Contacts of the strand formed by residues 428 - 435 (chain A) in PDB entry 3BMW
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 ASN 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASN* 3.9 15.3 - - - +
402A PRO* 3.5 24.4 - - + +
403A ALA* 3.4 6.6 - - + +
424A LYS* 3.4 5.2 - - - +
425A PHE* 2.9 49.8 + - - +
427A ASN* 1.3 77.1 - - - +
429A VAL* 1.3 62.1 + - - +
492A TYR 3.4 5.6 - - - +
493A VAL* 3.5 15.1 - - - +
494A SER* 3.0 26.5 + - - +
497A ASN* 3.0 26.9 + - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ASN* 3.3 7.1 + - - -
403A ALA* 3.8 4.5 - - - +
422A GLU* 3.8 32.1 - - + +
423A ARG 3.3 4.0 - - - -
424A LYS* 4.3 9.2 - - + -
427A ASN* 3.9 12.6 - - - +
428A ASN* 1.3 81.0 - - - +
430A ALA* 1.3 66.4 + - - +
431A LEU 4.5 0.2 - - - +
449A THR* 4.3 0.2 - - - +
450A ALA* 3.9 29.4 - - + +
451A LEU* 3.8 29.6 - - + +
452A PRO* 5.3 0.7 - - + -
491A GLN* 3.4 0.6 - - - -
492A TYR* 2.9 34.2 + - + +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ASN* 4.1 4.7 - - - +
403A ALA* 4.0 0.6 - - + +
404A ILE* 3.7 36.1 - - + -
421A TYR 3.9 0.5 - - - +
422A GLU* 3.3 4.2 - - - +
423A ARG* 2.8 46.4 + - + +
429A VAL* 1.3 78.5 - - - +
431A LEU* 1.3 60.9 + - - +
432A VAL* 4.9 8.1 - - + -
489A VAL* 5.2 2.5 - - + -
490A TRP 3.4 9.0 - - - +
491A GLN* 4.5 2.0 - - + -
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Residues in contact with LEU 431 (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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412A ARG* 4.1 11.9 - - + -
420A ILE* 3.8 18.2 - - + -
421A TYR 3.6 14.8 - - - +
422A GLU* 3.9 22.0 - - + +
429A VAL* 4.5 1.1 - - + +
430A ALA* 1.3 72.8 - - - +
432A VAL* 1.3 60.9 + - - +
447A LEU* 4.4 13.2 - - + -
448A TYR 5.0 0.2 - - - +
449A THR* 3.8 25.1 - - + +
451A LEU* 4.2 11.4 - - + -
469A ILE* 4.1 14.4 - - + -
489A VAL* 3.5 1.6 - - - -
490A TRP* 2.8 65.9 + - + +
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA 5.4 1.6 - - - +
351A THR* 3.8 28.7 - - + +
419A TYR 3.6 1.9 - - - +
420A ILE* 3.1 6.1 - - - -
421A TYR* 2.9 69.8 + - + +
423A ARG* 5.7 1.3 - - + -
430A ALA* 4.9 7.0 - - + +
431A LEU* 1.3 81.2 - - - +
433A ALA* 1.3 62.5 + - - +
434A ILE* 4.2 14.8 - - + -
487A VAL* 4.5 4.0 - - + -
488A ALA 3.4 9.6 - - - +
489A VAL* 4.1 21.5 - - + -
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Residues in contact with ALA 433 (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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419A TYR 3.6 3.4 - - - -
420A ILE* 3.7 22.9 - - + -
432A VAL* 1.3 72.8 - - - +
434A ILE* 1.3 65.7 + - - +
435A ASN 4.4 0.2 - - - -
480A PHE* 5.0 0.2 - - + -
482A LEU* 3.9 18.3 - - + +
486A GLU 3.8 1.1 - - - +
487A VAL* 3.2 5.7 - - - +
488A ALA 3.0 32.1 + - - +
490A TRP* 3.7 28.9 - - + -
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Residues in contact with ILE 434 (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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294A PHE* 3.8 27.6 - - + -
301A MET* 3.8 9.9 - - + -
344A GLN* 3.9 25.4 - - + +
348A PHE* 3.9 43.3 - - + +
417A ASP 3.6 1.0 - - - +
418A VAL* 3.2 6.6 - - - +
419A TYR* 2.9 38.3 + - + +
421A TYR* 4.1 12.3 - - + +
432A VAL* 4.2 6.5 - - + -
433A ALA* 1.3 80.3 - - - +
435A ASN* 1.3 62.6 + - - +
482A LEU* 4.1 3.5 - - - +
486A GLU 3.5 2.9 - - - -
487A VAL* 4.0 16.8 - - + -
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Residues in contact with ASN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLN* 2.8 18.9 + - - -
417A ASP 3.5 7.0 - - - +
418A VAL* 4.2 1.1 - - + -
434A ILE* 1.3 71.4 - - - +
436A ARG* 1.3 59.1 + - - +
437A ASN* 3.0 22.1 + - - +
440A THR 2.9 24.5 + - - -
442A TYR* 3.6 19.6 - - - -
482A LEU* 3.4 29.2 + - + +
483A SER 3.0 25.6 + - - +
484A ALA* 3.8 1.4 - - - +
485A GLY* 3.1 14.9 + - - -
486A GLU 2.9 10.7 + - - +
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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