 (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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398B ILE* 3.5 24.7 - - + -
400B MET* 3.9 18.5 - - + +
415B TYR* 2.8 39.8 + + - -
416B TRP* 3.5 44.0 + + - -
443B LYS 3.6 0.7 + - - +
444B LYS* 3.5 2.6 - - - -
445B THR* 2.7 52.4 + - - +
447B LEU* 4.0 19.7 - - + -
460B VAL 4.0 0.2 + - - -
461B THR* 1.3 72.4 - - - +
463B PHE* 1.3 62.4 + - - +
464B GLN* 4.1 9.9 + - + +
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Residues in contact with PHE 463 (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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397B VAL* 3.8 24.2 - - + -
398B ILE 2.8 9.8 + - - +
399B VAL* 3.5 0.8 - - - -
400B MET* 2.7 34.1 + - - +
442B TYR* 4.2 14.4 - + - -
443B LYS 3.4 1.8 - - - -
444B LYS* 3.6 33.7 - - + -
461B THR* 3.4 25.4 - - + -
462B HIS* 1.3 76.0 + - - +
464B GLN* 1.3 54.9 + - - +
465B PHE 4.1 0.7 - - - -
483B PHE* 3.7 21.8 - + + -
486B VAL* 3.5 28.5 - - + -
487B VAL* 4.0 15.5 - - + -
490B GLN* 3.7 29.8 - - + -
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Residues in contact with GLN 464 (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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400B MET* 3.3 25.7 - - + +
402B THR 2.9 28.6 + - - +
403B ARG* 3.7 12.3 - - - +
404B PHE* 4.8 7.2 - - - +
416B TRP* 4.0 15.9 - - - -
442B TYR* 3.1 6.9 - - - -
443B LYS* 2.9 48.0 + - + +
462B HIS* 4.1 12.5 + - + +
463B PHE* 1.3 72.3 - - - +
465B PHE* 1.3 60.3 - - - +
466B LEU* 3.6 25.4 + - + +
483B PHE* 4.2 0.4 - - - -
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Residues in contact with PHE 465 (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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400B MET 2.8 11.7 + - - +
401B THR* 4.0 22.1 - - + +
402B THR* 4.1 5.9 + - - +
441B HIS* 3.5 22.4 - + + -
464B GLN* 1.3 72.4 - - - +
466B LEU* 1.3 63.7 + - - +
467B SER* 3.5 15.7 - - - -
468B TRP* 3.5 55.3 + + + -
474B PRO* 4.9 4.7 - - + -
479B SER* 3.7 28.5 - - - -
480B LEU* 3.9 24.9 - - + -
483B PHE* 3.6 41.3 - + + -
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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