Contacts of the helix formed by residues 703 - 712 (chain B) in PDB entry 4UN5
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 THR 703 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670B ILE* 5.3 0.2 - - + -
671B ARG 3.8 8.1 - - - +
672B ASP* 2.9 21.9 + - - -
673B LYS* 3.4 44.8 - - + +
702B LEU* 1.3 72.1 - - - +
704B PHE* 1.3 68.5 + - + +
705B LYS 3.4 2.2 - - - -
706B GLU* 3.3 28.9 + - - +
707B ASP* 3.2 32.2 + - - +
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Residues in contact with PHE 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 6.1 2.5 - - + -
670B ILE* 3.7 39.2 - - + +
672B ASP* 3.7 17.9 - - + -
677B LYS 3.4 20.2 - - - -
678B THR 3.9 3.1 - - - -
679B ILE* 3.5 35.2 - - + -
682B PHE* 3.6 27.4 - + - -
696B LEU* 3.6 25.6 - - + +
697B ILE* 4.7 7.6 - - + -
702B LEU* 3.5 16.5 - - + -
703B THR* 1.3 79.5 - - + +
705B LYS* 1.3 58.7 + - - +
707B ASP* 3.2 6.9 + - - +
708B ILE* 2.9 37.0 + - + +
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Residues in contact with LYS 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LEU 4.7 0.6 + - - -
697B ILE 3.3 25.1 + - - +
698B HIS* 4.3 23.3 + - + +
699B ASP 4.5 11.2 + - - +
700B ASP* 2.9 35.4 + - - +
702B LEU 4.8 2.4 + - - +
703B THR 3.4 0.4 - - - -
704B PHE* 1.3 77.9 - - - +
706B GLU* 1.3 57.0 + - - +
708B ILE* 3.4 5.6 + - - +
709B GLN* 2.9 57.5 + - - +
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Residues in contact with GLU 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B LYS* 4.1 14.5 + - - -
702B LEU 5.2 1.5 + - - +
703B THR* 3.3 28.9 + - - +
705B LYS* 1.3 80.4 - - - +
707B ASP* 1.3 66.8 + - - +
709B GLN* 3.4 4.9 + - - +
710B LYS* 2.9 58.2 + - - +
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Residues in contact with ASP 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B LEU* 4.7 2.1 - - - +
670B ILE* 3.9 33.4 - - + +
671B ARG 5.0 1.4 - - - +
673B LYS* 5.7 1.4 + - - -
703B THR* 3.2 24.5 + - - +
704B PHE 3.2 6.5 + - - +
706B GLU* 1.3 90.1 - - - +
708B ILE* 1.3 58.4 + - - +
710B LYS* 3.3 11.2 + - - +
711B ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ASN* 3.6 48.2 - - + +
502B LEU* 4.5 9.2 - - + -
666B LEU* 4.2 10.8 - - + -
670B ILE* 5.2 4.3 - - + -
697B ILE* 3.6 38.1 - - + -
704B PHE* 2.9 25.5 + - + +
705B LYS* 3.8 6.1 - - - +
707B ASP* 1.3 72.9 - - - +
709B GLN* 1.3 66.8 + - + +
710B LYS 3.0 1.1 - - - -
711B ALA* 3.0 12.1 + - - +
712B GLN* 3.0 24.3 + - - +
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Residues in contact with GLN 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705B LYS* 2.9 46.7 + - - +
706B GLU* 3.9 4.2 - - - +
708B ILE* 1.3 79.5 - - + +
710B LYS* 1.3 60.8 - - - +
712B GLN* 3.8 17.7 + - - +
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B GLU* 2.9 56.1 + - - +
707B ASP* 3.4 13.0 - - - +
709B GLN* 1.3 78.2 - - - +
711B ALA* 1.3 59.1 + - - +
712B GLN 3.1 13.1 + - - +
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Residues in contact with ALA 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ASN 4.0 3.4 - - - +
502B LEU* 3.7 26.2 - - + -
503B PRO* 3.5 18.0 - - + +
504B ASN* 6.0 1.7 - - - -
707B ASP 2.9 16.5 + - - +
708B ILE 3.0 4.8 + - - +
710B LYS* 1.3 73.0 - - - +
712B GLN* 1.3 66.7 + - - +
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Residues in contact with GLN 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B LYS* 3.2 23.7 + - - +
501B ASN* 3.7 10.6 - - - +
503B PRO* 4.2 14.2 - - + +
708B ILE* 3.0 25.5 - - - +
709B GLN* 3.9 15.1 - - - +
710B LYS 3.1 8.5 + - - +
711B ALA* 1.3 82.9 - - - +
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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
------------------------------------------------------------
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