Contacts of the helix formed by residues 1114 - 1122 (chain A) in PDB entry 3U44
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 THR1114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110A GLN* 3.5 16.2 - - - +
1111A PHE* 2.6 27.8 + - - +
1112A PHE 4.1 0.2 - - - +
1113A HIS* 1.3 84.1 - - - +
1115A GLU* 1.3 63.9 + - - +
1117A GLY 3.0 11.3 + - - -
1118A GLY* 3.1 18.0 + - - -
1222A TYR* 4.3 8.1 - - + -
1227A GLY 4.6 8.1 - - - +
1229A ILE* 3.2 31.6 - - + +
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Residues in contact with GLU1115 (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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1114A THR* 1.3 70.1 - - - +
1116A ILE* 1.3 72.6 + - + +
1118A GLY* 3.0 5.3 + - - +
1119A GLN* 2.8 54.1 + - - +
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Residues in contact with ILE1116 (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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1111A PHE* 3.8 19.1 - - + -
1114A THR* 3.4 1.2 + - - -
1115A GLU* 1.3 80.3 - - + +
1117A GLY* 1.3 58.5 + - - +
1119A GLN* 3.2 16.0 + - - +
1120A LEU* 2.8 27.7 + - - +
1162A TYR* 3.9 23.2 + - + +
1169A TYR* 6.2 1.6 - - + -
1171A LEU* 4.1 17.7 - - + -
1220A ALA* 3.7 24.5 - - + -
1229A ILE* 3.5 31.9 - - + -
1231A THR* 5.0 8.7 - - + -
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Residues in contact with GLY1117 (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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1111A PHE* 3.3 39.9 - - - -
1112A PHE* 3.9 6.1 - - - -
1114A THR* 3.0 11.3 + - - -
1116A ILE* 1.3 76.0 - - - +
1118A GLY* 1.3 61.9 + - - +
1120A LEU* 2.9 14.7 + - - +
1121A ILE* 3.0 19.2 + - - +
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Residues in contact with GLY1118 (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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1076A VAL* 5.7 2.2 - - - -
1112A PHE 4.0 7.7 + - - -
1114A THR 3.1 10.6 + - - -
1115A GLU* 3.0 9.6 + - - -
1117A GLY* 1.3 73.0 - - - +
1119A GLN* 1.3 60.5 + - - +
1121A ILE* 3.4 10.9 + - - +
1122A GLY* 3.1 19.9 + - - -
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Residues in contact with GLN1119 (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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1115A GLU* 2.8 49.9 + - - +
1116A ILE* 3.4 17.2 - - - +
1118A GLY* 1.3 73.3 - - - +
1120A LEU* 1.3 65.1 + - - +
1122A GLY 2.5 28.7 - - - +
1123A ALA* 3.9 3.3 - - - +
1162A TYR* 3.8 28.0 + - + -
1164A THR* 4.6 7.4 - - + +
1169A TYR* 5.0 12.8 - - - -
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Residues in contact with LEU1120 (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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1073A LEU* 3.8 38.8 - - + -
1111A PHE* 3.7 17.5 - - + -
1112A PHE* 4.6 0.9 - - + -
1116A ILE 2.8 16.7 + - - +
1117A GLY 3.3 9.0 - - - +
1119A GLN* 1.3 73.1 - - - +
1121A ILE* 1.3 68.1 + - + +
1123A ALA* 3.8 5.9 - - - +
1126A LYS* 3.3 17.2 + - + -
1128A ARG* 5.6 0.4 - - - -
1160A CYS* 3.7 16.8 - - - -
1162A TYR* 3.7 36.2 - - + -
1171A LEU* 3.6 23.8 - - + -
1173A TYR* 4.1 7.4 - - - +
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Residues in contact with ILE1121 (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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1073A LEU* 3.7 26.2 - - + +
1074A SER 3.9 5.6 - - - +
1075A HIS* 3.8 34.5 - - - +
1076A VAL* 4.4 14.1 - - + +
1112A PHE* 3.4 34.8 - - + -
1117A GLY 3.0 16.5 + - - +
1118A GLY* 3.4 11.2 - - - +
1119A GLN 3.2 0.2 - - - -
1120A LEU* 1.3 75.3 - - + +
1122A GLY* 1.3 58.2 + - - +
1123A ALA 3.2 5.2 + - - +
1126A LYS* 2.8 22.3 + - - +
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Residues in contact with GLY1122 (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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1118A GLY 3.1 9.4 + - - -
1119A GLN* 2.5 20.1 - - - +
1121A ILE* 1.3 77.1 - - - +
1123A ALA* 1.3 59.7 + - - +
1164A THR* 4.4 6.9 - - - +
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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