Contacts of the helix formed by residues 1014 - 1024 (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 GLY1014 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979A ASN* 5.6 0.2 - - - -
1010A ILE* 2.7 9.4 + - - +
1013A ASN* 1.3 84.2 + - - +
1015A GLY* 1.3 66.2 + - - +
1017A GLN* 3.1 25.8 + - - -
1018A ALA* 3.2 24.6 - - - +
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Residues in contact with GLY1015 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979A ASN* 5.2 1.5 - - - +
981A GLY* 5.5 4.9 - - - -
985A ALA* 3.7 7.6 - - - -
1010A ILE 2.5 20.4 + - - +
1011A ALA* 3.3 20.1 + - - -
1013A ASN 3.4 2.8 + - - -
1014A GLY* 1.3 72.6 - - - +
1016A LYS* 1.3 53.1 + - - -
1019A LEU* 2.6 43.5 + - - +
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Residues in contact with LYS1016 (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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981A GLY* 5.8 1.4 - - - -
984A GLN* 3.3 47.8 - - + +
985A ALA* 3.7 12.7 - - + +
988A THR* 3.4 22.9 - - + +
991A ARG* 5.0 4.5 - - - +
1014A GLY 3.5 0.6 + - - -
1015A GLY* 1.3 68.1 - - - -
1017A GLN* 1.3 91.2 + - - +
1019A LEU* 3.0 8.4 + - - +
1020A GLU* 2.9 29.6 + - + +
21B C 3.3 25.1 + - - +
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Residues in contact with GLN1017 (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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1014A GLY* 3.1 20.9 + - - -
1016A LYS* 1.3 84.5 + - - +
1018A ALA* 1.3 69.9 + - + +
1019A LEU 2.9 0.3 + - - -
1020A GLU* 4.6 2.9 - - - +
1021A THR* 2.7 37.4 + - - +
21B C 3.4 38.0 + - - +
22B C 2.6 42.8 + - - +
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Residues in contact with ALA1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A ILE* 3.8 11.2 - - + -
1014A GLY* 3.2 35.9 + - - +
1015A GLY 3.4 0.4 + - - -
1016A LYS 3.4 0.2 - - - -
1017A GLN* 1.3 82.4 - - + +
1019A LEU* 1.3 57.7 + - - +
1021A THR* 4.1 4.8 - - - -
1022A VAL* 3.0 33.5 + - + +
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Residues in contact with LEU1019 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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985A ALA 4.0 6.5 - - - +
988A THR* 3.5 25.4 - - + +
989A VAL* 3.3 31.2 - - + +
992A LEU* 4.6 5.2 - - + -
996A LEU* 4.2 11.2 - - + +
1007A VAL* 3.7 28.5 - - + +
1010A ILE* 3.8 21.7 - - + +
1011A ALA* 4.1 9.0 - - + +
1015A GLY 2.6 27.1 + - - +
1016A LYS 3.0 5.6 - - - +
1017A GLN 2.9 1.0 + - - -
1018A ALA* 1.3 71.9 - - - +
1020A GLU* 1.3 66.7 + - - +
1022A VAL* 3.3 4.4 - - + +
1023A GLN* 3.1 19.2 + - - +
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Residues in contact with GLU1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988A THR* 4.0 10.2 + - + +
991A ARG* 3.9 25.4 + - - -
992A LEU* 3.4 28.4 - - + +
1016A LYS* 2.9 16.9 + - + +
1017A GLN* 4.2 2.7 - - - +
1019A LEU* 1.3 77.0 - - - +
1021A THR* 1.3 51.7 + - - +
1023A GLN* 2.7 18.4 + - - +
1024A ARG* 2.7 67.4 + - + +
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Residues in contact with THR1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017A GLN* 2.7 38.3 + - - +
1018A ALA* 4.1 4.5 - - - -
1020A GLU* 1.3 72.6 - - - +
1022A VAL* 1.3 57.3 + - - +
1024A ARG* 3.4 7.2 - - - +
1025A LEU* 2.9 48.2 + - + +
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Residues in contact with VAL1022 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996A LEU* 4.6 11.2 - - + -
1002A LEU* 5.1 6.5 - - + -
1010A ILE* 4.4 22.4 - - + -
1018A ALA* 3.0 27.9 + - + +
1019A LEU* 3.3 6.1 - - + +
1021A THR* 1.3 75.6 - - - +
1023A GLN* 1.3 68.1 + - - +
1024A ARG 2.8 2.3 + - - -
1025A LEU* 2.9 14.8 + - - -
1026A LEU* 3.0 34.5 + - + +
1040A VAL* 4.7 8.5 - - + +
1042A ALA 4.0 19.7 - - - +
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Residues in contact with GLN1023 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992A LEU* 3.8 25.8 - - + +
995A VAL* 4.3 21.9 - - + +
996A LEU* 3.3 39.7 - - + -
1000A HIS* 3.0 25.1 + - + -
1019A LEU 3.1 6.1 + - - +
1020A GLU* 2.7 18.0 + - - +
1022A VAL* 1.3 76.4 - - - +
1024A ARG* 1.3 90.2 + - - +
1025A LEU 3.8 0.2 + - - -
1027A PRO* 4.1 2.8 - - - +
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Residues in contact with ARG1024 (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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1020A GLU* 2.7 47.7 + - - +
1021A THR* 3.4 6.8 - - - +
1022A VAL 2.8 0.4 + - - -
1023A GLN* 1.3 103.4 - - - +
1025A LEU* 1.3 64.0 + - - +
1027A PRO* 4.4 6.1 - - - -
1028A VAL* 6.0 0.3 - - - +
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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