Contacts of the helix formed by residues 1114 - 1123 (chain A) in PDB entry 3UON
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 PHE1114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A MET* 4.1 8.3 - - + -
1106A MET* 3.4 26.0 - - - -
1110A GLY 3.6 11.0 - - - -
1111A VAL* 2.9 22.0 + - - +
1113A GLY* 1.3 78.0 - - - +
1115A THR* 1.3 53.5 + - - +
1116A ASN* 3.1 3.6 - - - -
1117A SER* 3.0 11.4 + - - +
1118A LEU* 2.7 46.9 + - + +
1133A LEU* 3.6 27.8 - - + -
1136A SER* 3.6 33.9 - - - -
1138A TRP* 4.0 22.7 - + + -
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Residues in contact with THR1115 (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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1083A LYS* 4.3 17.4 - - + +
1112A ALA 2.9 18.1 + - - -
1113A GLY 3.2 4.2 + - - -
1114A PHE* 1.3 74.7 - - - +
1116A ASN* 1.3 60.0 + - - +
1118A LEU* 3.6 10.6 - - + +
1119A ARG* 2.9 45.3 + - + +
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Residues in contact with ASN1116 (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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1113A GLY 5.1 0.4 + - - -
1114A PHE* 3.1 1.0 - - - -
1115A THR* 1.3 80.1 - - - +
1117A SER* 1.3 60.5 + - - +
1119A ARG* 3.4 31.5 + - - +
1120A MET* 3.0 27.8 + - + +
1132A ASN* 4.0 12.1 - - - +
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Residues in contact with SER1117 (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 PHE* 3.0 12.7 + - - -
1116A ASN* 1.3 74.3 - - - +
1118A LEU* 1.3 66.5 + - - +
1120A MET* 2.9 19.6 + - - +
1121A LEU* 3.0 18.4 + - - +
1129A ALA* 4.4 4.5 - - - +
1132A ASN* 2.5 35.2 + - - +
1133A LEU* 3.5 37.0 - - - +
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Residues in contact with LEU1118 (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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1083A LYS* 4.4 11.9 - - + +
1084A LEU* 3.9 21.8 - - + -
1087A VAL* 3.7 16.4 - - + +
1099A LEU* 4.3 19.3 - - + -
1102A MET* 5.8 4.5 - - + -
1111A VAL* 3.7 21.3 - - + +
1112A ALA* 4.7 2.5 - - - +
1114A PHE* 2.7 37.4 + - + +
1115A THR* 3.6 10.5 - - - +
1117A SER* 1.3 74.2 - - - +
1119A ARG* 1.3 61.4 + - - +
1121A LEU* 3.1 32.7 + - + +
1122A GLN* 3.1 23.5 + - - +
1133A LEU* 6.1 1.6 - - + -
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Residues in contact with ARG1119 (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 THR* 2.9 36.5 + - + +
1116A ASN* 3.6 33.1 + - - +
1117A SER 3.2 0.2 - - - -
1118A LEU* 1.3 76.4 - - - +
1120A MET* 1.3 60.4 + - + +
1122A GLN* 3.5 16.0 + - + +
1123A GLN* 3.1 51.6 + - + +
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Residues in contact with MET1120 (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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1116A ASN* 3.0 16.8 - - - +
1117A SER* 2.9 10.4 + - - +
1119A ARG* 1.3 75.3 - - + +
1121A LEU* 1.3 63.6 + - - +
1123A GLN* 3.5 14.6 + - - +
1124A LYS 3.4 2.9 + - - -
1125A ARG* 3.2 40.3 + - + +
1128A GLU* 3.3 45.5 - - + +
1129A ALA* 3.9 12.6 - - + +
1132A ASN* 3.6 37.0 - - - +
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Residues in contact with LEU1121 (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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1087A VAL* 3.9 14.8 - - + -
1091A LEU* 4.5 7.2 - - + -
1099A LEU* 5.7 0.9 - - + -
1117A SER* 3.0 14.2 + - - +
1118A LEU* 3.3 30.5 - - + +
1120A MET* 1.3 76.9 - - - +
1122A GLN* 1.3 56.9 + - - +
1124A LYS* 2.8 35.6 + - - -
1126A TRP* 3.8 27.3 - - + -
1129A ALA* 3.8 20.2 - - + -
1133A LEU* 5.3 5.6 - - + -
1153A PHE* 4.1 49.6 - - + -
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Residues in contact with GLN1122 (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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1083A LYS 5.0 4.6 + - - -
1086A PRO* 3.5 24.9 - - - +
1087A VAL* 3.5 38.5 + - + +
1090A SER* 4.0 10.5 + - - +
1118A LEU* 3.1 19.3 + - - +
1119A ARG* 3.8 18.1 - - + +
1120A MET 3.4 0.2 - - - -
1121A LEU* 1.3 75.9 - - - +
1123A GLN* 1.3 59.8 + - + +
1124A LYS* 3.4 19.1 + - - +
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Residues in contact with GLN1123 (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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1119A ARG* 3.1 38.8 + - + +
1120A MET* 3.7 9.9 - - - +
1121A LEU 3.1 1.0 - - - -
1122A GLN* 1.3 77.1 - - + +
1124A LYS* 1.3 71.3 + - - +
1125A ARG* 3.1 47.8 + - + +
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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