Contacts of the helix formed by residues 434 - 439 (chain F) in PDB entry 5UHA
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 434 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400D LYS* 4.3 12.5 + - - +
410D GLN* 4.1 29.5 + - - +
423F LEU 4.4 6.1 - - - +
424F ASP* 4.2 23.0 - - - +
425F GLN 3.8 3.6 - - - +
426F THR* 3.7 18.3 - - + +
427F ILE* 5.7 1.3 - - - -
432F ASP 3.4 9.3 + - - +
433F SER* 1.3 74.1 - - - +
435F LEU* 1.3 66.5 + - - +
436F GLY* 4.4 1.8 - - - +
437F ASP* 2.9 46.4 + - - +
438F PHE* 4.2 6.6 + - - -
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Residues in contact with LEU 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D LEU* 4.6 9.4 - - + -
336D ALA* 4.0 23.8 - - + -
421F ILE* 4.0 16.8 - - + -
422F SER 3.9 17.3 - - - +
423F LEU* 3.6 16.6 - - + +
425F GLN* 3.2 18.7 + - + +
426F THR* 4.7 0.4 - - - +
427F ILE* 5.4 10.0 - - + +
433F SER 4.3 1.0 + - - -
434F GLN* 1.3 69.6 - - - +
436F GLY* 1.3 57.5 + - - +
438F PHE* 2.9 37.8 + - + +
439F ILE* 3.7 15.9 + - + +
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Residues in contact with GLY 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050C SER* 5.0 6.4 + - - -
1051C MET* 5.4 0.7 + - - +
1052C ILE* 5.1 12.2 - - - +
1057C LEU* 5.2 0.5 - - - +
423F LEU* 3.4 33.6 + - - -
434F GLN* 3.0 3.5 + - - +
435F LEU* 1.3 78.3 - - - +
437F ASP* 1.3 60.0 + - - +
438F PHE 3.0 5.0 + - - -
439F ILE* 3.2 18.7 + - - +
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Residues in contact with ASP 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050C SER* 5.8 2.0 - - - -
1057C LEU* 3.5 23.0 - - - +
1058C GLY 4.7 4.2 + - - -
410D GLN* 5.6 0.3 - - - +
432F ASP 4.2 4.2 - - - +
433F SER* 5.0 0.7 - - - -
434F GLN* 2.9 47.3 + - - +
436F GLY* 1.3 77.4 - - - +
438F PHE* 1.3 73.8 + - + +
439F ILE 3.6 0.4 - - - -
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Residues in contact with PHE 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057C LEU* 3.9 12.2 - - - +
1058C GLY 4.2 10.3 - - - -
1059C GLY* 6.1 0.2 - - - -
1062C GLN* 4.2 37.6 + - - +
427F ILE* 5.7 7.9 - - + -
433F SER* 5.2 8.5 - - - -
434F GLN 4.9 6.1 - - - -
435F LEU* 2.9 24.4 + - + +
437F ASP* 1.3 97.5 - - + +
439F ILE* 1.3 61.8 + - + +
440F GLU* 3.0 10.1 + - - +
19G G 3.8 32.8 - + - -
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Residues in contact with ILE 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049C TYR 4.3 0.7 - - - +
1051C MET* 3.7 47.3 + - + +
1057C LEU* 4.4 5.0 - - - +
328D VAL* 4.2 17.7 - - + -
330D LEU* 3.6 30.5 - - + -
423F LEU* 3.8 25.8 - - + -
435F LEU* 3.9 19.1 - - + +
436F GLY* 3.2 11.8 + - - +
437F ASP 3.6 0.2 - - - -
438F PHE* 1.3 76.4 - - + +
440F GLU* 1.3 67.6 + - - +
441F ASP 3.4 2.1 + - - -
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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