Contacts of the helix formed by residues 1165 - 1176 (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 ALA1165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1164A ASP* 1.3 70.6 - - - +
1166A GLY* 1.3 57.1 + - - +
1167A LEU 3.1 0.7 - - - -
1168A GLY* 2.8 22.7 + - - +
1169A SER* 2.9 13.4 + - - -
2200A ARG* 5.3 9.2 - - + +
2204A GLU* 4.8 18.4 - - + -
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Residues in contact with GLY1166 (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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1164A ASP* 3.2 2.4 - - - +
1165A ALA* 1.3 78.2 - - - +
1167A LEU* 1.3 55.3 + - - +
1168A GLY 3.2 0.2 - - - -
1169A SER* 3.7 7.9 + - - -
1170A ASP* 2.9 26.7 + - - +
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Residues in contact with LEU1167 (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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1164A ASP* 3.1 26.1 + - + +
1166A GLY* 1.3 73.9 - - - +
1168A GLY* 1.3 56.4 + - - +
1170A ASP* 3.7 9.2 - - + +
1171A HIS* 2.9 25.9 + - - +
2218A VAL* 5.8 9.0 - - + -
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Residues in contact with GLY1168 (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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1164A ASP 3.7 2.4 + - - -
1165A ALA* 2.8 13.9 + - - -
1167A LEU* 1.3 75.8 - - - +
1169A SER* 1.3 57.9 + - - -
1170A ASP 3.2 1.1 - - - -
1171A HIS* 3.1 8.0 + - - +
1172A GLU* 2.9 27.2 + - - +
2196A GLN* 5.0 1.0 - - - +
2197A SER* 5.5 4.0 - - - -
2200A ARG* 4.3 24.0 - - - +
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Residues in contact with SER1169 (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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1165A ALA 2.9 10.2 + - - -
1166A GLY* 4.0 9.6 - - - -
1168A GLY* 1.3 75.9 - - - +
1170A ASP* 1.3 57.6 + - - +
1172A GLU* 3.6 6.9 + - - +
1173A SER* 2.9 24.9 + - - -
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Residues in contact with ASP1170 (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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1166A GLY 2.9 20.7 + - - +
1167A LEU* 3.8 10.3 - - + +
1169A SER* 1.3 75.3 - - - +
1171A HIS* 1.3 59.8 + - - +
1173A SER* 3.5 10.1 - - - -
1174A ASP* 2.9 25.6 + - - +
1213A ALA* 6.0 6.5 - - + -
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Residues in contact with HIS1171 (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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1167A LEU 2.9 20.3 + - - +
1168A GLY* 3.1 11.6 + - - +
1170A ASP* 1.3 78.3 - - - +
1172A GLU* 1.3 56.6 + - - +
1174A ASP* 3.1 10.7 + - - +
1175A THR* 2.9 23.6 + - - -
2193A ILE* 5.7 6.2 - - - +
2196A GLN* 4.6 20.9 - - + +
2197A SER* 5.7 1.3 - - - +
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Residues in contact with GLU1172 (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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1168A GLY 2.9 15.1 + - - +
1169A SER* 3.9 7.6 - - - +
1171A HIS* 1.3 73.5 - - - +
1173A SER* 1.3 60.5 + - - +
1175A THR* 3.1 11.2 + - - -
1176A LEU* 2.9 28.1 + - - +
2193A ILE 6.0 1.1 - - - -
2197A SER* 5.5 12.0 - - - -
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Residues in contact with SER1173 (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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1169A SER 2.9 19.8 + - - -
1170A ASP* 3.5 12.6 - - - -
1171A HIS 3.2 0.2 - - - -
1172A GLU* 1.3 76.0 - - - +
1174A ASP* 1.3 50.5 + - - +
1176A LEU* 3.4 5.1 - - - +
1177A THR* 2.6 39.6 + - - -
1209A PRO* 6.0 2.0 - - - -
1212A ALA* 5.5 10.8 - - - -
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Residues in contact with ASP1174 (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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1170A ASP 2.9 14.2 + - - +
1171A HIS* 3.1 13.0 + - - +
1173A SER* 1.3 73.7 - - - +
1175A THR* 1.3 63.0 + - - +
1177A THR* 3.5 11.9 + - - -
1178A ILE* 3.5 17.3 + - - +
1185A ASN* 3.8 30.1 - - + +
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Residues in contact with THR1175 (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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1171A HIS 2.9 12.5 + - - -
1172A GLU* 3.1 14.8 + - - -
1174A ASP* 1.3 79.1 - - - +
1176A LEU* 1.3 57.3 + - - +
1177A THR 3.2 2.8 + - - -
1178A ILE* 4.2 5.5 + - - +
1179A ASP* 5.2 3.3 + - - +
2193A ILE* 4.2 28.3 - - - -
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Residues in contact with LEU1176 (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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1172A GLU 2.9 14.9 + - - +
1173A SER* 3.4 6.3 - - - +
1174A ASP 3.4 0.2 - - - -
1175A THR* 1.3 75.1 - - - +
1177A THR* 1.3 56.8 + - - +
1178A ILE 3.9 0.2 - - - -
1179A ASP* 5.1 4.2 + - - +
1180A VAL* 5.5 4.7 + - - +
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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