Contacts of the helix formed by residues 867 - 876 (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 THR 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830A HIS* 5.6 0.2 - - - -
865A GLY 3.0 9.2 + - - +
866A LEU* 1.3 79.3 - - - +
868A PRO* 1.3 76.9 - - + +
869A ALA* 3.0 12.6 + - - +
870A GLN* 3.1 35.6 + - - +
871A VAL* 3.4 7.3 + - - +
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Residues in contact with PRO 868 (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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830A HIS* 3.0 38.3 - - + +
831A GLY* 3.3 35.4 - - - +
836A GLN* 5.6 0.4 - - - +
857A LEU* 4.2 11.0 - - + -
866A LEU 3.6 0.6 - - - -
867A THR* 1.3 90.6 - - + +
869A ALA* 1.3 53.8 + - + +
871A VAL* 3.1 11.2 + - + +
872A VAL* 2.8 39.2 + - - +
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Residues in contact with ALA 869 (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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836A GLN* 4.4 13.5 - - - +
867A THR* 3.6 14.8 - - - +
868A PRO* 1.3 82.2 - - + +
870A GLN* 1.3 64.3 + - + +
872A VAL* 2.9 14.7 + - - +
873A ALA* 2.9 13.3 + - - +
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Residues in contact with GLN 870 (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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865A GLY 4.7 0.5 - - - -
866A LEU* 3.0 45.8 - - + +
867A THR* 3.1 18.8 + - - +
869A ALA* 1.3 79.5 - - + +
871A VAL* 1.3 62.8 + - - +
873A ALA* 3.2 10.8 + - - +
874A ILE* 3.1 24.3 + - - +
902A LEU* 3.5 22.7 - - - +
903A ALA* 5.2 6.7 - - - +
906A VAL* 3.9 23.9 - - + +
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Residues in contact with VAL 871 (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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853A VAL* 3.5 32.3 - - + -
856A LEU 5.5 0.2 - - - +
857A LEU* 3.9 30.3 - - + +
860A LEU* 4.6 13.5 - - + -
866A LEU* 3.1 32.9 - - + +
867A THR 3.4 1.6 + - - +
868A PRO 3.1 13.2 + - - +
870A GLN* 1.3 78.8 - - - +
872A VAL* 1.3 62.7 + - + +
874A ILE* 2.7 25.0 + - - +
875A ALA* 3.1 10.9 + - - +
884A LEU* 4.2 9.5 - - + +
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Residues in contact with VAL 872 (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* 3.4 31.2 - - + -
836A GLN* 3.5 38.6 - - + +
839A ALA* 5.5 1.3 - - + -
840A ILE* 3.3 24.2 - - + +
853A VAL* 5.2 0.7 - - + -
868A PRO 2.8 23.3 + - - +
869A ALA 2.9 7.2 + - - +
871A VAL* 1.3 81.5 - - + +
873A ALA* 1.3 51.5 + - - +
876A SER* 2.6 44.8 + - - -
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Residues in contact with ALA 873 (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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869A ALA 2.9 10.8 + - - +
870A GLN* 3.3 14.4 - - - +
871A VAL 3.0 0.4 + - - -
872A VAL* 1.3 74.3 - - - +
874A ILE* 1.3 65.5 + - - +
875A ALA 3.4 0.2 + - - -
876A SER* 3.9 10.5 + - - -
877A ASN* 3.3 20.6 + - - -
906A VAL* 5.7 2.5 - - + -
910A SER* 3.6 15.3 - - - +
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Residues in contact with ILE 874 (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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866A LEU* 4.1 19.1 - - + -
870A GLN 3.1 17.0 - - - +
871A VAL* 2.7 11.6 + - - +
873A ALA* 1.3 73.9 - - - +
875A ALA* 1.3 59.1 + - - +
877A ASN* 3.8 12.3 - - - +
880A GLY* 4.3 2.3 - - - -
883A ALA* 3.6 33.4 - - + +
884A LEU* 3.7 15.3 - - + -
887A VAL* 3.8 24.9 - - + -
906A VAL* 4.1 18.8 - - + -
909A ALA* 3.4 24.0 - - + +
910A SER* 3.9 13.7 - - - -
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Residues in contact with ALA 875 (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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840A ILE* 3.4 30.8 - - + +
849A ALA* 3.9 10.5 - - + +
853A VAL* 4.6 7.9 - - + -
871A VAL 3.1 7.7 + - - +
872A VAL* 4.8 0.2 - - - -
874A ILE* 1.3 78.4 - - - +
876A SER* 1.3 56.5 + - - +
877A ASN 2.8 17.8 + - - +
880A GLY* 4.2 10.5 - - - -
884A LEU* 3.6 31.9 - - + -
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Residues in contact with SER 876 (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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839A ALA* 3.6 29.9 - - - +
840A ILE* 3.7 7.9 - - - +
843A ASN* 2.3 25.9 + - - +
872A VAL* 2.6 27.3 + - - -
873A ALA* 4.1 9.6 + - - -
874A ILE 3.7 0.8 - - - -
875A ALA* 1.3 68.9 - - - +
877A ASN* 1.3 55.7 + - - +
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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