Contacts of the helix formed by residues 458 - 462 (chain 3) in PDB entry 6Q8W
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 LEU 458 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4013 ASP* 3.5 19.5 - - - +
4023 PRO* 4.2 14.4 - - + -
4033 THR* 3.1 25.4 - - - +
4103 HIS* 4.0 25.6 - - + +
4133 LEU* 3.8 32.5 - - + -
4483 MET* 4.4 9.3 - - + +
4503 LEU* 3.8 15.0 - - + -
4563 ALA* 3.0 4.8 + - + -
4573 PRO* 1.3 76.2 - - - +
4593 MET* 1.3 56.4 + - - +
4603 LYS 3.0 6.3 - - - -
4613 TRP* 2.8 41.5 + - + +
4623 ALA* 3.3 10.0 + - - +
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Residues in contact with MET 459 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4503 LEU* 3.6 31.6 - - + +
4523 ALA 4.1 11.0 - - - +
4543 TYR 3.5 19.7 - - - +
4553 ARG* 3.6 33.4 - - + -
4563 ALA 2.8 16.1 + - - +
4583 LEU* 1.3 76.8 - - - +
4603 LYS* 1.3 62.0 + - - +
4613 TRP 3.2 0.2 - - - -
4623 ALA* 3.2 22.7 - - - +
4653 HIS* 3.5 45.4 + - + -
4663 GLU 4.1 9.0 - - - +
4673 VAL* 4.1 19.3 - - + -
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Residues in contact with LYS 460 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542 GLY* 6.4 0.2 - - - -
4453 THR* 4.6 8.8 - - - +
4563 ALA 4.4 0.6 + - - -
4573 PRO 4.1 11.1 + - - +
4583 LEU 3.0 1.0 - - - -
4593 MET* 1.3 81.1 - - - +
4613 TRP* 1.3 77.2 + - + +
4623 ALA 3.7 1.2 + - - -
4633 ALA* 5.2 0.5 + - - -
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Residues in contact with TRP 461 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1953 PRO 3.4 22.7 - - - -
1963 GLY* 3.5 21.5 - - - -
4103 HIS* 4.1 15.5 - + - -
4133 LEU* 5.7 1.3 - - + -
4143 SER* 4.7 12.1 - - - -
4173 VAL* 4.6 12.3 - - + -
4433 ARG* 3.3 59.4 - - + +
4443 ARG 3.0 27.1 - - - +
4453 THR* 3.5 10.9 - - - -
4483 MET* 4.0 17.3 - - - +
4573 PRO 4.9 8.3 - - - -
4583 LEU* 2.8 31.2 + - + +
4603 LYS* 1.3 95.7 - - + +
4623 ALA* 1.3 58.1 + - - +
4633 ALA 3.8 1.1 - - - -
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Residues in contact with ALA 462 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4483 MET* 3.8 28.0 - - + +
4503 LEU* 3.9 32.8 - - + +
4583 LEU 3.3 10.3 + - - +
4593 MET* 3.2 10.1 + - - +
4603 LYS 3.4 1.7 - - - -
4613 TRP* 1.3 76.1 - - - +
4633 ALA* 1.3 53.8 + - - +
4643 ILE 3.3 3.0 + - - +
4653 HIS* 2.7 30.4 + - + -
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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