Contacts of the strand formed by residues 464 - 471 (chain D) in PDB entry 4OMC
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 ARG 464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D ASP 5.1 0.2 - - - +
461D ILE* 3.2 10.6 + - - +
463D LYS* 1.3 85.4 + - + +
465D LEU* 1.3 65.9 + - - +
466D GLU* 2.9 39.1 + - - +
550D GLU* 3.5 38.2 + - - +
551D ILE 3.3 13.0 - - - +
552D GLU* 4.5 15.8 + - + +
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Residues in contact with LEU 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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459D LYS* 3.8 36.6 - - + +
460D ASP 3.6 18.2 - - - +
461D ILE* 4.0 15.7 - - + +
464D ARG* 1.3 80.9 - - - +
466D GLU* 1.3 72.4 + - - +
467D VAL* 4.1 9.4 - - + -
549D LEU 3.8 0.3 - - - +
550D GLU* 3.5 3.3 - - - -
551D ILE* 2.8 48.4 + - + +
563D LEU* 4.0 28.3 - - + -
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Residues in contact with GLU 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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464D ARG* 2.9 35.9 + - - +
465D LEU* 1.3 81.9 - - - +
467D VAL* 1.3 64.0 + - - +
468D ARG* 2.7 44.5 + - + +
548D VAL* 3.7 20.2 - - + -
549D LEU 3.4 3.6 - - - +
550D GLU* 4.2 8.7 - - + +
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Residues in contact with VAL 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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454D ILE* 4.1 26.2 - - + -
455D LEU* 4.1 17.3 - - + -
459D LYS* 4.8 12.3 - - + +
465D LEU* 4.1 25.8 - - + -
466D GLU* 1.3 77.6 - - - +
468D ARG* 1.3 65.4 + - - +
469D LYS* 5.6 0.2 - - - +
547D TRP 3.8 0.9 - - - +
548D VAL* 3.3 4.2 - - - -
549D LEU* 2.9 51.4 + - + +
563D LEU* 4.4 14.4 - - + -
566D PHE* 4.3 8.6 - - + -
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Residues in contact with ARG 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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454D ILE* 4.9 0.7 - - - +
466D GLU* 2.7 36.0 + - - +
467D VAL* 1.3 83.1 - - - +
469D LYS* 1.3 66.3 + - - +
546D GLU* 3.2 40.0 + - - +
547D TRP 3.5 3.4 - - - -
548D VAL* 3.7 24.2 - - + +
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Residues in contact with LYS 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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452D ILE* 4.7 7.4 - - - -
453D ASP 5.3 2.4 + - - -
454D ILE* 3.5 54.7 + - + +
468D ARG* 1.3 79.0 - - - +
470D THR* 1.3 76.7 + - - +
471D VAL* 3.7 15.4 + - + +
545D GLY 3.6 1.2 - - - +
546D GLU* 3.4 2.9 - - - +
547D TRP* 2.9 37.7 + - + +
566D PHE* 5.8 1.6 - - + -
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Residues in contact with THR 470 (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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469D LYS* 1.3 91.0 + - - +
471D VAL* 1.3 66.0 + - - +
472D THR* 5.6 3.0 - - + +
545D GLY* 3.3 20.0 - - - -
546D GLU* 3.6 19.5 + - + +
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Residues in contact with VAL 471 (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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452D ILE* 3.8 37.7 - - + -
454D ILE* 4.6 0.7 - - + -
469D LYS* 3.8 24.0 - - + +
470D THR* 1.3 83.1 - - - +
472D THR* 1.3 65.5 + - - +
473D ALA* 3.8 9.6 - - + +
543D PRO 3.5 23.3 - - - +
544D SER* 3.6 1.9 - - - -
545D GLY* 2.8 34.6 + - - +
547D TRP* 3.7 15.5 - - + +
568D LEU* 4.5 4.7 - - + -
570D LEU* 4.9 0.9 - - + -
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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