Contacts of the helix formed by residues 480 - 494 (chain B) in PDB entry 3V4R
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 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479B ILE* 1.4 75.3 - - - +
481B THR* 1.4 65.7 + - - +
482B LEU* 3.3 7.6 - - + +
483B GLU* 3.2 15.9 + - + +
484B ARG* 3.0 22.2 + - - +
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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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482A LEU* 4.1 14.8 - - + -
68B THR* 3.4 21.7 + - - +
480B LYS* 1.4 72.2 - - - +
482B LEU* 1.4 58.2 + - - +
484B ARG* 3.5 20.4 + - - +
485B ILE* 3.1 49.2 + - + +
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Residues in contact with LEU 482 (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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481A THR 4.0 6.5 - - - +
482A LEU* 3.7 31.2 - - + +
485A ILE* 3.6 37.2 - - + -
480B LYS* 3.3 5.0 - - + +
481B THR* 1.4 79.4 - - - +
483B GLU* 1.3 56.0 + - - +
485B ILE* 3.3 9.4 + - + +
486B GLU* 2.9 65.5 + - - +
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Residues in contact with GLU 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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476B HIS* 4.3 18.3 - - - -
478B GLU 4.1 4.3 - - - +
479B ILE* 3.3 31.1 - - + +
480B LYS* 3.2 18.2 + - + +
482B LEU* 1.3 72.9 - - - +
484B ARG* 1.4 56.9 + - - +
486B GLU* 3.8 11.3 - - + +
487B ILE* 2.9 45.7 + - + +
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Residues in contact with ARG 484 (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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68B THR* 3.9 17.6 + - - +
72B GLN* 5.5 3.6 - - - +
479B ILE* 5.1 10.0 - - + +
480B LYS 3.0 13.1 + - - +
481B THR* 3.5 31.8 + - - +
483B GLU* 1.4 73.1 - - - +
485B ILE* 1.4 81.3 + - - +
487B ILE* 2.9 33.3 + - + +
488B ILE* 3.1 28.7 + - + +
506B ARG* 4.9 12.8 - - + +
507B GLU* 3.1 49.7 + - - +
508B GLY* 4.2 3.4 - - - +
509B LEU* 6.1 0.7 - - + -
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Residues in contact with ILE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 4.4 20.9 - - + +
485A ILE* 4.6 18.8 - - + -
486A GLU* 5.3 7.9 - - + -
489A ARG* 3.5 34.0 + - - +
481B THR* 3.1 37.3 + - + +
482B LEU* 3.6 7.4 - - + +
484B ARG* 1.4 98.1 - - - +
486B GLU* 1.4 55.4 + - - +
488B ILE* 4.0 7.6 - - - +
489B ARG* 3.2 27.3 + - + +
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Residues in contact with GLU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ILE* 4.2 14.4 - - + +
482B LEU* 2.9 43.9 + - + +
483B GLU* 3.8 8.2 - - - +
485B ILE* 1.4 73.5 - - - +
487B ILE* 1.3 62.5 - - + +
489B ARG* 3.3 42.9 + - - +
490B ASP* 3.0 31.0 + - - +
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Residues in contact with ILE 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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473B ASN* 3.4 41.7 - - + +
475B LEU* 3.8 28.7 - - + -
483B GLU* 2.9 23.7 + - + +
484B ARG* 2.9 22.7 + - + +
486B GLU* 1.3 77.5 - - + +
488B ILE* 1.3 60.3 + - + +
490B ASP* 3.5 4.6 + - + +
491B LEU* 3.0 28.3 + - - +
496B TYR* 3.9 18.3 - - + +
499B LEU* 4.6 6.4 - - + +
509B LEU* 5.5 1.1 - - + -
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Residues in contact with ILE 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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489A ARG* 6.2 3.4 - - - +
484B ARG* 3.1 32.0 + - + +
485B ILE* 4.0 7.2 - - - +
487B ILE* 1.3 73.6 - - + +
489B ARG* 1.4 57.0 + - - +
491B LEU* 3.2 11.7 + - + +
492B ARG* 2.8 40.0 + - + +
499B LEU* 5.6 0.2 - - - -
507B GLU 3.5 24.9 - - - +
508B GLY* 3.8 16.4 - - - +
509B LEU* 3.7 24.7 - - + -
511B ILE* 3.8 26.2 - - + -
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ILE* 3.6 31.0 + - - +
489A ARG* 3.8 41.7 - - + +
492A ARG* 6.2 4.5 - - - +
493A LEU* 5.3 3.1 - - + +
485B ILE* 3.2 18.5 + - - +
486B GLU* 3.3 43.4 + - - +
488B ILE* 1.4 79.9 - - - +
490B ASP* 1.4 56.4 + - - +
492B ARG* 3.3 10.2 + - - +
493B LEU* 2.9 37.3 + - + +
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Residues in contact with ASP 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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486B GLU 3.0 17.1 + - - +
487B ILE* 3.6 2.2 - - + +
489B ARG* 1.4 81.4 - - - +
491B LEU* 1.4 54.9 + - - +
493B LEU* 3.4 5.0 + - - +
494B GLY 2.9 9.7 + - - -
495B LYS* 2.9 48.9 + - + +
496B TYR* 3.6 28.3 - - + +
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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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447B ARG* 3.0 34.9 + - + +
448B VAL 4.6 1.1 - - - +
449B LEU* 3.8 15.9 - - + -
487B ILE 3.0 15.5 + - - +
488B ILE* 3.2 11.0 + - - +
490B ASP* 1.4 71.2 - - - +
492B ARG* 1.4 58.2 + - - +
494B GLY 3.5 2.6 + - - -
496B TYR* 3.5 26.8 - - + +
497B ASP 4.0 19.7 - - - +
498B VAL 4.1 5.8 - - - +
499B LEU* 3.7 39.9 - - + +
509B LEU* 5.5 2.5 - - + -
511B ILE* 3.8 24.9 - - + -
514B VAL* 4.3 2.2 - - + -
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Residues in contact with ARG 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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489A ARG* 6.3 0.4 - - - +
493A LEU* 3.6 47.0 + - + +
447B ARG* 3.3 17.8 + - - -
488B ILE* 2.8 24.9 + - - +
489B ARG* 3.4 10.3 - - - +
491B LEU* 1.4 70.1 - - - +
493B LEU* 1.4 61.6 + - - +
494B GLY 3.2 0.9 - - - -
511B ILE* 3.9 35.6 - - + +
512B PRO* 3.8 35.2 - - - +
513B GLU* 4.9 11.7 - - - +
589B ASN* 4.1 27.3 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG* 5.3 19.5 - - + +
493A LEU* 4.7 8.0 - - + +
447B ARG* 4.2 3.5 + - - -
489B ARG* 2.9 24.4 + - + +
490B ASP* 4.0 6.1 - - - +
492B ARG* 1.4 72.1 - - - +
494B GLY* 1.3 58.1 + - - +
495B LYS* 3.6 2.7 - - + +
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Residues in contact with GLY 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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447B ARG* 3.8 25.1 - - - -
471B LYS* 5.3 0.7 - - - +
490B ASP 2.9 4.3 + - - -
491B LEU 3.5 0.2 + - - -
492B ARG 3.2 4.4 - - - -
493B LEU* 1.3 77.2 - - - +
495B LYS* 1.4 64.9 + - - +
496B TYR 3.1 11.2 + - - +
497B ASP* 4.1 10.8 - - - +
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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