Contacts of the helix formed by residues 482 - 490 (chain B) in PDB entry 4K9P
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 482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480B GLY 4.2 0.8 - - - -
481B ILE* 1.3 69.0 - - - +
483B PHE* 1.3 59.0 + - - +
484B ARG* 3.3 15.4 + - - +
485B ALA* 3.2 25.7 + - + -
486B LEU* 3.1 23.5 + - - +
520B GLU* 4.0 5.6 - - - +
488D LYS* 3.6 29.2 + - + +
489D GLY* 2.7 24.3 + - - +
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Residues in contact with PHE 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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428B ASP* 3.5 44.4 - - + -
431B ALA* 3.8 22.2 - - + -
432B ASN* 4.2 8.7 - - - -
435B ILE* 5.0 6.3 - - + -
452B ILE* 4.0 19.5 - - + -
454B ASN* 4.0 7.0 - - - -
481B ILE* 3.5 35.9 - - + -
482B ASP* 1.3 70.0 + - - +
484B ARG* 1.3 59.9 + - - +
485B ALA 3.1 1.6 - - - -
486B LEU* 3.2 16.3 + - + +
487B ALA* 2.8 30.3 + - - +
518B LEU* 4.3 19.1 - - + +
520B GLU* 3.3 30.1 + - + +
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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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482B ASP* 3.3 10.0 + - - +
483B PHE* 1.3 76.2 - - - +
485B ALA* 1.3 57.5 + - - +
487B ALA* 3.5 1.7 + - - +
488B LYS* 2.9 28.5 + - - +
494B ALA* 3.7 26.6 + - + +
495B LEU* 3.7 18.7 - - - +
496B LYS* 3.5 45.5 - - - +
518B LEU* 4.8 1.3 - - + +
520B GLU* 3.5 15.9 + - + +
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Residues in contact with ALA 485 (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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482B ASP* 3.2 27.8 + - - +
483B PHE 3.1 0.6 - - - -
484B ARG* 1.3 78.2 - - - +
486B LEU* 1.3 59.8 + - - +
488B LYS* 3.3 8.7 + - + +
489B GLY 2.8 24.6 + - - -
485D ALA* 3.4 27.1 - - + +
488D LYS* 4.1 16.8 - - + -
489D GLY 3.6 10.8 - - - +
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Residues in contact with LEU 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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435B ILE* 4.2 24.5 - - + -
438B LEU* 4.7 2.2 - - - -
481B ILE* 4.1 6.1 - - + -
482B ASP 3.1 16.0 + - - +
483B PHE* 3.2 29.4 + - + +
485B ALA* 1.3 75.0 - - - +
487B ALA* 1.3 62.7 + - - +
489B GLY* 3.2 10.7 + - - -
490B TYR* 3.2 20.1 + - - -
518B LEU* 6.2 0.4 - - + -
435D ILE* 6.2 0.2 - - + -
486D LEU* 3.7 33.3 - - + +
489D GLY* 3.9 4.5 - - - -
490D TYR* 3.6 50.9 - - + +
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Residues in contact with ALA 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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438B LEU* 4.3 12.6 - - - +
483B PHE 2.8 21.0 + - - +
484B ARG 3.6 5.2 - - - +
486B LEU* 1.3 70.5 - - - +
488B LYS* 1.3 61.8 + - - +
490B TYR* 3.2 3.8 + - - +
491B GLY 3.0 5.2 + - - -
492B VAL* 2.8 43.6 + - + +
494B ALA* 3.7 13.2 - - + -
518B LEU* 4.1 22.4 - - + -
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Residues in contact with LYS 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 ARG 2.9 19.4 + - - +
485B ALA* 3.5 7.6 - - + +
487B ALA* 1.3 75.2 - - - +
489B GLY* 1.3 64.2 + - - +
491B GLY* 3.0 14.6 + - - +
492B VAL 3.8 6.7 + - - +
494B ALA* 5.0 1.3 - - + +
480D GLY 5.4 0.2 - - - +
482D ASP* 4.0 22.3 + - + +
485D ALA* 4.0 14.6 - - + +
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Residues in contact with GLY 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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485B ALA 2.8 15.5 + - - -
486B LEU 3.2 4.4 + - - -
488B LYS* 1.3 76.2 - - - +
490B TYR* 1.3 59.7 + - - +
480D GLY 3.7 0.9 - - - +
481D ILE* 3.4 10.0 - - - +
482D ASP* 2.8 45.3 + - - -
485D ALA* 3.7 5.3 - - - +
486D LEU* 3.8 10.5 - - - -
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Residues in contact with TYR 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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45B LEU* 3.6 20.4 - - + -
435B ILE* 4.0 23.3 - - + -
436B SER* 3.5 31.2 - - - -
438B LEU* 4.0 14.0 - - + +
439B TRP* 3.6 43.1 - + + +
442B ALA* 3.4 17.5 - - - +
486B LEU* 3.2 12.7 + - + +
487B ALA 3.2 1.7 + - - +
488B LYS 3.2 0.4 - - - -
489B GLY* 1.3 79.5 - - - +
491B GLY* 1.3 59.6 + - - +
492B VAL 3.5 2.0 - - - -
432D ASN* 3.1 24.0 + - - +
435D ILE* 4.0 12.5 - - + +
480D GLY 4.0 9.3 - - - +
481D ILE* 4.1 5.4 - - + -
486D LEU* 3.5 35.5 - - + +
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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