Contacts of the helix formed by residues 792 - 799 (chain A) in PDB entry 6UMW
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 ALA 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790A TRP 4.0 0.4 + - - -
791A THR* 1.3 78.6 - - - +
793A PRO* 1.3 75.7 - - + +
794A GLU* 3.4 27.6 - - - +
795A ALA* 3.0 4.9 + - + +
796A ILE* 2.9 19.2 + - - +
805A SER* 3.5 21.5 + - - -
808A TRP* 3.7 25.7 - - + +
868A ARG* 3.8 1.8 - - - +
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Residues in contact with PRO 793 (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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791A THR 3.7 0.4 - - - -
792A ALA* 1.3 88.0 - - + +
794A GLU* 1.3 60.1 + - - +
796A ILE* 3.3 11.5 + - + +
797A ALA* 2.8 37.1 + - - +
808A TRP* 3.6 37.0 - - + -
837A ILE* 3.9 18.8 - - + -
842A ARG* 5.4 0.4 - - - +
863A LYS* 5.3 11.7 - - + +
868A ARG* 3.9 2.2 - - - +
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Residues in contact with GLU 794 (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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792A ALA* 3.4 13.2 - - - +
793A PRO* 1.3 76.6 - - - +
795A ALA* 1.3 60.2 + - - +
798A TYR* 2.7 51.9 + - + +
799A ARG 3.2 4.2 + - - -
800A LYS* 3.6 28.4 + - + +
802A THR* 4.9 0.3 + - - -
805A SER* 3.7 8.8 + - - -
863A LYS 4.3 4.8 - - - +
865A ARG* 3.6 24.2 - - + +
868A ARG* 2.7 45.6 + - - -
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Residues in contact with ALA 795 (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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786A ILE* 5.8 0.2 - - - +
791A THR* 3.4 20.4 - - + -
792A ALA 3.0 11.6 + - - +
794A GLU* 1.3 79.9 - - - +
796A ILE* 1.3 62.7 + - - +
799A ARG* 3.1 21.4 + - - +
800A LYS 3.6 21.8 - - - +
801A PHE* 3.7 24.4 - - + -
805A SER* 4.2 10.5 - - - -
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Residues in contact with ILE 796 (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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786A ILE* 4.7 11.4 - - + -
788A VAL* 3.7 31.4 - - + +
791A THR* 3.3 36.1 - - + +
792A ALA 2.9 13.5 + - - +
793A PRO* 3.7 8.1 - - + +
795A ALA* 1.3 80.8 - - - +
797A ALA* 1.3 65.8 + - + +
799A ARG* 4.3 8.3 + - - +
833A VAL* 6.5 0.2 - - + -
834A ILE* 4.0 31.6 - - + -
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Residues in contact with ALA 797 (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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793A PRO 2.8 21.8 + - - +
796A ILE* 1.3 78.7 - - + +
798A TYR* 1.3 85.3 + - + +
799A ARG* 5.8 0.2 - - - +
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Residues in contact with TYR 798 (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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794A GLU* 2.7 28.6 + - + +
797A ALA* 1.3 93.8 - - + +
799A ARG* 1.3 67.3 + - - +
800A LYS* 3.1 42.2 + - + +
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Residues in contact with ARG 799 (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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743A ARG* 5.0 3.1 + - - +
786A ILE* 4.3 23.8 - - - +
795A ALA 3.1 20.0 + - - +
796A ILE 5.0 6.8 + - - +
797A ALA 3.8 0.6 - - - -
798A TYR* 1.3 78.1 - - - +
800A LYS* 1.3 58.9 + - - +
801A PHE* 3.2 33.3 + - - -
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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