Contacts of the helix formed by residues 1110 - 1119 (chain A) in PDB entry 5UGW
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 THR1110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108A PRO* 3.0 10.8 + - - -
1109A GLY* 1.3 76.5 + - - +
1111A THR* 1.3 48.7 + - - -
1112A LEU* 2.6 18.2 + - - +
1113A THR* 2.8 34.3 + - - +
1114A ALA 3.9 0.2 + - - -
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Residues in contact with THR1111 (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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994A LEU* 3.7 28.5 - - + -
998A CYS* 5.9 0.4 - - - -
1065A LEU* 5.8 2.0 - - + -
1109A GLY* 2.7 21.2 + - - -
1110A THR* 1.3 69.2 - - - +
1112A LEU* 1.3 52.2 + - - +
1113A THR 3.2 1.1 - - - -
1114A ALA* 3.0 22.5 + - + -
1115A LEU* 2.8 46.8 + - + +
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Residues in contact with LEU1112 (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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1072A TRP* 4.6 14.0 - - + +
1103A LEU 4.8 0.4 - - - +
1104A SER* 3.5 40.2 - - - +
1107A LEU* 3.7 21.5 - - + +
1108A PRO* 3.8 20.0 - - + -
1109A GLY 4.4 2.0 - - - +
1110A THR* 2.6 10.3 + - - +
1111A THR* 1.3 73.5 - - - +
1113A THR* 1.3 59.8 + - + +
1115A LEU* 3.3 15.1 + - + +
1116A GLU* 3.0 52.3 + - + +
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Residues in contact with THR1113 (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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1110A THR* 2.8 27.6 + - - +
1112A LEU* 1.3 77.7 - - + +
1114A ALA* 1.3 60.1 + - - +
1115A LEU 3.3 0.9 - - - -
1116A GLU* 3.4 26.2 + - - +
1117A ALA* 3.1 24.3 + - - +
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Residues in contact with ALA1114 (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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994A LEU* 5.4 3.6 - - + -
995A GLN* 3.2 35.9 + - - +
998A CYS* 4.9 3.4 - - - +
1111A THR* 3.0 32.7 + - + +
1113A THR* 1.3 76.8 + - - +
1115A LEU* 1.3 64.1 + - - +
1117A ALA* 3.9 6.1 - - - -
1118A ALA* 3.6 3.5 + - - +
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Residues in contact with LEU1115 (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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998A CYS* 3.9 24.5 - - - -
1065A LEU* 4.7 3.1 - - + -
1069A ALA* 3.8 42.4 - - + +
1072A TRP* 3.8 30.1 - - + -
1073A LEU* 3.9 16.6 - - + +
1107A LEU* 6.0 3.6 - - + -
1111A THR* 2.8 28.8 + - + +
1112A LEU* 3.3 16.2 - - + +
1113A THR 3.3 0.2 - - - -
1114A ALA* 1.3 76.7 - - - +
1116A GLU* 1.3 63.7 + - - +
1117A ALA 3.2 0.2 - - - -
1118A ALA* 3.1 18.4 + - - +
1119A ALA* 3.2 13.7 + - - +
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Residues in contact with GLU1116 (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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1072A TRP* 3.4 30.0 - - + -
1112A LEU* 3.0 31.1 + - - +
1113A THR* 3.4 30.8 - - - +
1114A ALA 3.5 0.2 - - - -
1115A LEU* 1.3 73.9 - - - +
1117A ALA* 1.3 61.7 + - - +
1119A ALA* 3.4 5.6 + - - +
1120A ASN* 3.4 24.3 + - - +
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Residues in contact with ALA1117 (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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995A GLN* 3.5 20.1 + - - +
1113A THR 3.1 16.4 + - - +
1114A ALA* 3.7 6.7 - - - +
1115A LEU 3.2 0.2 - - - -
1116A GLU* 1.3 76.1 - - - +
1118A ALA* 1.3 57.6 + - - +
1120A ASN* 3.3 9.0 + - - +
1121A PRO* 3.0 23.9 - - - +
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Residues in contact with ALA1118 (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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995A GLN* 3.3 13.5 - - - +
998A CYS* 3.8 18.8 - - + +
999A THR* 3.6 38.8 + - - +
1002A TYR* 3.5 16.9 - - - -
1073A LEU* 4.5 3.8 - - + -
1114A ALA 3.6 2.6 + - - +
1115A LEU 3.1 10.8 + - - +
1117A ALA* 1.3 77.8 - - - +
1119A ALA* 1.3 57.7 + - - +
1120A ASN 3.2 0.9 - - - -
1121A PRO* 3.4 15.3 - - - +
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Residues in contact with ALA1119 (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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1002A TYR* 3.5 44.1 + - + -
1072A TRP* 4.5 4.5 - - + -
1073A LEU* 4.7 0.4 - - + -
1076A GLN* 3.7 25.1 + - + +
1080A LEU* 4.7 8.1 - - - +
1115A LEU 3.2 13.8 + - - +
1116A GLU* 3.4 7.6 + - - +
1117A ALA 3.3 0.4 - - - -
1118A ALA* 1.3 76.0 - - - +
1120A ASN* 1.3 58.9 + - - +
1121A PRO* 3.8 1.0 - - - +
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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