Contacts of the helix formed by residues 935 - 944 (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 935 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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929A CYS* 4.1 4.9 - - - -
933A GLY 4.9 2.9 - - - +
934A LEU* 1.3 79.6 - - - +
936A GLN* 1.3 65.8 + - - +
937A ASP* 4.0 8.0 + - - +
938A GLN* 2.8 49.0 + - - +
939A VAL* 3.0 22.3 + - - +
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Residues in contact with GLN 936 (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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898A HIS* 2.4 34.2 + - - +
899A GLY* 4.7 1.5 - - - -
900A LEU* 3.3 26.5 + - + +
904A GLN* 4.1 7.3 + - - +
925A LEU* 4.7 13.8 - - + +
929A CYS* 3.8 22.3 - - - -
935A THR* 1.3 73.2 - - - +
937A ASP* 1.3 64.5 + - - +
939A VAL* 3.2 4.7 + - - +
940A VAL* 3.0 30.4 + - - +
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Residues in contact with ASP 937 (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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904A GLN* 3.3 20.3 - - - +
935A THR* 3.4 6.6 + - - +
936A GLN* 1.3 77.2 + - - +
938A GLN* 1.3 57.6 + - - +
940A VAL* 3.9 11.2 - - + +
941A ALA* 2.7 35.9 + - - +
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Residues in contact with GLN 938 (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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933A GLY 4.3 1.7 - - - +
934A LEU* 3.6 11.1 - - + +
935A THR* 2.8 59.4 + - - +
937A ASP* 1.3 75.7 - - - +
939A VAL* 1.3 62.8 + - - +
941A ALA* 3.5 5.6 - - - +
942A ILE* 3.0 31.2 + - - +
971A ASP* 2.8 33.6 + - - +
974A VAL* 3.9 37.0 - - + +
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Residues in contact with VAL 939 (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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921A VAL* 3.9 19.7 - - + -
924A LEU 5.3 2.2 - - - +
925A LEU* 3.5 29.6 - - + -
928A LEU* 3.7 29.2 - - + -
929A CYS* 5.8 0.4 - - - -
934A LEU* 3.9 13.0 - - + -
935A THR 3.0 9.4 + - - +
936A GLN 3.2 7.4 + - - +
938A GLN* 1.3 74.9 - - - +
940A VAL* 1.3 62.8 + - + +
942A ILE* 3.1 10.6 + - - +
943A ALA* 2.8 33.1 + - - +
952A LEU* 3.9 17.4 - - + +
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Residues in contact with VAL 940 (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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900A LEU* 3.3 44.2 - - + -
904A GLN* 4.3 28.3 - - + +
907A ALA* 5.5 2.0 - - + -
908A ILE* 3.6 18.5 - - + +
921A VAL* 5.1 1.3 - - + -
925A LEU* 5.4 0.4 - - + -
936A GLN 3.0 13.2 + - - +
937A ASP* 3.9 8.5 - - + +
939A VAL* 1.3 85.9 - - + +
941A ALA* 1.3 51.7 - - - +
943A ALA* 3.2 2.8 + - - +
944A SER* 2.3 44.5 + - - +
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Residues in contact with ALA 941 (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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937A ASP 2.7 23.3 + - - +
938A GLN* 3.5 8.1 - - - +
940A VAL* 1.3 68.4 - - - +
942A ILE* 1.3 65.0 + - + +
943A ALA 3.0 1.8 - - - -
944A SER* 2.7 27.1 + - - -
945A ASN* 4.0 1.9 + - - +
974A VAL* 6.0 1.1 - - + -
978A SER* 3.0 19.9 + - - +
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Residues in contact with ILE 942 (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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934A LEU* 4.2 11.4 - - + -
938A GLN 3.0 17.7 - - - +
939A VAL* 3.1 8.5 + - - +
941A ALA* 1.3 78.1 - - + +
943A ALA* 1.3 59.5 + - - +
945A ASN* 4.2 8.1 + - - +
948A GLY* 3.8 11.4 - - - -
951A ALA* 3.8 10.5 - - + +
952A LEU* 3.7 33.7 - - + +
955A VAL* 4.5 12.1 - - + -
974A VAL* 3.7 46.9 - - + +
977A ALA* 3.6 18.6 - - + +
978A SER* 3.3 11.8 + - - -
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Residues in contact with ALA 943 (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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908A ILE* 3.4 29.3 - - + +
911A ASN* 4.8 0.3 + - - -
917A ALA* 4.4 14.1 - - + +
921A VAL* 3.9 18.2 - - + -
939A VAL 2.8 15.5 + - - +
940A VAL 4.2 0.2 - - - -
942A ILE* 1.3 76.0 - - - +
944A SER* 1.3 55.0 + - - +
945A ASN 2.9 18.9 + - - +
948A GLY* 3.8 13.8 - - - -
952A LEU* 4.1 13.9 - - + -
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Residues in contact with SER 944 (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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907A ALA* 4.2 28.3 - - - -
908A ILE* 4.3 4.3 - - - -
911A ASN* 3.2 19.6 + - - +
940A VAL* 2.3 31.3 + - - +
941A ALA* 2.7 21.3 + - - -
943A ALA* 1.3 70.4 - - - +
945A ASN* 1.3 68.0 + - - +
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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