Contacts of the strand formed by residues 427 - 436 (chain A) in PDB entry 2VIF
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 LYS 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A PHE 3.9 0.2 - - - +
423A ARG* 3.4 13.1 - - - +
424A SER 2.9 33.8 + - - +
425A HIS* 3.1 32.6 + - - +
426A GLY* 1.3 82.6 - - - +
428A THR* 1.3 61.1 + - - +
429A LEU* 4.0 22.7 + - + +
472A TYR* 4.0 20.4 - - - -
474A ARG* 6.3 0.9 - - - +
567P ASN* 5.7 4.9 - - - +
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Residues in contact with THR 428 (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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395A GLU* 3.9 26.9 + - + +
398A LEU* 3.6 41.3 - - + +
421A SER* 4.3 1.1 - - - -
422A PHE 3.4 6.3 - - - +
423A ARG* 3.3 20.5 + - - +
427A LYS* 1.3 72.7 - - - +
429A LEU* 1.3 66.8 + - - +
430A HIS* 3.8 24.7 + - + -
567P ASN* 3.4 25.6 + - - +
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Residues in contact with LEU 429 (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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421A SER* 3.3 3.5 - - - -
422A PHE* 2.8 61.0 + - + +
424A SER* 4.7 9.0 - - - -
427A LYS* 4.1 28.9 - - + +
428A THR* 1.3 80.9 - - - +
430A HIS* 1.3 65.9 + - - +
472A TYR* 3.4 46.4 - - + +
567P ASN* 3.4 19.7 - - + +
569P VAL* 4.1 13.2 - - + -
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Residues in contact with HIS 430 (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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391A ARG* 3.4 32.0 - - + +
394A ALA* 4.3 0.9 - - + -
395A GLU* 2.8 31.7 + - + +
409A ARG* 3.2 9.6 + - - +
420A LEU 3.2 6.5 - - - +
421A SER* 2.8 27.1 + - - -
422A PHE* 4.7 1.3 - - - -
428A THR* 3.8 13.4 + - + -
429A LEU* 1.3 75.3 - - - +
431A THR* 1.3 62.3 + - - +
566P ASN 3.5 22.9 - - - -
567P ASN* 2.9 13.6 + - + -
568P PTR 3.2 25.9 - + + -
569P VAL* 2.9 28.9 + - - +
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Residues in contact with THR 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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419A SER* 3.3 4.1 - - - -
420A LEU* 2.8 46.7 + - + +
422A PHE* 4.6 2.0 - - + -
430A HIS* 1.3 77.1 - - - +
432A ARG* 1.3 65.7 + - - +
442A PHE* 3.6 34.2 - - + +
443A TYR* 3.3 12.1 - - - -
568P PTR 4.1 4.7 - - - -
569P VAL* 2.9 23.0 + - - -
571P ILE* 4.0 25.9 + - + +
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Residues in contact with ARG 432 (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 SER* 4.0 1.6 - - - +
413A ASP* 3.7 22.6 + - - +
415A ARG* 3.8 13.3 - - - +
416A TYR* 3.7 32.8 - - + -
418A LEU 3.7 4.3 - - - +
419A SER* 3.4 16.4 - - - +
431A THR* 1.3 79.5 + - - +
433A ILE* 1.3 62.6 + - - +
442A PHE* 3.5 6.6 - - - -
443A TYR* 2.9 68.6 + - + -
566P ASN* 4.8 7.5 - - - +
568P PTR 2.8 56.5 + - + +
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Residues in contact with ILE 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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408A VAL* 4.4 15.3 - - + -
416A TYR* 3.6 15.6 - - - +
417A LEU 4.7 2.1 + - - -
418A LEU* 2.9 45.6 + - + +
419A SER 4.1 15.3 - - - +
420A LEU* 4.2 11.9 - - + +
432A ARG* 1.3 77.6 - - - +
434A GLU* 1.3 71.8 + - - +
435A HIS* 4.1 2.4 + - + +
440A PHE* 4.1 19.1 - - + -
441A SER 3.4 11.2 - - - +
442A PHE* 4.0 20.2 - - + -
454A ILE* 4.9 8.5 - - + -
457A LEU* 4.1 13.2 - - + -
458A ILE* 5.8 1.8 - - + -
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Residues in contact with GLU 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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416A TYR* 3.2 35.6 + - + -
433A ILE* 1.3 76.9 - - - +
435A HIS* 1.3 61.3 + - - +
436A SER* 4.2 3.2 - - - +
439A ARG 4.4 0.2 - - - -
440A PHE* 3.2 6.1 - - - -
441A SER* 2.8 42.2 + - - +
442A PHE 3.8 3.4 - - - +
443A TYR* 3.2 28.2 - - + +
444A GLU* 3.6 9.7 + - - +
445A GLN 5.3 0.6 + - - +
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Residues in contact with HIS 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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372A LEU* 3.6 35.1 - - + +
417A LEU* 5.7 9.9 - - + +
418A LEU* 6.5 0.4 - - + -
433A ILE* 4.1 3.0 + - + +
434A GLU* 1.3 74.8 + - - +
436A SER* 1.3 67.2 + - - +
438A GLY* 4.1 15.4 + - - -
439A ARG 3.1 20.0 - - - -
440A PHE* 3.3 37.1 - + + -
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Residues in contact with SER 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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434A GLU* 4.2 3.3 - - - +
435A HIS* 1.3 80.0 - - - +
437A ASN* 1.3 81.7 + - - +
438A GLY 3.1 2.2 - - - -
439A ARG* 2.9 22.5 + - - +
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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