Contacts of the helix formed by residues 488 - 499 (chain B) in PDB entry 3VRY
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 PRO 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A GLU* 4.7 10.5 - - + +
529A GLU* 4.2 21.5 - - + +
360B LEU* 3.6 22.9 - - + -
364B ILE* 4.9 0.7 - - + -
483B ARG* 4.3 2.0 - - - +
486B ASN 3.7 7.9 - - - +
487B CYS* 1.3 89.8 - - - +
489B GLU* 1.3 65.1 + - - +
490B GLU* 3.3 12.8 - - - +
491B LEU* 3.2 28.7 + - + +
492B TYR* 3.0 18.2 + - - +
519B PHE* 4.6 15.0 - - + -
601B CA 4.7 1.8 - - - -
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Residues in contact with GLU 489 (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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181A THR* 4.6 2.1 + - - -
204A LYS* 3.8 35.5 + - + +
206A ARG* 2.5 46.9 + - - +
527A PTR 5.0 9.0 - - + -
528A GLU 5.9 2.5 - - - +
529A GLU* 6.2 0.6 - - - +
483B ARG* 2.7 27.1 + - - +
487B CYS 3.8 0.2 + - - -
488B PRO* 1.3 71.7 - - - +
490B GLU* 1.3 68.2 + - - +
492B TYR* 3.1 14.0 + - - +
493B ASN* 2.8 38.8 + - - +
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Residues in contact with GLU 490 (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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523A THR* 3.0 41.1 - - + +
524A GLU* 3.1 11.2 - - - +
526A GLN* 3.6 17.7 - - + +
527A PTR 2.8 37.9 + - + +
488B PRO* 3.9 5.2 - - - +
489B GLU* 1.3 78.1 + - - +
491B LEU* 1.3 59.6 + - - +
493B ASN* 3.7 13.1 + - - +
494B ILE* 3.5 26.2 + - - +
519B PHE* 4.1 5.8 - - + -
601B CA 2.9 26.4 - - - -
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Residues in contact with LEU 491 (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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364B ILE* 3.9 25.8 - - + -
367B SER* 5.5 0.7 - - - +
452B LEU* 3.6 27.6 - - + +
456B VAL* 4.0 27.6 - - + -
487B CYS* 4.0 1.6 - - - -
488B PRO* 3.2 26.7 + - + +
489B GLU 3.1 0.2 - - - -
490B GLU* 1.3 75.4 - - - +
492B TYR* 1.3 66.9 + - - +
494B ILE* 3.2 12.7 + - + +
495B MET* 3.4 23.7 + - + +
516B LEU* 4.3 20.4 - - + -
519B PHE* 3.9 13.6 - - + -
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Residues in contact with TYR 492 (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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181A THR* 6.5 1.3 - - + -
453B MET* 4.3 8.5 - - + -
480B ARG* 4.5 2.8 + - - +
481B MET 2.3 33.7 + - - -
482B PRO* 3.7 3.2 - - - +
483B ARG* 3.4 49.9 + - + -
484B PRO* 4.8 0.2 - - + -
487B CYS* 4.1 1.3 - - - -
488B PRO 3.0 12.6 + - - +
489B GLU* 3.4 18.4 - - - +
491B LEU* 1.3 75.3 - - - +
493B ASN* 1.3 69.1 + - - +
494B ILE 3.1 0.2 + - - -
495B MET* 3.1 22.5 + - + +
496B MET* 2.9 55.5 + - + +
499B TRP* 4.5 4.3 - + - -
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Residues in contact with ASN 493 (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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180A THR* 3.1 49.5 + - + +
181A THR* 5.0 0.7 + - - -
204A LYS* 4.5 7.1 + - - +
526A GLN* 5.7 1.8 + - - -
527A PTR 5.6 4.4 - - - -
489B GLU* 2.8 30.7 + - - +
490B GLU* 3.9 14.1 - - - +
491B LEU 3.3 0.2 - - - -
492B TYR* 1.3 78.1 - - - +
494B ILE* 1.3 54.4 + - + +
496B MET* 3.1 14.2 + - - +
