Contacts of the helix formed by residues 452 - 463 (chain D) in PDB entry 5UHE
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 PHE 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443D LEU* 4.4 20.6 - - + -
448D ALA 2.9 20.6 + - - +
449D LEU 3.9 3.6 - - - -
451D LEU* 1.3 79.5 - - + +
453D LYS* 1.3 57.4 + - - +
454D PRO* 3.4 3.1 - - - -
455D PHE* 3.1 14.4 + + + -
456D VAL* 2.9 29.0 + - - +
487D LEU* 4.3 5.6 - - + -
490D VAL* 3.7 28.9 - - + -
491D ILE* 3.4 29.8 - - + -
494D HIS* 3.4 43.5 - + + -
496D VAL* 4.2 6.3 - - + -
514D PRO* 4.9 0.4 - - + -
545D LEU* 3.6 31.0 - - + -
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Residues in contact with LYS 453 (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* 5.7 5.3 + - - -
1045C SER* 3.9 8.9 + - - +
1063C PHE* 6.1 1.2 - - - -
1103C TYR* 4.9 4.7 - - - +
449D LEU 3.3 15.1 + - - +
450D GLU* 3.6 39.2 + - - +
451D LEU 3.2 0.6 - - - -
452D PHE* 1.3 78.0 - - - +
454D PRO* 1.3 71.0 - - + +
456D VAL* 4.1 3.7 - - - +
457D MET* 3.2 44.5 + - + +
473D LYS* 3.5 29.2 - - - +
476D VAL* 4.0 23.3 - - + -
477D GLU* 3.6 22.7 + - - +
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Residues in contact with PRO 454 (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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1045C SER* 4.3 4.7 - - - +
1103C TYR* 4.1 17.3 - - + -
1106C ILE* 3.7 28.6 - - + +
1107C VAL* 3.9 20.4 - - + +
424D TYR* 4.0 25.4 - - + +
451D LEU 4.2 8.1 - - - +
452D PHE 3.7 1.6 - - - -
453D LYS* 1.3 95.2 - - + +
455D PHE* 1.3 68.1 + - + +
457D MET* 3.6 11.7 + - + -
458D LYS* 3.1 22.7 + - - +
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Residues in contact with PHE 455 (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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1106C ILE* 3.7 43.5 - - + -
424D TYR* 5.5 0.2 - + - -
451D LEU 4.9 0.7 - - - -
452D PHE* 3.1 25.5 + + + +
454D PRO* 1.3 86.5 - - + +
456D VAL* 1.3 57.3 + - - +
458D LYS* 3.4 20.3 - - + +
459D ARG* 3.5 6.6 + - - +
490D VAL* 3.5 29.9 - - + +
494D HIS* 4.1 26.0 - + - -
545D LEU* 4.5 7.9 - - + -
547D LEU* 4.1 25.6 - - + -
552D GLN* 5.6 1.8 - - - -
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Residues in contact with VAL 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LEU* 4.1 15.9 - - + -
452D PHE 2.9 20.8 + - - +
453D LYS 4.1 3.6 - - - +
454D PRO 3.2 0.2 - - - -
455D PHE* 1.3 74.7 - - - +
457D MET* 1.3 58.2 + - - +
458D LYS 3.0 4.5 - - - -
459D ARG* 3.2 2.3 + - - +
460D LEU* 2.9 39.6 + - + +
476D VAL* 3.9 19.7 - - + -
483D VAL* 4.4 8.7 - - + +
486D VAL* 4.3 9.3 - - + +
487D LEU* 3.8 31.6 - - + -
490D VAL* 3.8 19.1 - - + -
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Residues in contact with MET 457 (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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1103C TYR* 3.1 36.6 - - + +
1107C VAL* 4.2 7.0 - - + -
453D LYS* 3.2 19.6 + - - +
454D PRO* 3.6 19.1 - - + +
456D VAL* 1.3 77.0 - - - +
458D LYS* 1.3 62.5 + - - +
460D LEU* 3.9 2.7 - - - -
461D VAL* 3.5 21.1 + - - +
469D ILE* 3.8 17.6 - - + +
472D ALA* 3.6 26.8 - - + +
473D LYS* 3.6 32.5 - - - -
476D VAL* 3.7 18.2 - - + -
448F VAL* 4.7 2.7 - - + -
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Residues in contact with LYS 458 (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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1106C ILE 3.9 12.1 - - - +
1107C VAL* 3.3 25.1 - - - +
1108C LYS 4.0 4.7 - - - -
1109C GLY* 3.6 29.3 - - - +
454D PRO 3.1 14.5 + - - +
455D PHE* 3.4 16.2 - - + +
457D MET* 1.3 77.2 - - - +
459D ARG* 1.3 63.4 + - + +
460D LEU 3.2 0.2 - - - -
461D VAL* 3.2 15.5 - - + +
462D ASP* 2.8 50.4 + - - +
469D ILE* 4.7 0.8 - - - +
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Residues in contact with ARG 459 (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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455D PHE 3.5 9.5 + - - +
456D VAL 3.2 2.4 + - - -
458D LYS* 1.3 80.9 - - + +
460D LEU* 1.3 62.3 + - - +
462D ASP* 3.7 17.7 - - + +
463D LEU* 3.3 61.8 + - + +
486D VAL* 3.9 18.8 - - + +
489D GLU* 2.9 34.9 + - - +
490D VAL* 4.6 12.1 - - + +
88E GLN* 3.2 42.2 - - - +
90E LYS* 5.7 5.0 - - - +
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Residues in contact with LEU 460 (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* 2.9 24.8 + - + +
457D MET 4.1 4.3 - - - +
458D LYS 3.2 0.4 - - - -
459D ARG* 1.3 75.8 - - - +
461D VAL* 1.3 60.2 + - - +
462D ASP 3.1 4.9 + - - -
463D LEU 3.7 1.0 + - - -
464D ASN 3.4 2.6 + - - -
465D HIS* 3.0 54.3 + - + +
466D ALA* 3.3 5.1 + - + -
472D ALA* 3.8 29.4 - - + +
475D MET* 3.9 18.8 - - + -
476D VAL* 4.0 8.3 - - + -
483D VAL* 3.7 27.1 - - + -
486D VAL* 3.7 27.1 - - + -
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Residues in contact with VAL 461 (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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1107C VAL 5.6 2.9 - - - +
457D MET 3.5 13.1 + - - +
458D LYS* 3.2 19.1 - - + +
460D LEU* 1.3 77.2 - - - +
462D ASP* 1.3 68.1 + - - +
464D ASN* 3.7 11.8 + - - +
466D ALA* 3.4 22.2 - - - +
467D GLN 3.8 4.7 - - - +
468D ASN* 3.6 36.8 - - - +
469D ILE* 4.3 8.1 - - + +
472D ALA* 4.7 0.4 - - - +
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Residues in contact with ASP 462 (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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458D LYS* 2.8 53.1 + - - +
459D ARG* 3.7 16.3 - - + +
460D LEU 3.1 0.2 - - - -
461D VAL* 1.3 81.8 - - - +
463D LEU* 1.3 68.2 + - + +
464D ASN* 3.0 16.4 + - - +
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Residues in contact with LEU 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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459D ARG* 3.3 51.7 + - + +
460D LEU 3.7 0.2 + - - -
462D ASP* 1.3 82.1 - - + +
464D ASN* 1.3 69.0 + - - +
465D HIS* 3.1 32.2 + - + +
486D VAL* 5.1 9.2 - - + -
489D GLU* 4.3 8.3 - - - +
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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