Contacts of the helix formed by residues 969 - 977 (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 969 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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963A CYS* 4.0 1.1 - - - -
968A LEU* 1.3 74.2 - - - +
970A PRO* 1.3 65.7 - - + +
971A ASP* 2.6 22.4 + - - +
972A GLN* 2.6 50.2 + - - +
973A VAL* 3.2 11.3 + - - +
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Residues in contact with PRO 970 (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* 4.5 17.5 - - - +
934A LEU* 4.7 8.9 - - + +
959A LEU* 6.1 7.0 - - + -
963A CYS* 3.3 22.6 - - - -
969A THR* 1.3 86.1 - - + -
971A ASP* 1.3 66.7 + - - +
973A VAL* 3.4 9.8 - - + +
974A VAL* 2.9 32.6 + - - +
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Residues in contact with ASP 971 (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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938A GLN* 2.8 29.2 + - - +
969A THR* 2.6 13.4 + - - +
970A PRO* 1.3 82.9 - - - +
972A GLN* 1.3 60.1 + - + +
973A VAL 3.1 1.3 - - - -
974A VAL* 3.3 6.6 + - - +
975A ALA* 2.8 30.7 + - - +
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Residues in contact with GLN 972 (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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968A LEU* 3.4 24.1 - - + +
969A THR* 2.6 44.8 + - - +
971A ASP* 1.3 77.0 - - + +
973A VAL* 1.3 63.1 + - - +
975A ALA* 3.1 10.5 + - - +
976A ILE* 3.1 25.5 + - - +
1004A LEU* 5.5 0.2 - - - +
1005A ASP* 3.1 26.5 + - - -
1008A VAL* 3.6 26.5 - - + +
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Residues in contact with VAL 973 (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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955A VAL* 4.9 20.2 - - + -
958A LEU 5.5 5.8 - - - +
959A LEU* 5.4 7.6 - - + +
962A LEU* 4.2 28.9 - - + -
963A CYS* 5.6 1.8 - - - -
968A LEU* 4.3 15.5 - - + +
969A THR 3.2 12.7 + - - +
970A PRO* 3.4 14.1 - - + +
971A ASP 3.1 0.2 - - - -
972A GLN* 1.3 75.4 - - - +
974A VAL* 1.3 69.3 + - + +
975A ALA 2.9 1.1 - - - -
976A ILE* 2.8 24.3 + - + +
977A ALA* 3.0 11.6 + - - +
986A LEU* 3.8 14.0 - - + +
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Residues in contact with VAL 974 (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* 3.4 30.3 - - + -
938A GLN* 3.9 33.0 - - + +
941A ALA* 6.0 1.6 - - + -
942A ILE* 3.7 29.8 - - + +
955A VAL* 5.6 2.9 - - + -
970A PRO 2.9 23.7 + - - +
971A ASP 3.3 5.6 + - - +
973A VAL* 1.3 76.5 - - + +
975A ALA* 1.3 57.7 + - - +
977A ALA* 3.3 4.4 + - - +
978A SER* 3.2 30.0 + - - -
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Residues in contact with ALA 975 (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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971A ASP 2.8 17.7 + - - +
972A GLN* 3.1 12.1 - - - +
973A VAL 2.9 0.4 - - - -
974A VAL* 1.3 77.5 - - - +
976A ILE* 1.3 55.6 + - - +
978A SER* 4.2 7.5 + - - -
979A ASN* 4.8 5.5 + - - +
1008A VAL* 5.3 1.6 - - + -
1012A SER* 2.3 28.8 + - - +
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Residues in contact with ILE 976 (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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968A LEU* 4.9 8.7 - - + -
972A GLN 3.3 12.6 - - - +
973A VAL* 2.8 16.4 + - + +
975A ALA* 1.3 75.4 - - - +
977A ALA* 1.3 60.7 + - - +
978A SER 3.1 9.2 + - - -
979A ASN* 3.5 17.8 + - - +
982A GLY 4.1 6.2 + - - -
985A ALA* 3.9 14.4 - - + +
986A LEU* 3.5 23.1 - - + +
989A VAL* 4.3 15.9 - - + -
1008A VAL* 3.6 27.4 - - + -
1011A ALA* 3.4 39.5 - - + +
1012A SER* 3.6 7.0 - - - -
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Residues in contact with ALA 977 (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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942A ILE* 3.6 10.9 - - + +
951A ALA* 3.5 24.5 - - - +
955A VAL* 3.7 29.8 - - + -
973A VAL 3.0 13.2 + - - +
974A VAL* 3.7 7.0 - - - +
976A ILE* 1.3 78.1 - - - +
978A SER* 1.3 58.0 + - - +
979A ASN 3.5 1.4 + - - +
982A GLY* 4.0 12.6 - - - +
986A LEU* 3.9 14.1 - - + -
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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