Contacts of the helix formed by residues 480 - 492 (chain B) in PDB entry 3V42
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 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366B TRP* 3.8 7.9 - - + -
369B LEU* 4.4 5.6 - - + -
370B MET* 3.5 28.7 - - + -
479B GLY* 1.3 88.3 - - - +
481B THR* 1.3 65.3 + - - +
482B ILE* 4.3 3.8 - - + +
483B LEU* 3.0 31.8 + - + +
484B ASN* 3.2 11.6 + - - -
545B ASP* 3.7 13.7 - - + -
546B ASN* 3.3 15.0 - - - +
549B LEU* 3.8 23.6 - - + -
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Residues in contact with THR 481 (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 PRO* 1.3 70.6 - - - +
482B ILE* 1.3 63.8 + - - +
484B ASN* 3.1 14.1 + - + +
485B LYS* 3.0 50.8 + - + +
511B TRP* 3.7 22.3 - - + -
540B GLY 4.3 3.8 + - - +
543B GLU* 4.2 7.8 + - - -
546B ASN* 2.8 28.7 + - - +
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 4.2 13.0 - - + -
394B MET 5.1 2.0 - - - +
480B PRO* 4.3 1.8 - - + +
481B THR* 1.3 78.3 - - - +
483B LEU* 1.3 59.2 + - - +
485B LYS* 3.3 6.4 + - - +
486B ILE* 2.9 44.5 + - + +
504B LEU* 4.6 1.6 - - + -
507B LEU* 3.9 42.8 - - + +
508B LYS* 4.1 8.3 - - + +
511B TRP* 4.2 21.3 - - + +
549B LEU* 3.9 28.3 - - + -
553B TRP* 4.1 20.4 - - + -
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Residues in contact with LEU 483 (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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361B PHE* 5.4 3.1 - - + -
362B ARG* 3.3 43.1 - - - +
365B ALA* 3.7 24.0 - - + -
366B TRP* 3.9 32.5 - - + +
369B LEU* 3.7 18.2 - - + -
394B MET* 5.3 0.2 - - - -
479B GLY 3.9 7.0 - - - +
480B PRO* 3.0 15.7 + - + +
482B ILE* 1.3 78.6 - - - +
484B ASN* 1.3 59.4 + - - +
486B ILE* 3.2 13.9 + - + -
487B GLU* 2.8 32.2 + - + +
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Residues in contact with ASN 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 2.7 40.3 + - - +
477B ARG 4.3 1.0 - - - +
478B VAL* 2.9 26.3 + - - +
479B GLY* 4.1 0.8 - - - -
480B PRO 3.2 10.9 + - - -
481B THR* 3.1 15.6 + - + +
483B LEU* 1.3 73.5 - - - +
485B LYS* 1.3 64.4 + - + +
487B GLU* 3.8 1.8 - - - +
488B ALA* 3.1 24.8 + - - +
543B GLU* 5.8 1.4 + - - -
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Residues in contact with LYS 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B THR* 3.0 37.8 + - + +
482B ILE* 3.7 5.8 - - - +
484B ASN* 1.3 74.8 - - + +
486B ILE* 1.3 65.2 + - - +
488B ALA* 3.4 5.7 + - - +
489B ALA* 3.0 22.5 + - - +
507B LEU* 3.9 35.4 - - + +
510B GLU* 4.8 11.9 + - - -
511B TRP* 5.3 3.3 - - - +
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Residues in contact with ILE 486 (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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349B LEU* 4.5 10.5 - - + -
361B PHE* 5.0 2.7 - - + -
369B LEU* 4.9 5.6 - - + -
394B MET* 4.1 26.5 - - + -
482B ILE* 2.9 35.8 + - + +
483B LEU* 3.6 13.2 - - + +
485B LYS* 1.3 75.5 - - - +
487B GLU* 1.3 68.7 + - - +
489B ALA* 3.1 14.3 + - - +
490B LEU* 3.1 33.8 + - + +
500B VAL* 6.5 0.2 - - + -
504B LEU* 3.8 32.3 - - + -
507B LEU* 4.8 6.3 - - + -
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Residues in contact with GLU 487 (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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353B ARG* 3.3 33.5 + - - +
358B ALA* 4.6 5.2 - - - +
361B PHE* 5.7 4.2 - - + -
362B ARG* 2.8 51.7 + - - +
477B ARG 5.2 0.3 - - - +
483B LEU* 2.8 22.4 + - + +
484B ASN 3.8 4.0 - - - +
486B ILE* 1.3 81.4 - - - +
488B ALA* 1.3 62.7 + - - +
490B LEU* 3.2 8.0 + - - +
491B THR* 3.1 25.3 + - - +
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Residues in contact with ALA 488 (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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484B ASN 3.1 17.5 + - - +
485B LYS* 3.8 5.4 - - - +
487B GLU* 1.3 77.3 - - - +
489B ALA* 1.3 62.3 + - - +
491B THR* 3.4 14.5 + - - +
492B ASN* 3.4 13.2 + - - +
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Residues in contact with ALA 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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350B ARG* 3.0 16.4 + - - -
485B LYS 3.0 13.8 + - - +
486B ILE* 3.1 10.3 + - - +
488B ALA* 1.3 76.8 - - - +
490B LEU* 1.3 63.7 + - + +
492B ASN* 3.2 8.4 + - - +
495B LEU* 3.5 25.2 - - + +
500B VAL* 4.3 13.5 - - + -
503B ALA* 6.3 2.7 - - + -
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Residues in contact with LEU 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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349B LEU* 3.9 23.8 - - + +
350B ARG* 2.9 50.7 + - + +
353B ARG* 3.9 19.3 + - - -
361B PHE* 3.6 37.0 - - + -
486B ILE* 3.1 23.9 + - + +
487B GLU* 3.8 6.3 - - - +
489B ALA* 1.3 78.7 - - - +
491B THR* 1.3 60.9 + - - +
492B ASN 4.4 0.2 - - - -
493B GLN* 5.3 0.2 - - - -
500B VAL* 4.1 24.7 - - + -
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Residues in contact with THR 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 3.3 28.9 + - - +
487B GLU* 3.1 14.4 + - - +
488B ALA* 3.5 13.9 - - - +
490B LEU* 1.3 79.7 - - - +
492B ASN* 1.3 56.8 + - - +
493B GLN* 3.2 9.9 + - - +
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Residues in contact with ASN 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG* 2.9 22.0 + - - -
488B ALA 3.4 8.6 + - - +
489B ALA* 3.2 10.4 + - - +
491B THR* 1.3 77.3 - - - +
493B GLN* 1.3 58.1 + - - +
494B ASN* 3.1 33.8 + - - +
495B LEU* 3.2 25.7 + - + +
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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