Contacts of the helix formed by residues 1136 - 1145 (chain N) in PDB entry 4G7Z
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 LYS1136 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124N GLN* 4.5 3.8 - - - +
1133N ARG* 4.1 23.6 - - - +
1134N LEU 3.9 0.4 + - - -
1135N ARG* 1.3 73.9 - - - +
1137N ARG* 1.3 68.8 + - - +
1138N ALA* 3.5 2.9 - - + +
1139N ASP* 3.4 23.5 + - - +
1140N ILE* 3.1 22.5 + - - +
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Residues in contact with ARG1137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134N LEU* 6.2 1.8 - - - -
1135N ARG 3.9 0.4 + - - -
1136N LYS* 1.3 71.5 - - - +
1138N ALA* 1.3 59.9 + - - +
1140N ILE* 3.0 6.3 + - - +
1141N GLU* 2.9 43.9 + - - +
1172N HIS* 2.9 40.7 + - - +
1175N ILE* 3.8 40.4 - - - +
1179N GLU* 5.6 1.8 + - - -
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Residues in contact with ALA1138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136N LYS* 3.5 2.5 - - + +
1137N ARG* 1.3 80.6 - - + +
1139N ASP* 1.3 62.7 + - - +
1141N GLU* 3.8 3.8 - - - -
1142N ALA* 2.9 29.8 + - - +
1362N LYS* 3.3 30.8 + - + +
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Residues in contact with ASP1139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124N GLN* 5.3 5.5 + - - -
1135N ARG* 3.6 35.4 + - - +
1136N LYS* 3.4 28.8 + - - +
1137N ARG 3.1 0.6 - - - -
1138N ALA* 1.3 81.5 - - - +
1140N ILE* 1.3 59.3 + - - +
1142N ALA* 3.4 7.6 + - - +
1143N GLY* 3.1 21.5 + - - -
1357N ARG* 3.1 46.4 + - - +
1365N ASP* 4.5 0.3 - - - +
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Residues in contact with ILE1140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120N VAL* 6.0 2.5 - - + -
1121N PRO 5.4 0.2 - - - +
1122N LEU* 3.6 46.7 - - + +
1134N LEU* 4.1 14.1 - - + -
1135N ARG* 3.5 38.6 - - + +
1136N LYS 3.1 11.2 - - - +
1137N ARG 3.0 5.3 + - - +
1139N ASP* 1.3 74.2 - - - +
1141N GLU* 1.3 61.4 + - - +
1143N GLY* 3.3 1.6 + - - -
1144N LEU* 2.8 39.7 + - + +
1171N VAL* 4.6 1.6 - - + -
1175N ILE* 4.2 28.3 - - + -
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Residues in contact with GLU1141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137N ARG* 2.9 38.9 + - - +
1138N ALA* 3.8 4.3 - - - +
1140N ILE* 1.3 75.3 - - - +
1142N ALA* 1.3 58.6 + - - +
1145N TYR* 3.0 33.9 + - + +
1168N MET* 3.6 32.2 - - + +
1171N VAL* 4.2 14.1 - - + -
1172N HIS* 3.4 19.8 - - + -
1175N ILE* 4.8 4.0 - - + -
1362N LYS* 3.3 24.7 + - - +
1364N HIS* 5.0 0.2 - - - -
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Residues in contact with ALA1142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138N ALA 2.9 20.1 + - - +
1139N ASP* 3.5 9.4 - - - +
1140N ILE 3.2 0.2 - - - -
1141N GLU* 1.3 77.6 - - - +
1143N GLY* 1.3 58.0 + - - +
1353N GLN* 4.9 3.1 - - - +
1357N ARG* 5.8 1.8 - - - +
1362N LYS* 4.7 8.2 - - + +
1363N LEU 3.7 24.9 - - - +
1364N HIS* 3.2 33.4 + - - +
1365N ASP* 3.4 12.5 + - - +
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Residues in contact with GLY1143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120N VAL* 4.6 14.6 - - - +
1139N ASP 3.1 13.4 + - - -
1140N ILE 3.7 2.0 - - - -
1141N GLU 3.2 0.2 - - - -
1142N ALA* 1.3 78.5 - - - +
1144N LEU* 1.3 61.5 + - - +
1147N ARG* 3.0 33.1 + - - +
1364N HIS* 3.8 1.3 - - - -
1365N ASP* 3.2 22.6 + - - -
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Residues in contact with LEU1144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120N VAL* 4.0 22.7 - - + -
1122N LEU* 3.6 29.4 - - + -
1140N ILE* 2.8 28.4 + - + +
1143N GLY* 1.3 73.6 - - - +
1145N TYR* 1.3 67.8 + - - +
1146N GLY 3.3 0.5 + - - -
1147N ARG* 3.0 21.1 + - - +
1166N LEU* 4.1 14.9 - - + +
1171N VAL* 3.8 19.5 - - + +
1174N LEU* 4.2 16.6 - - + -
1186N VAL* 3.8 36.1 - - + -
1188N VAL* 4.8 6.7 - - + -
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Residues in contact with TYR1145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775N GLY* 4.0 21.1 - - - -
916N TYR* 3.1 33.4 + + - -
1141N GLU* 3.0 25.7 + - + +
1143N GLY 3.8 0.4 - - - -
1144N LEU* 1.3 71.6 - - - +
1146N GLY* 1.3 64.9 + - - +
1147N ARG* 3.7 0.2 - - - +
1167N SER 4.3 0.2 - - - -
1168N MET* 3.7 42.2 - - + -
1171N VAL* 3.8 13.3 - - + +
1207N TYR* 3.6 21.3 - + - -
1209N LEU* 3.4 31.6 + - + +
1212N ALA* 3.6 24.1 - - - +
1364N HIS* 2.8 34.0 + + + +
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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