Contacts of the strand formed by residues 432 - 437 (chain A) in PDB entry 3VI4
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 ASP 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.8 2.5 - - - -
25A PHE* 4.0 5.4 - - - -
358A LEU* 4.6 2.9 - - - +
361A LEU* 5.6 1.4 - - - +
421A GLY* 3.6 17.5 - - - -
422A GLY 3.6 5.7 + - - -
423A ARG 2.9 8.3 + - - +
424A ASP* 3.5 0.2 - - - +
425A LEU* 2.7 52.1 + - + +
426A ASP* 3.7 1.4 + - - +
430A TYR 3.0 2.8 - - - +
431A PRO* 1.3 73.2 - - - +
433A LEU* 1.3 66.6 + - - +
446A TYR 3.1 14.6 - - - +
447A ARG* 3.6 7.9 - - - -
448A GLY 2.8 24.5 + - - +
2004A CA 2.3 27.1 - - - -
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Residues in contact with LEU 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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3A LEU* 3.7 27.6 - - + -
25A PHE* 4.2 1.6 - - - -
356A THR* 5.0 0.4 - - - +
358A LEU* 3.6 32.3 - - + -
361A LEU* 6.2 0.4 - - + -
370A ALA* 4.5 9.6 - - + -
384A VAL* 5.1 1.3 - - + -
386A VAL* 5.1 0.4 - - + -
402A LEU* 4.9 8.1 - - + -
419A LEU* 4.3 9.2 - - + -
420A ARG 3.3 25.1 - - - +
425A LEU* 5.0 0.4 - - - +
432A ASP* 1.3 76.6 - - - +
434A ILE* 1.3 70.9 + - - +
435A VAL* 3.8 20.4 - - + -
444A VAL 3.5 1.6 - - - +
445A VAL* 3.5 2.0 - - - -
446A TYR* 2.6 51.2 + - + +
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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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23A VAL* 3.5 28.9 - - + +
24A GLU* 3.8 26.0 - - - +
25A PHE* 3.5 39.7 - - + -
35A VAL* 3.7 35.4 - - + -
419A LEU* 3.4 5.4 - - - -
420A ARG* 2.9 33.0 + - + +
425A LEU* 5.1 0.4 - - + -
433A LEU* 1.3 75.3 - - - +
435A VAL* 1.3 61.0 + - - +
443A ALA* 4.5 9.4 - - + -
444A VAL 3.3 10.1 - - - +
445A VAL* 4.4 7.2 - - + -
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Residues in contact with VAL 435 (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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384A VAL* 3.6 15.3 - - + -
402A LEU* 5.7 1.1 - - + -
415A PHE* 3.7 17.0 - - + -
416A GLY* 3.6 29.6 - - - +
418A ALA 3.6 4.0 - - - +
419A LEU* 3.7 16.4 - - + -
433A LEU* 3.8 16.6 - - + -
434A ILE* 1.3 77.5 - - - +
436A GLY* 1.3 62.0 + - - +
437A SER 3.9 0.7 + - - -
443A ALA* 3.5 1.8 - - - -
444A VAL* 2.8 37.7 + - + +
446A TYR* 3.7 27.8 - - + -
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Residues in contact with GLY 436 (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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20A GLY* 3.3 20.9 - - - -
23A VAL* 4.3 10.2 - - - +
414A PHE 3.3 5.7 - - - +
416A GLY 3.2 18.4 + - - -
417A SER* 3.7 9.4 + - - -
418A ALA 2.8 17.3 + - - -
434A ILE 4.2 0.2 - - - -
435A VAL* 1.3 72.9 - - - +
437A SER* 1.3 59.9 + - - -
438A PHE 3.6 4.0 + - - -
442A LYS 4.1 3.6 - - - -
443A ALA* 4.4 0.4 - - - -
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Residues in contact with SER 437 (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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406A TRP* 3.6 25.3 - - - -
413A ASP* 3.0 27.6 + - - +
415A PHE* 3.5 27.1 - - - +
435A VAL 3.9 2.3 + - - -
436A GLY* 1.3 71.0 - - - -
438A PHE* 1.3 63.5 + - - +
439A GLY 3.0 3.9 + - - -
440A VAL* 3.2 12.0 + - - +
442A LYS 2.8 29.3 + - - -
444A VAL* 5.5 0.9 - - - -
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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