Contacts of the helix formed by residues 1114 - 1122 (chain A) in PDB entry 5XJY
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 SER1114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1098A GLY 6.0 0.7 - - - -
1099A ASP 3.3 23.9 + - - -
1100A ARG* 3.8 6.5 - - - +
1101A ILE* 5.2 0.9 - - - -
1113A GLY* 1.3 78.1 - - - +
1115A SER* 1.3 61.8 + - - +
1116A LEU* 3.2 9.4 - - - -
1117A PHE* 3.0 23.3 + - - +
1118A LEU* 3.2 11.1 + - - +
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Residues in contact with SER1115 (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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1094A ALA 5.6 1.3 - - - -
1095A ASP* 5.1 20.6 - - - -
1097A LEU 5.8 2.7 - - - -
1100A ARG* 5.3 1.6 - - - +
1101A ILE* 5.6 5.5 - - - +
1114A SER* 1.3 71.1 - - - +
1116A LEU* 1.3 60.6 + - - +
1118A LEU* 3.9 6.5 - - - +
1119A LYS* 2.9 28.9 + - - +
1130A LEU* 5.4 14.2 - - - +
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Residues in contact with LEU1116 (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 SER* 3.2 6.7 - - - -
1115A SER* 1.3 78.5 - - - +
1117A PHE* 1.3 58.8 + - - +
1119A LYS* 3.4 6.8 - - - +
1120A ASN* 2.9 31.9 + - - +
1195A ARG* 4.8 18.4 - - + -
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Residues in contact with PHE1117 (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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1112A VAL 5.2 3.6 - - - +
1113A GLY* 4.7 6.1 - - - -
1114A SER* 3.0 21.9 + - - +
1116A LEU* 1.3 80.7 - - - +
1118A LEU* 1.3 51.6 + - - +
1120A ASN* 4.8 1.1 - - - +
1121A GLN* 2.6 38.5 + - - +
1146A SER* 5.2 13.5 - - - +
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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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1113A GLY 5.6 1.3 - - - +
1114A SER 3.2 10.7 + - - +
1115A SER* 4.3 6.3 - - - +
1117A PHE* 1.3 75.1 - - - +
1119A LYS* 1.3 59.7 + - - +
1121A GLN* 3.8 6.3 - - - -
1122A LEU* 2.8 32.1 + - + +
1130A LEU* 6.0 7.2 - - + -
1133A LYS* 5.7 5.4 - - + +
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Residues in contact with LYS1119 (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 SER 2.9 21.1 + - - +
1116A LEU* 3.2 10.1 + - - +
1118A LEU* 1.3 76.7 - - - +
1120A ASN* 1.3 58.6 + - - +
1122A LEU 3.0 27.3 - - - +
1129A THR* 6.6 0.2 - - - -
1130A LEU* 6.3 2.9 - - + +
2229A HIS* 5.0 7.3 + - - +
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Residues in contact with ASN1120 (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 LEU 2.9 16.4 + - - +
1117A PHE* 4.8 1.3 - - - +
1119A LYS* 1.3 71.0 - - - +
1121A GLN* 1.3 62.8 + - - +
1122A LEU 4.2 3.3 - - - +
2229A HIS* 6.1 1.8 - - - +
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Residues in contact with GLN1121 (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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1117A PHE 2.6 26.0 + - - +
1118A LEU* 3.9 5.4 - - - -
1120A ASN* 1.3 80.0 - - - +
1122A LEU* 1.3 59.8 + - + +
1144A ASN* 4.9 18.4 - - + -
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Residues in contact with LEU1122 (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 LEU* 2.8 18.3 + - + +
1119A LYS* 3.0 18.2 - - - +
1120A ASN* 4.2 3.3 - - - +
1121A GLN* 1.3 80.5 - - + +
1133A LYS* 4.9 17.0 - - + -
1137A SER* 6.4 2.0 - - - -
2229A HIS* 4.2 16.2 + - - -
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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