Contacts of the helix formed by residues 445 - 452 (chain D) in PDB entry 5UHF
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 LYS 445 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B ARG* 6.3 0.2 - - - +
185B GLN* 3.5 25.3 + - - +
187B THR* 4.3 13.1 - - - +
443D LEU 3.6 0.6 + - - -
444D PRO* 1.3 71.6 - - - +
446D LEU* 1.3 64.6 + - + +
448D ALA* 3.4 2.8 + - - +
449D LEU 3.2 19.2 + - - -
484D TRP* 3.7 49.1 + - + +
487D LEU* 4.0 0.9 - - - +
488D GLU* 5.3 3.6 - - - -
516D LEU* 4.1 29.4 - - + -
517D VAL 3.3 27.6 + - - +
518D GLU* 2.9 41.9 + - - +
519D GLY 4.4 2.3 + - - +
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Residues in contact with LEU 446 (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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1041C ILE* 4.7 11.7 - - + -
1043C ALA* 5.8 0.2 - - - +
444D PRO* 3.2 1.0 - - - +
445D LYS* 1.3 78.5 - - + +
447D MET* 1.3 61.8 + - - +
449D LEU* 4.2 8.4 + - + +
450D GLU* 4.3 9.5 + - - +
479D GLN* 3.7 32.8 - - - +
484D TRP* 3.9 14.8 - - + -
519D GLY 4.7 6.4 + - - +
520D LYS* 3.6 38.6 - - + +
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Residues in contact with MET 447 (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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1041C ILE* 3.6 25.4 - - + -
1042C HIS 3.9 4.9 - - - +
1043C ALA* 3.8 20.2 - - + +
426D GLY* 3.7 30.7 - - - -
427D ARG 3.9 3.1 - - - +
428D SER* 4.0 12.3 - - - -
443D LEU* 4.9 4.0 - - + -
444D PRO* 3.2 20.7 + - + +
446D LEU* 1.3 79.6 - - - +
448D ALA* 1.3 63.9 + - - +
450D GLU* 3.4 6.9 + - - +
451D LEU* 3.3 32.7 + - + +
522D ILE* 3.9 28.0 - - - -
543D VAL* 4.0 17.7 - - + -
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Residues in contact with ALA 448 (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* 4.3 17.9 - - + +
444D PRO 3.0 15.3 + - - +
445D LYS 3.4 0.6 + - - +
447D MET* 1.3 78.2 - - - +
449D LEU* 1.3 64.2 + - - +
451D LEU* 3.0 15.1 + - - -
452D PHE* 3.1 27.8 + - + +
487D LEU* 3.8 12.8 - - + -
491D ILE* 4.7 1.8 - - + -
516D LEU* 3.6 24.9 - - + -
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Residues in contact with LEU 449 (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 3.2 13.9 + - - +
446D LEU* 4.4 6.5 - - + +
447D MET 3.3 0.6 - - - -
448D ALA* 1.3 78.1 - - - +
450D GLU* 1.3 59.3 + - - +
452D PHE 4.0 1.4 - - - -
453D LYS* 3.5 19.4 + - - +
456D VAL* 4.6 14.6 - - + -
476D VAL* 3.8 37.0 - - + +
479D GLN* 4.5 10.8 - - + +
483D VAL* 4.0 31.4 - - + -
484D TRP* 3.9 24.7 - - + -
487D LEU* 3.5 21.0 - - + +
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Residues in contact with GLU 450 (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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841C HIS* 5.1 6.3 + - - -
1043C ALA* 4.0 9.4 - - + +
1044C ARG* 3.7 15.7 - - - +
1045C SER* 2.8 45.2 + - - +
1046C THR 4.5 0.2 - - - +
1063C PHE* 3.2 25.5 - - + -
446D LEU 4.3 6.4 + - - +
447D MET 3.4 8.8 + - - +
448D ALA 3.1 0.4 - - - -
449D LEU* 1.3 77.0 - - - +
451D LEU* 1.3 64.3 + - - +
452D PHE 3.2 2.0 - - - -
453D LYS* 3.2 39.2 + - - +
476D VAL* 5.8 2.1 - - - +
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Residues in contact with LEU 451 (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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1043C ALA* 4.6 7.2 - - + -
1044C ARG 3.9 5.8 - - - +
424D TYR* 3.4 53.1 - - - +
425D SER* 3.4 16.4 - - - +
443D LEU* 4.4 15.5 - - + -
447D MET* 3.3 17.2 + - + +
448D ALA 3.0 8.4 + - - +
450D GLU* 1.3 80.3 - - - +
452D PHE* 1.3 70.0 + - + +
453D LYS 3.3 1.7 + - - -
454D PRO* 4.5 0.9 - - - +
455D PHE* 4.6 1.4 - - - -
496D VAL* 5.2 1.6 - - + -
543D VAL* 3.7 30.5 - - + +
545D LEU* 3.3 27.6 - - + +
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Residues in contact with PHE 452 (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* 4.7 4.9 - - + -
448D ALA* 3.1 27.4 + - + +
449D LEU 4.0 3.6 - - - -
451D LEU* 1.3 85.0 - - + +
453D LYS* 1.3 52.6 + - - +
454D PRO* 3.5 2.7 - - - -
455D PHE* 2.9 15.2 + + + -
456D VAL* 2.7 36.2 + - - +
487D LEU* 4.1 7.2 - - + -
490D VAL* 3.7 27.6 - - + -
491D ILE* 3.5 32.1 - - + -
494D HIS* 3.7 32.8 - + + -
496D VAL* 4.3 14.8 - - + -
514D PRO* 5.0 0.9 - - + -
545D LEU* 3.5 36.1 - - + -
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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