Contacts of the strand formed by residues 429 - 438 (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 LEU 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B ARG* 4.8 3.6 - - + +
387B TRP* 3.7 16.6 - - + +
388B LEU* 3.6 45.8 - - + +
391B TRP* 4.1 17.0 - - + -
424B ILE 4.1 0.3 - - - +
425B ARG* 3.4 2.2 - - - +
426B PHE* 2.6 49.8 + - + +
427B GLY 3.2 0.4 - - - -
428B PHE* 1.3 101.4 - - + +
430B THR* 1.3 60.4 + - - +
431B VAL* 5.0 2.0 - - + -
449B ILE* 4.3 13.0 - - + -
450B HIS 3.4 1.6 - - - -
451B ASN* 3.9 21.8 - - + +
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Residues in contact with THR 430 (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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423B ARG* 4.5 9.6 - - + -
424B ILE 3.4 11.0 - - - +
425B ARG* 3.6 21.6 - - + +
428B PHE 5.3 0.2 - - - -
429B LEU* 1.3 75.2 - - - +
431B VAL* 1.3 65.6 + - - +
432B THR* 4.1 16.1 + - - +
448B GLU* 3.4 1.7 - - - +
449B ILE* 3.4 3.5 - - - -
450B HIS* 2.8 49.7 + - + +
452B THR* 4.6 9.4 - - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B TRP* 3.8 55.6 - - + +
417B PRO* 3.6 26.8 - - + +
423B ARG* 3.2 2.8 - - - -
424B ILE 2.8 38.9 + - - +
426B PHE* 4.6 9.0 - - + -
429B LEU* 5.0 1.3 - - + +
430B THR* 1.3 78.2 - - - +
432B THR* 1.3 62.4 + - - +
447B LEU* 4.2 14.4 - - + -
448B GLU 3.3 7.6 - - - +
449B ILE* 4.4 11.2 - - + -
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Residues in contact with THR 432 (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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417B PRO* 4.3 0.2 - - - -
421B ASP* 4.3 11.2 - - - +
422B SER 3.4 11.7 - - - +
423B ARG* 3.9 11.1 - - + +
430B THR* 4.1 9.7 + - - +
431B VAL* 1.3 76.7 + - - +
433B ASN* 1.3 72.3 + - - +
434B LEU* 3.5 16.6 + - + +
447B LEU* 3.2 9.4 - - - -
448B GLU* 2.9 46.9 + - - -
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Residues in contact with ASN 433 (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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417B PRO* 2.9 29.3 + - + +
418B LEU 3.0 22.4 + - - -
419B GLU 3.2 23.0 - - - +
420B LYS* 3.4 5.6 - - - +
421B ASP* 2.7 31.4 + - - +
422B SER 2.9 11.9 + - - +
432B THR* 1.3 72.4 - - - +
434B LEU* 1.3 58.8 + - - +
435B GLY* 2.9 24.3 + - - +
436B VAL* 3.7 3.2 - - - +
445B THR* 3.5 19.7 - - - +
446B THR 3.8 2.9 - - - -
447B LEU* 3.9 4.0 - - + -
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Residues in contact with LEU 434 (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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420B LYS* 3.5 19.7 - - - -
421B ASP* 5.5 1.3 - - - -
432B THR* 3.9 24.0 - - + +
433B ASN* 1.3 78.6 - - - +
435B GLY* 1.3 54.6 + - - +
446B THR* 2.7 43.7 + - + +
447B LEU 4.2 1.3 - - - +
448B GLU* 4.0 29.8 - - + +
459B GLN* 3.9 15.0 - - + +
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Residues in contact with GLY 435 (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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420B LYS* 4.0 15.7 - - - -
433B ASN* 2.9 8.7 + - - +
434B LEU* 1.3 82.0 - - - +
436B VAL* 1.3 63.2 + - - +
437B GLU* 5.5 2.0 - - - -
444B LYS 3.8 1.0 - - - +
445B THR* 3.3 3.8 - - - -
446B THR* 2.9 29.9 + - - +
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Residues in contact with VAL 436 (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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418B LEU 3.8 11.0 - - - +
420B LYS* 4.7 8.9 - - + +
433B ASN* 3.7 24.5 - - - +
435B GLY* 1.3 79.2 - - - +
437B GLU* 1.3 76.8 + - - +
438B ASN* 4.2 3.8 + - + +
443B LYS* 4.5 20.2 - - + -
444B LYS 3.3 7.4 - - - +
445B THR* 3.8 13.9 - - - +
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Residues in contact with GLU 437 (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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435B GLY 5.5 1.3 - - - -
436B VAL* 1.3 80.3 - - - +
438B ASN* 1.3 60.5 - - - +
439B MET* 3.6 16.8 + - + +
443B LYS* 3.3 4.9 - - - +
444B LYS* 2.8 66.0 + - + +
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Residues in contact with ASN 438 (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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436B VAL* 4.1 4.8 + - + -
437B GLU* 1.3 69.8 - - - +
439B MET* 1.3 69.5 + - - +
442B TYR 4.1 3.1 - - - -
443B LYS* 4.3 22.0 - - + -
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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