Contacts of the helix formed by residues 834 - 842 (chain A) in PDB entry 3UGM
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 PRO 834 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A GLY 5.5 7.0 - - - +
798A LEU* 6.2 1.6 - - + -
802A GLN* 5.3 2.9 - - - +
823A LEU* 4.9 11.4 - - + +
827A CYS* 4.9 5.2 - - - -
833A THR* 1.3 93.1 - - - +
835A ASP* 1.3 68.7 + - - +
836A GLN 3.4 0.2 - - - -
837A VAL* 3.9 3.1 + - - +
838A VAL* 2.9 32.0 + - + +
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Residues in contact with ASP 835 (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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802A GLN* 4.8 9.6 + - - +
833A THR* 3.3 8.7 - - + +
834A PRO* 1.3 82.4 - - - +
836A GLN* 1.3 66.4 + - + +
838A VAL* 3.1 11.1 - - - +
839A ALA* 3.1 21.5 + - - +
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Residues in contact with GLN 836 (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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831A GLY 3.3 20.8 + - - +
832A LEU* 3.6 15.4 - - + -
833A THR* 2.9 43.7 + - + +
835A ASP* 1.3 75.3 - - + +
837A VAL* 1.3 65.6 + - - +
839A ALA* 2.8 18.8 + - - +
840A ILE* 2.9 12.9 + - - +
868A PRO* 5.6 0.5 - - - +
869A ALA* 4.4 12.1 - - - +
872A VAL* 3.5 35.1 - - + +
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Residues in contact with VAL 837 (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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819A VAL* 4.5 9.4 - - + -
823A LEU* 3.6 30.3 - - + +
826A LEU* 3.4 32.3 - - + -
827A CYS* 5.1 2.0 - - - -
832A LEU* 3.4 32.7 - - + +
833A THR 4.5 5.4 - - - +
834A PRO 3.9 5.3 + - - +
836A GLN* 1.3 77.7 - - - +
838A VAL* 1.3 66.6 + - - +
840A ILE* 2.9 9.5 + - - +
841A ALA* 2.9 19.8 + - - +
850A LEU* 3.7 19.5 - - + -
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Residues in contact with VAL 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A LEU* 3.7 26.9 - - + -
802A GLN* 3.7 29.6 - - + +
805A ALA* 5.9 0.4 - - + -
806A ILE* 3.8 25.6 - - + +
823A LEU* 5.1 7.4 - - + -
834A PRO 2.9 22.6 + - - +
835A ASP 3.1 9.2 + - - +
837A VAL* 1.3 77.9 - - - +
839A ALA* 1.4 57.0 + - - +
841A ALA* 3.0 4.5 + - - +
842A SER* 2.9 39.0 + - - +
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Residues in contact with ALA 839 (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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835A ASP 3.1 10.0 + - - +
836A GLN* 2.8 15.0 + - - +
838A VAL* 1.4 70.5 - - - +
840A ILE* 1.3 65.5 + - - +
841A ALA 3.4 0.2 + - - -
842A SER* 3.6 12.1 + - - -
843A ASN* 3.6 16.1 + - - -
872A VAL* 5.5 1.8 - - + -
876A SER* 3.6 16.7 - - - +
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Residues in contact with ILE 840 (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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832A LEU* 4.1 8.7 - - + -
836A GLN 2.9 15.1 + - - +
837A VAL* 3.0 16.4 - - - +
839A ALA* 1.3 78.3 - - - +
841A ALA* 1.3 56.5 + - - +
843A ASN* 3.9 11.3 + - - +
846A GLY* 4.8 1.4 - - - -
849A ALA* 4.0 21.9 - - + +
850A LEU* 3.6 31.2 - - + +
853A VAL* 4.3 10.3 - - + -
872A VAL* 3.3 42.8 - - + +
875A ALA* 3.4 22.2 - - + +
876A SER* 3.3 13.5 - - - +
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Residues in contact with ALA 841 (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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806A ILE* 3.9 29.0 - - + +
809A ASN* 4.3 0.7 + - - -
815A ALA* 4.8 6.4 - - + +
819A VAL* 4.1 20.6 - - + -
837A VAL 2.9 14.4 + - - +
838A VAL 3.5 4.5 - - - +
840A ILE* 1.3 76.1 - - - +
842A SER* 1.3 55.3 + - - +
843A ASN 2.9 17.2 + - - +
846A GLY* 4.7 11.1 - - - -
850A LEU* 4.2 14.8 - - + -
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Residues in contact with SER 842 (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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805A ALA* 4.1 13.4 - - - +
806A ILE* 3.9 22.9 + - - +
809A ASN* 2.8 25.4 + - - +
838A VAL* 2.9 20.3 + - - +
839A ALA* 3.6 10.4 + - - -
840A ILE 3.6 1.8 - - - -
841A ALA* 1.3 73.7 - - - +
843A ASN* 1.3 63.1 + - - +
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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