Contacts of the helix formed by residues 582 - 586 (chain C) 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 SER 582 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG* 3.3 26.6 - - - +
480C TYR* 5.0 0.7 + - - -
503C TYR* 3.7 30.9 + - - -
544C ALA* 3.5 10.0 - - - +
580C ASP* 4.1 2.3 - - - +
581C VAL* 1.3 81.2 - - - +
583C PRO* 1.3 81.7 - - - +
584C ARG* 3.3 13.1 - - - +
585C GLN* 3.1 20.9 + - - +
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Residues in contact with PRO 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 3.9 27.8 - - - +
45C ARG* 5.3 6.5 - - + -
480C TYR* 4.6 1.3 + - - +
544C ALA* 3.5 16.4 - - + -
545C ASN* 4.8 7.6 - - + -
581C VAL 4.7 0.4 - - - +
582C SER* 1.3 92.9 - - - +
584C ARG* 1.3 57.8 + - + +
585C GLN* 2.8 8.5 + - - +
586C MET 4.5 1.0 + - - -
976C VAL 4.0 2.7 - - - +
977C PHE* 3.4 49.5 - - + +
978C ASP* 4.5 9.6 - - + +
846D VAL* 4.0 20.2 - - + +
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Residues in contact with ARG 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASN* 5.5 2.8 - - - +
45C ARG* 3.2 36.9 - - - +
50C VAL* 3.6 15.9 - - - +
502C VAL* 4.8 3.1 - - - +
503C TYR* 3.1 35.7 + - - +
582C SER* 3.3 17.1 + - - +
583C PRO* 1.3 76.3 - - + +
585C GLN* 1.3 55.9 + - - +
586C MET 3.7 1.3 - - - -
587C VAL* 3.5 25.7 - - + +
592C ALA* 5.4 2.5 - - + -
628C THR* 4.0 18.6 + - - -
629C GLY* 4.7 3.0 - - - -
630C MET* 4.2 29.0 - - - +
975C PRO* 4.7 17.3 - - - +
976C VAL* 3.6 28.9 + - + +
977C PHE* 4.5 6.5 - - - -
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Residues in contact with GLN 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C TYR* 4.8 7.5 - - + +
481C GLY* 3.1 21.8 - - - +
501C SER* 3.7 9.0 - - - -
502C VAL 4.7 1.7 + - - -
503C TYR* 4.1 23.2 + - + -
514C THR* 2.9 26.3 + - - +
515C PRO* 3.3 17.5 + - - -
516C TYR* 3.7 16.2 + - - -
580C ASP* 3.5 10.5 + - - +
581C VAL* 2.8 31.4 + - - -
582C SER 3.1 17.5 + - - +
583C PRO 2.8 8.2 + - - +
584C ARG* 1.3 71.3 - - - +
586C MET* 1.3 64.8 + - - +
587C VAL 3.2 3.9 + - - +
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Residues in contact with MET 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C TYR* 3.6 25.6 - - + -
481C GLY 3.6 11.5 + - - +
483C MET 3.9 1.4 - - - +
484C CYS* 3.7 0.2 - - - -
485C PRO* 3.4 38.4 - - + +
486C ILE* 5.1 4.3 - - + -
501C SER* 2.9 15.4 + - - -
583C PRO 4.5 0.4 + - - -
585C GLN* 1.3 79.2 - - - +
587C VAL* 1.3 73.1 + - + +
597C LEU* 6.3 0.2 - - + -
977C PHE* 3.6 24.7 - - + -
846D VAL* 3.9 22.9 - - + +
849D TYR* 4.4 16.4 - - + +
850D PHE* 3.5 43.1 - - + +
853D THR* 4.9 0.4 - - - +
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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