Contacts of the helix formed by residues 462 - 469 (chain D) in PDB entry 5U03
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 SER 462 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PHE* 4.3 0.2 - - - -
459D THR* 4.2 5.8 - - - -
460D LYS 2.8 5.5 + - - +
461D ASN* 1.3 77.1 + - - +
463D VAL* 1.3 61.7 + - - +
464D MET* 3.8 1.4 - - - +
465D ARG* 3.0 27.7 + - - +
466D LYS* 3.1 27.7 + - - +
500D VAL* 3.4 27.8 - - - +
513D GLU* 2.6 27.0 + - - -
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Residues in contact with VAL 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D ASN* 6.1 0.9 - - - +
462D SER* 1.3 72.9 + - - +
464D MET* 1.3 60.2 + - + +
466D LYS* 3.0 15.6 + - + +
467D LEU* 2.9 43.2 + - + +
513D GLU* 3.2 18.5 + - - +
519D PHE* 5.8 5.2 - - + -
551D LEU* 5.2 11.4 - - + -
555D LEU* 4.5 19.3 - - + -
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Residues in contact with MET 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PHE* 4.8 5.2 - - + -
462D SER* 3.8 1.8 - - - +
463D VAL* 1.3 76.2 - - + +
465D ARG* 1.3 65.9 + - - +
467D LEU* 2.9 21.0 + - - +
468D TYR* 2.8 55.2 + - + -
511D ILE* 4.6 18.2 - - + -
513D GLU* 3.0 22.8 + - + +
519D PHE* 5.3 4.5 - - - -
521D VAL* 4.8 18.8 - - + -
523D VAL* 5.3 3.1 - - + -
525D TYR* 4.1 8.1 - - - +
538D PRO* 4.0 4.5 - - + -
539D PRO* 3.6 43.3 - - + -
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Residues in contact with ARG 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PHE* 3.4 41.3 + - + +
459D THR 3.6 12.4 + - - -
460D LYS* 3.5 33.4 - - - +
462D SER* 3.0 25.1 + - - +
464D MET* 1.3 74.9 - - - +
466D LYS* 1.3 53.5 + - - +
468D TYR* 3.0 4.3 + - - +
469D GLY 2.7 30.8 + - - -
470D ASP* 2.8 46.3 + - - -
471D ALA 2.9 29.6 + - - +
472D ASP* 2.7 32.9 + - - +
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Residues in contact with LYS 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D LYS 4.9 7.9 - - - +
461D ASN* 4.5 16.0 + - - +
462D SER 3.1 21.6 + - - +
463D VAL* 3.0 15.8 + - + +
465D ARG* 1.3 77.4 - - + +
467D LEU* 1.3 61.7 + - - +
469D GLY* 3.1 12.7 + - - +
470D ASP* 4.3 5.8 - - - +
555D LEU* 4.6 22.8 - - + +
559D CYS* 3.5 17.7 - - + -
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Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D VAL* 2.9 28.6 + - + +
464D MET* 2.9 33.6 + - - +
466D LYS* 1.3 76.1 - - - +
468D TYR* 1.3 62.4 + - - +
469D GLY* 4.4 0.5 - - - -
519D PHE* 5.2 3.1 - - + -
538D PRO* 3.7 35.2 - - + +
541D PHE* 5.6 3.6 - - + -
542D GLY* 4.3 13.5 - - - +
545D LEU* 5.1 0.7 - - + -
551D LEU* 4.4 12.3 - - + -
554D TYR* 4.0 19.1 + - + +
555D LEU* 3.9 22.2 - - + -
559D CYS* 4.4 8.2 - - - -
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Residues in contact with TYR 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PHE* 3.8 20.4 - + + -
464D MET* 2.8 45.1 + - + +
465D ARG* 3.4 8.3 - - - +
467D LEU* 1.3 76.7 - - - +
469D GLY* 1.3 59.3 + - - +
471D ALA* 4.8 14.5 - - + +
474D LEU* 3.4 27.3 - - + +
476D GLU* 2.8 27.5 + - - -
511D ILE* 5.2 0.4 - - + -
525D TYR* 2.9 21.1 + - - -
538D PRO* 3.5 30.0 - - + +
539D PRO* 4.5 2.3 - - - +
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Residues in contact with GLY 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ARG 2.7 5.3 + - - -
466D LYS 3.1 10.8 + - - -
467D LEU 4.4 0.7 - - - -
468D TYR* 1.3 78.6 - - - +
470D ASP* 1.3 76.1 + - - +
471D ALA* 3.3 3.8 + - - +
559D CYS* 5.7 1.8 - - - -
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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