Contacts of the strand formed by residues 418 - 425 (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 VAL 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A MET* 3.6 5.6 - - - +
413A TRP* 3.7 26.0 - - + -
414A ILE* 3.3 5.4 - - - -
415A ASN* 2.8 38.4 + - - +
417A ASP* 1.3 81.0 - - - +
419A TYR* 1.3 62.8 + - - +
420A ILE* 3.9 13.0 - - + -
434A ILE 3.2 2.9 - - - +
435A ASN* 4.2 3.4 - - - +
442A TYR* 3.4 39.7 - - + -
444A ILE* 4.3 1.3 - - + -
482A LEU* 3.6 32.3 - - + -
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Residues in contact with TYR 419 (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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301A MET* 3.8 23.0 - - + +
304A LEU* 3.9 23.8 - - + -
305A ASP* 2.7 45.0 + - + -
308A ILE* 4.0 16.8 - - + +
309A GLN* 4.9 0.2 + - - -
348A PHE* 3.9 18.2 - + - -
409A THR* 4.6 3.3 - - + +
411A GLN* 3.9 16.8 + - + +
413A TRP 3.6 4.3 - - - -
414A ILE* 4.0 14.6 - - + -
418A VAL* 1.3 73.7 - - - +
420A ILE* 1.3 65.5 + - - +
421A TYR* 3.5 39.4 - + + +
432A VAL 3.6 2.1 - - - +
433A ALA* 3.6 1.0 - - - -
434A ILE* 2.9 34.8 + - + +
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Residues in contact with ILE 420 (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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411A GLN* 3.8 1.9 - - - -
412A ARG* 2.7 30.5 + - + -
413A TRP* 2.8 40.1 + - + +
418A VAL* 3.9 8.7 - - + -
419A TYR* 1.3 77.5 - - - +
421A TYR* 1.3 55.2 + - - +
431A LEU* 3.8 26.0 - - + -
432A VAL 3.1 14.4 - - - +
433A ALA* 3.7 22.9 - - + -
444A ILE* 3.9 31.4 - - + -
447A LEU* 4.0 21.1 - - + -
480A PHE* 4.3 4.7 - - + -
482A LEU* 4.7 0.7 - - + -
490A TRP* 4.9 0.4 - - + -
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Residues in contact with TYR 421 (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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348A PHE* 3.3 38.7 + + - -
351A THR* 2.7 32.5 + - - -
352A SER* 4.0 12.1 - - - -
409A THR* 4.2 18.2 - - + -
410A GLN 3.3 10.3 - - - +
412A ARG 4.3 0.2 - - - +
419A TYR* 3.5 42.6 - + + +
420A ILE* 1.3 74.9 - - - +
422A GLU* 1.3 60.2 - - - +
423A ARG* 4.5 9.6 - - + -
430A ALA 3.9 0.5 - - - +
431A LEU* 3.6 5.4 - - - +
432A VAL* 2.9 69.2 + - + +
434A ILE* 4.1 6.9 - - + +
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Residues in contact with GLU 422 (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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408A THR* 3.4 1.4 + - - +
409A THR* 3.3 4.9 - - - -
410A GLN* 2.8 49.6 + - + +
412A ARG* 2.9 36.4 + - + +
421A TYR* 1.3 74.9 - - - +
423A ARG* 1.3 69.1 + - - +
424A LYS* 4.1 11.2 + - + +
429A VAL* 3.8 18.4 - - + -
430A ALA 3.3 3.6 - - - +
431A LEU* 3.9 5.3 - - + +
449A THR* 2.7 33.3 + - - -
450A ALA* 2.8 23.9 + - - +
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Residues in contact with ARG 423 (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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319A ASN* 4.7 0.8 + - - -
351A THR 2.9 32.7 + - - +
352A SER* 3.2 14.0 - - - +
353A ARG* 3.6 21.2 - - - +
403A ALA* 3.4 28.5 + - + +
404A ILE* 2.8 32.2 + - + +
405A ALA 4.5 1.0 - - - -
406A TYR 4.0 2.4 - - - +
407A GLY 2.8 24.5 + - - +
408A THR 3.1 16.2 + - - -
409A THR* 3.4 25.6 + - - -
421A TYR* 4.5 11.0 - - + -
422A GLU* 1.3 72.3 - - - +
424A LYS* 1.3 60.8 + - - +
429A VAL* 3.3 7.4 - - - +
430A ALA* 2.8 44.7 + - + +
432A VAL* 5.7 1.6 - - + -
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Residues in contact with LYS 424 (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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403A ALA* 4.3 0.4 - - - -
407A GLY* 3.1 3.1 - - - -
408A THR* 3.0 43.2 + - - +
410A GLN* 6.0 0.9 - - - +
422A GLU* 4.1 12.5 - - + +
423A ARG* 1.3 76.4 - - - +
425A PHE* 1.3 62.7 + - - +
426A GLY* 2.8 30.1 + - - +
427A ASN* 4.8 6.8 + - - +
428A ASN 3.4 7.6 - - - +
429A VAL* 4.3 6.1 - - + -
450A ALA* 3.6 31.4 - - + -
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Residues in contact with PHE 425 (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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402A PRO* 3.7 31.2 - - + +
403A ALA* 3.7 20.4 - - - +
406A TYR* 3.8 22.4 - + + -
407A GLY* 4.0 2.9 - - - -
424A LYS* 1.3 75.3 - - - +
426A GLY* 1.3 63.2 + - - +
428A ASN* 2.9 38.2 + - + -
500A LEU* 3.5 43.5 - - + -
501A ILE 3.7 7.6 - - - -
502A GLY* 3.6 30.3 - - - -
519A GLY* 4.2 2.0 - - - -
520A ARG* 4.1 16.4 - - + -
571A ASN* 5.4 1.8 - - - -
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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