Contacts of the helix formed by residues 901 - 910 (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 901 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895A CYS* 3.5 12.5 - - - -
899A GLY 3.1 6.4 + - - +
900A LEU* 1.3 79.0 - - - +
902A LEU* 1.3 73.4 + - + +
903A ALA* 4.0 12.5 - - + +
904A GLN* 2.8 30.9 + - - +
905A VAL* 3.7 9.2 + - - +
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Residues in contact with LEU 902 (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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864A HIS* 3.3 40.2 - - + -
865A GLY* 4.5 15.9 - - - +
866A LEU* 3.7 11.9 - - + +
870A GLN* 3.5 20.9 - - - +
891A LEU* 5.1 4.3 - - + -
895A CYS* 4.9 5.2 - - - -
901A THR* 1.3 79.9 - - + +
903A ALA* 1.3 70.5 + - + +
905A VAL* 2.6 20.8 + - - +
906A VAL* 2.9 17.1 + - + -
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Residues in contact with ALA 903 (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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870A GLN* 5.2 6.7 - - - +
901A THR* 4.0 6.2 - - + +
902A LEU* 1.3 82.4 - - + +
904A GLN* 1.3 64.0 + - + +
906A VAL* 4.0 7.2 - - - +
907A ALA* 2.8 25.6 + - - +
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Residues in contact with GLN 904 (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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899A GLY 4.4 0.8 + - - -
900A LEU* 2.9 34.1 - - + +
901A THR* 2.8 40.5 + - - +
902A LEU 2.8 4.6 + - - -
903A ALA* 1.3 78.4 - - + +
905A VAL* 1.3 62.6 + - - +
907A ALA* 3.1 6.9 + - - +
908A ILE* 3.1 25.8 + - - +
936A GLN* 4.1 4.7 + - - +
937A ASP* 3.3 23.2 - - - +
940A VAL* 4.3 18.6 - - + +
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Residues in contact with VAL 905 (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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887A VAL* 4.5 12.3 - - + -
891A LEU* 3.6 30.1 - - + -
894A LEU* 3.3 30.3 - - + -
895A CYS* 4.5 0.9 - - - -
900A LEU* 4.2 17.5 - - + -
901A THR 3.7 13.9 + - - +
902A LEU* 2.6 13.0 + - + +
904A GLN* 1.3 75.4 - - - +
906A VAL* 1.3 62.6 + - + +
908A ILE* 3.3 9.6 - - - +
909A ALA* 3.1 24.4 + - - +
918A LEU* 4.4 13.2 - - + -
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Residues in contact with VAL 906 (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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864A HIS* 5.0 1.6 - - + -
866A LEU* 3.5 28.9 - - + -
870A GLN* 3.9 33.2 - - + +
873A ALA* 5.7 2.2 - - + -
874A ILE* 4.1 18.2 - - + -
887A VAL* 5.6 1.1 - - + -
902A LEU* 2.9 21.9 + - + +
903A ALA* 4.0 7.0 - - - +
905A VAL* 1.3 79.9 - - + +
907A ALA* 1.3 59.7 + - - +
908A ILE 3.1 1.3 - - - -
909A ALA* 4.4 2.5 - - - +
910A SER* 2.3 42.7 + - - +
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Residues in contact with ALA 907 (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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903A ALA 2.8 12.6 + - - +
904A GLN* 3.4 12.3 - - - +
906A VAL* 1.3 78.5 - - - +
908A ILE* 1.3 62.1 + - - +
910A SER* 3.9 6.1 + - - -
911A ASN* 3.1 22.9 + - - -
940A VAL* 5.5 3.1 - - + -
944A SER* 4.2 17.7 - - - -
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Residues in contact with ILE 908 (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* 5.4 2.9 - - + -
904A GLN 3.1 14.7 + - - +
905A VAL* 3.3 12.3 - - - +
907A ALA* 1.3 80.9 - - - +
909A ALA* 1.3 61.6 - - - +
910A SER 3.4 0.7 + - - -
911A ASN* 3.8 13.3 + - - +
914A GLY* 4.5 1.0 - - - -
917A ALA* 3.9 24.0 - - + +
918A LEU* 3.4 35.7 - - + +
921A VAL* 4.3 11.2 - - + -
940A VAL* 3.6 27.4 - - + +
943A ALA* 3.4 38.4 - - + +
944A SER* 4.0 4.0 - - - +
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Residues in contact with ALA 909 (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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874A ILE* 3.4 24.1 - - + +
883A ALA* 3.7 13.2 - - - +
887A VAL* 3.4 34.1 - - + -
905A VAL 3.1 12.2 + - - +
906A VAL 3.5 0.9 + - - +
907A ALA 3.5 0.2 - - - -
908A ILE* 1.3 80.2 - - - +
910A SER* 1.3 58.2 + - - +
911A ASN 3.4 8.5 + - - +
914A GLY* 3.9 9.0 - - - -
918A LEU* 3.7 13.0 - - + -
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Residues in contact with SER 910 (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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873A ALA* 3.6 28.0 - - - +
874A ILE* 3.9 13.0 - - - +
877A ASN* 2.5 28.3 + - - +
906A VAL* 2.3 33.9 + - - +
907A ALA* 4.0 4.7 + - - -
908A ILE 3.3 1.0 - - - -
909A ALA* 1.3 77.3 - - - +
911A ASN* 1.3 59.1 + - - +
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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