Contacts of the helix formed by residues 482 - 491 (chain D) in PDB entry 5UH8
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 GLN 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D LEU* 5.0 1.3 - - + -
465D HIS* 3.8 31.3 + - + +
475D MET* 3.6 30.6 - - + +
480D ARG* 2.9 22.7 + - - +
481D PRO* 1.3 84.1 - - - +
483D VAL* 1.3 65.9 + - - +
485D ASP* 3.0 23.7 + - - +
486D VAL* 3.4 11.3 + - + +
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Residues in contact with VAL 483 (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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449D LEU* 4.0 33.4 - - + -
456D VAL* 4.5 2.6 - - + +
460D LEU* 3.7 30.7 - - + -
475D MET* 4.3 20.0 - - + +
476D VAL* 4.3 9.4 - - + -
479D GLN* 4.6 5.4 - - - -
480D ARG 3.2 17.9 - - - +
482D GLN* 1.3 75.9 - - - +
484D TRP* 1.3 67.4 + - + +
486D VAL* 2.9 11.4 + - - +
487D LEU* 2.6 37.6 + - - +
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Residues in contact with TRP 484 (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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185B GLN* 4.3 33.1 - - + +
797C ARG* 5.6 1.1 - - - -
445D LYS* 3.3 55.6 - - + +
446D LEU* 3.7 25.8 - - + -
449D LEU* 4.3 17.5 - - + -
479D GLN* 3.9 27.3 + - + -
480D ARG 4.2 6.8 + - - -
481D PRO* 3.7 27.0 - - + +
482D GLN 3.1 0.8 + - - -
483D VAL* 1.3 83.8 - - + +
485D ASP* 1.3 62.7 + - - +
487D LEU* 4.2 13.6 - - + +
488D GLU* 3.5 22.0 + - - +
516D LEU* 4.9 5.3 - - + +
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Residues in contact with ASP 485 (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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184B GLU 4.8 8.8 - - - +
481D PRO 3.9 10.0 - - - +
482D GLN* 3.0 14.8 + - - +
484D TRP* 1.3 79.6 - - - +
486D VAL* 1.3 64.6 + - + +
488D GLU* 3.7 11.2 + - - +
489D GLU* 3.8 17.4 - - - +
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Residues in contact with VAL 486 (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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456D VAL* 3.7 23.8 - - + +
459D ARG* 3.7 33.2 - - + +
460D LEU* 3.7 23.8 - - + -
463D LEU* 5.2 7.0 - - + -
465D HIS* 4.8 15.0 - - + +
482D GLN 3.6 14.4 - - - +
483D VAL* 2.9 6.2 + - - +
485D ASP* 1.3 78.3 - - + +
487D LEU* 1.3 66.0 + - - +
489D GLU* 3.1 20.9 + - - +
490D VAL* 3.2 12.4 + - + +
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Residues in contact with LEU 487 (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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445D LYS 4.1 9.0 - - - +
448D ALA* 3.8 28.7 - - + +
449D LEU* 4.0 18.6 - - + +
452D PHE* 3.9 13.7 - - + -
456D VAL* 3.6 28.9 - - + +
483D VAL 2.6 20.1 + - - +
484D TRP* 4.2 13.7 - - + +
486D VAL* 1.3 73.2 - - - +
488D GLU* 1.3 63.1 + - - +
489D GLU 3.1 0.7 + - - -
490D VAL* 3.1 10.4 + - + +
491D ILE* 3.2 31.6 + - + +
516D LEU* 3.8 20.2 - - + -
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Residues in contact with GLU 488 (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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182B ARG* 3.6 42.6 + - - +
445D LYS* 5.4 2.8 - - - -
484D TRP 3.5 15.4 + - - +
485D ASP* 3.9 8.5 - - - +
486D VAL 3.2 0.4 - - - -
487D LEU* 1.3 78.5 - - - +
489D GLU* 1.3 61.6 + - + +
491D ILE* 3.9 14.2 - - - +
492D ALA* 4.3 5.9 + - - +
516D LEU* 3.2 37.2 + - - +
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Residues in contact with GLU 489 (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 ARG* 2.8 38.8 + - - +
463D LEU* 4.5 6.2 - - - +
485D ASP 3.8 16.2 - - - +
486D VAL* 3.1 9.8 + - - +
487D LEU 3.0 0.2 - - - -
488D GLU* 1.3 80.0 - - + +
490D VAL* 1.3 64.4 + - - +
491D ILE 3.3 0.2 - - - -
492D ALA* 3.2 23.1 + - - +
88E GLN* 3.4 39.8 + - + +
90E LYS* 4.0 6.4 + - - -
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Residues in contact with VAL 490 (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 PHE* 3.9 17.7 - - + -
455D PHE* 3.6 47.6 - - + +
456D VAL* 4.0 16.8 - - + -
459D ARG* 4.3 18.2 - - - +
486D VAL* 3.4 14.6 - - + +
487D LEU 3.1 6.4 + - - +
489D GLU* 1.3 77.1 - - - +
491D ILE* 1.3 58.1 + - + +
492D ALA 3.0 5.0 + - - -
494D HIS* 4.3 9.2 + - - +
90E LYS* 3.4 23.5 - - - +
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Residues in contact with ILE 491 (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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443D LEU* 6.0 0.2 - - + -
448D ALA* 4.9 3.1 - - + -
452D PHE* 3.5 39.9 - - + -
487D LEU* 3.4 29.8 - - + +
488D GLU* 3.9 15.5 - - - +
490D VAL* 1.3 74.9 - - - +
492D ALA* 1.3 63.6 + - - +
493D GLU 3.0 4.3 + - - -
494D HIS* 3.5 16.4 + - - -
514D PRO* 3.4 42.6 - - + +
515D MET* 4.7 0.4 - - - -
516D LEU* 3.6 31.9 - - + +
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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