Contacts of the helix formed by residues 703 - 711 (chain A) in PDB entry 3UEO
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 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702A GLY* 1.3 70.0 - - - -
704A LYS* 1.3 60.7 + - - +
706A GLU* 3.2 9.6 + - - +
707A ALA* 3.0 27.8 + - - +
4F SEP 4.7 0.2 + - - -
5F ASP* 3.0 23.6 + - - -
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Residues in contact with LYS 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A SER* 5.2 1.3 - - - -
653A PHE 3.1 21.3 + - - +
654A SER* 3.8 23.8 + - - +
661A LYS* 5.7 0.2 - - - +
677A GLU* 3.8 24.0 + - - -
678A TYR* 5.6 0.4 - - - +
679A PHE* 3.6 31.7 - - + +
695A LEU* 3.8 22.2 - - + -
702A GLY 3.3 1.0 - - - -
703A SER* 1.3 78.6 - - - +
705A TYR* 1.3 67.8 + - - +
707A ALA* 3.1 8.4 + - - +
708A ALA* 2.9 21.7 + - - +
6F TPO 3.0 33.9 + - - +
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Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A SER* 5.3 0.6 + - - -
695A LEU* 3.7 10.6 - - - +
697A LEU* 3.8 14.3 - - + +
700A ARG* 3.6 15.2 - - + +
701A GLY* 3.3 44.8 + - - +
702A GLY 3.1 2.7 + - - +
704A LYS* 1.3 79.4 - - - +
706A GLU* 1.3 75.9 + - - +
708A ALA* 3.2 3.2 + - - +
709A LYS* 3.1 51.7 + - + +
715A ALA* 4.8 5.6 - - + -
738A ILE* 3.5 33.2 - - + -
739A GLU* 2.7 34.3 + - - -
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Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A GLY* 5.3 1.0 - - - -
702A GLY 3.0 26.1 + - - +
703A SER* 3.6 8.1 - - - +
705A TYR* 1.3 89.7 - - - +
707A ALA* 1.3 57.1 + - - +
709A LYS* 3.2 25.7 + - - +
710A LYS* 2.9 30.1 + - - +
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Residues in contact with ALA 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 4.0 5.2 - - + -
703A SER 3.0 13.3 + - - +
704A LYS* 3.1 9.8 + - - +
706A GLU* 1.3 76.6 - - - +
708A ALA* 1.3 51.4 + - - +
710A LYS* 3.1 8.4 + - - +
711A TRP* 2.7 75.7 + - + +
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Residues in contact with ALA 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.6 24.3 - - + -
695A LEU* 4.3 12.3 - - + -
704A LYS 2.9 13.7 + - - +
705A TYR 3.2 7.4 + - - +
707A ALA* 1.3 74.3 - - - +
709A LYS* 1.3 58.3 + - - +
711A TRP* 4.4 0.9 - - - +
712A ASN* 2.8 26.2 + - - -
713A LEU* 3.0 30.9 + - + +
715A ALA* 4.4 10.5 - - + -
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Residues in contact with LYS 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A TYR* 3.1 51.4 + - + +
706A GLU* 3.5 26.5 + - - +
708A ALA* 1.3 77.7 - - - +
710A LYS* 1.3 63.5 + - - +
712A ASN* 3.4 10.3 + - - +
713A LEU 5.3 0.4 - - - -
739A GLU* 4.8 8.3 + - - +
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Residues in contact with LYS 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A ARG* 4.7 5.9 + - - +
706A GLU 2.9 14.3 + - - +
707A ALA* 3.5 10.5 - - - +
709A LYS* 1.3 79.3 - - - +
711A TRP* 1.3 76.9 + - + +
712A ASN* 3.5 1.4 + - - +
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Residues in contact with TRP 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.4 57.0 - + - -
680A VAL* 3.6 3.4 - - - -
681A ARG* 3.3 85.8 + - + +
707A ALA* 2.7 34.2 + - + +
708A ALA 4.1 0.2 - - - +
710A LYS* 1.3 93.3 - - + +
712A ASN* 1.3 70.2 + - - +
713A LEU* 3.9 22.6 - - + +
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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