497B ARG* 2.8 41.9 + - + +
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Residues in contact with ILE 494 (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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523A THR* 5.3 0.9 - - + -
448B PHE* 5.2 0.2 - - + -
452B LEU* 3.8 17.5 - - + -
490B GLU 3.5 17.0 - - - +
491B LEU* 3.2 9.6 + - + +
492B TYR 3.1 0.6 - - - -
493B ASN* 1.3 76.4 - - + +
495B MET* 1.3 60.8 + - - +
497B ARG* 3.3 12.2 + - - +
498B CYS* 2.9 35.7 + - - -
507B PRO* 5.2 0.8 - - + +
511B TYR* 6.1 3.6 - - + -
512B ILE* 4.5 22.0 - - + +
515B VAL* 3.4 34.5 - - + -
516B LEU* 4.1 17.0 - - + -
519B PHE* 4.5 6.7 - - + -
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Residues in contact with MET 495 (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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449B GLY* 4.1 12.6 - - - +
452B LEU* 3.7 30.1 - - + +
453B MET* 3.7 32.3 - - + +
456B VAL* 4.5 2.9 - - + -
487B CYS* 3.5 32.5 - - - -
491B LEU* 3.4 23.8 - - + +
492B TYR* 3.4 13.0 - - - +
494B ILE* 1.3 77.2 - - - +
496B MET* 1.3 53.1 + - - +
498B CYS* 2.7 29.4 + - - +
499B TRP* 2.8 44.1 + - + -
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Residues in contact with MET 496 (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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480B ARG* 4.0 30.7 - - + +
492B TYR* 2.9 57.3 + - + +
493B ASN* 3.2 18.8 - - - +
495B MET* 1.3 76.9 - - - +
497B ARG* 1.3 58.7 + - + +
499B TRP* 3.2 28.8 + - - +
500B LYS* 3.6 15.3 + - - +
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Residues in contact with ARG 497 (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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510A GLU* 4.7 12.7 + - - -
493B ASN* 2.8 25.3 + - + +
494B ILE* 3.7 13.5 - - - +
496B MET* 1.3 72.5 - - + +
498B CYS* 1.3 61.2 + - - +
499B TRP 3.5 0.3 + - - -
500B LYS* 3.6 31.0 - - + +
505B GLU 5.1 6.4 + - - +
506B ARG* 3.7 4.0 - - - +
507B PRO* 3.2 51.7 - - + +
511B TYR* 3.6 31.9 + - - -
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Residues in contact with CYS 498 (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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445B VAL* 3.4 30.5 - - - +
446B TRP* 3.2 20.6 - - - -
448B PHE* 4.1 7.0 - - - -
449B GLY* 3.7 21.8 - - - -
494B ILE* 2.9 23.0 + - - +
495B MET* 2.7 14.4 + - - +
497B ARG* 1.3 74.2 - - - +
499B TRP* 1.3 59.4 + - + +
500B LYS 3.5 0.2 - - - -
506B ARG* 3.6 14.3 + - - -
507B PRO* 4.8 1.1 - - - -
512B ILE* 3.7 30.5 - - - -
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Residues in contact with TRP 499 (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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446B TRP* 3.4 41.7 + + + -
449B GLY* 3.3 24.7 - - - -
450B ILE* 3.2 39.2 - - + +
453B MET* 3.9 15.0 - - + -
463B TYR* 5.7 1.1 - - - -
480B ARG* 2.8 47.0 + - + +
481B MET* 4.4 23.8 - - + -
492B TYR* 4.5 2.2 - + - -
495B MET* 2.8 47.0 + - + +
496B MET* 3.2 30.5 + - - +
497B ARG 3.2 0.4 - - - -
498B CYS* 1.3 82.3 - - - +
500B LYS* 1.3 59.8 + - - +
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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