Contacts of the helix formed by residues 1208 - 1221 (chain A) in PDB entry 5J68
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 GLY1208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1203A SER 3.9 2.1 - - - +
1204A GLU 3.3 12.1 + - - -
1205A ASP 4.7 0.6 + - - -
1206A GLU 3.7 1.0 - - - -
1207A LEU* 1.3 82.0 - - - +
1209A PRO* 1.3 73.6 - - - +
1210A ARG* 3.5 3.1 - - - -
1211A LYS* 3.7 2.7 + - - +
1212A ALA* 3.0 24.1 + - - +
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Residues in contact with PRO1209 (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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1204A GLU* 3.1 40.4 - - + +
1208A GLY* 1.3 85.5 - - - +
1210A ARG* 1.3 59.0 + - - +
1212A ALA* 3.6 9.0 - - + -
1213A HIS* 2.3 46.2 + - + +
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Residues in contact with ARG1210 (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 TYR* 5.0 4.0 + - - -
1208A GLY 3.5 0.8 - - - -
1209A PRO* 1.3 76.6 - - - +
1211A LYS* 1.3 77.9 + - + +
1213A HIS* 3.4 5.8 - - - +
1214A LEU* 2.5 66.3 + - + +
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Residues in contact with LYS1211 (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 GLN* 5.3 4.0 - - - +
1168A GLN* 3.9 22.3 + - - +
1171A TYR* 3.6 57.5 - - + -
1207A LEU* 3.6 29.4 - - + +
1208A GLY 3.7 8.0 + - - +
1210A ARG* 1.3 102.9 - - + +
1212A ALA* 1.3 57.1 + - - +
1214A LEU* 3.3 5.0 + - - +
1215A ILE* 2.8 35.6 + - - +
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Residues in contact with ALA1212 (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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1200A VAL 4.8 0.7 - - - +
1203A SER* 4.3 4.0 - - - -
1204A GLU* 3.8 26.9 - - + +
1207A LEU* 5.1 0.8 - - - +
1208A GLY 3.0 19.5 + - - +
1209A PRO* 3.6 11.7 - - + +
1211A LYS* 1.3 73.2 - - - +
1213A HIS* 1.3 53.2 + - + +
1215A ILE* 2.6 35.4 + - - +
1216A LEU* 2.7 33.9 + - + +
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Residues in contact with HIS1213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A GLU* 4.2 10.3 - - - -
1209A PRO* 2.3 51.1 + - + +
1210A ARG* 3.7 6.4 - - - +
1212A ALA* 1.3 72.3 - - + +
1214A LEU* 1.3 57.7 + - - +
1216A LEU* 3.6 13.7 - - + +
1217A ARG* 2.8 30.1 + - - +
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Residues in contact with LEU1214 (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 TYR* 3.2 28.7 - - + +
1175A MET* 4.0 10.4 - - - +
1210A ARG* 2.5 60.3 + - + +
1211A LYS* 3.4 7.4 - - - +
1212A ALA 2.9 0.4 + - - -
1213A HIS* 1.3 71.7 - - + +
1215A ILE* 1.3 64.5 + - - +
1217A ARG* 3.4 19.2 + - + +
1218A ARG* 3.3 21.7 + - - +
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Residues in contact with ILE1215 (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 TYR* 4.5 9.2 - - + -
1174A LEU* 3.8 26.7 - - + -
1175A MET* 3.6 20.8 - - + +
1182A LEU* 3.3 30.6 - - + +
1199A PHE* 4.0 20.0 - - + -
1203A SER* 4.4 9.4 - - - +
1207A LEU* 3.9 20.9 - - + -
1211A LYS 2.8 22.3 + - - +
1212A ALA* 2.6 15.0 + - - +
1214A LEU* 1.3 71.1 - - - +
1216A LEU* 1.3 74.6 + - + +
1218A ARG* 3.2 9.9 + - - +
1219A LEU* 3.3 3.9 + - + +
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Residues in contact with LEU1216 (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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1199A PHE* 5.1 0.7 - - + -
1200A VAL* 3.5 50.7 - - + -
1203A SER* 6.0 0.9 - - - -
1212A ALA* 2.7 45.6 + - + +
1213A HIS* 3.6 14.4 - - + +
1215A ILE* 1.3 79.8 - - + +
1217A ARG* 1.4 65.1 + - - +
1219A LEU* 3.1 34.1 + - + +
1220A GLU* 3.1 17.3 - - - +
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Residues in contact with ARG1217 (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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1213A HIS 2.8 21.3 + - - +
1214A LEU* 3.4 18.4 + - - +
1216A LEU* 1.4 72.1 - - - +
1218A ARG* 1.3 59.3 + - - +
1220A GLU* 2.9 34.8 + - + +
1221A ARG* 3.5 19.3 + - + +
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Residues in contact with ARG1218 (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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1174A LEU 4.2 1.0 + - - -
1175A MET* 2.9 66.0 + - + +
1177A VAL 3.5 13.1 + - - -
1178A SER* 5.1 0.4 - - - +
1179A ALA* 3.4 39.8 - - + +
1182A LEU* 3.6 15.9 - - + -
1214A LEU 3.3 9.3 + - - +
1215A ILE 3.2 11.8 + - - +
1216A LEU 3.2 0.6 - - - -
1217A ARG* 1.3 78.2 - - - +
1219A LEU* 1.3 62.5 + - - +
1221A ARG* 3.1 35.6 + - - +
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Residues in contact with LEU1219 (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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1179A ALA 4.4 0.9 - - - +
1182A LEU* 3.6 17.9 - - + +
1183A PHE* 3.5 48.9 - - + +
1186A GLN* 3.6 29.6 - - - +
1199A PHE* 4.7 3.1 - - + -
1200A VAL* 4.9 0.2 - - + -
1215A ILE* 3.3 13.2 + - + +
1216A LEU* 3.1 36.9 + - + +
1218A ARG* 1.3 76.2 - - - +
1220A GLU* 1.3 63.4 + - + +
1221A ARG 3.4 0.5 + - - -
1222A VAL* 3.4 23.3 + - - +
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Residues in contact with GLU1220 (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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1216A LEU* 3.1 19.9 - - - +
1217A ARG* 2.9 20.9 + - + +
1219A LEU* 1.3 74.9 - - - +
1221A ARG* 1.3 63.4 + - + +
1222A VAL 3.2 5.8 + - - +
1223A SER* 5.6 0.2 - - - -
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Residues in contact with ARG1221 (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 ASP* 4.6 2.8 - - - +
1179A ALA* 4.3 9.8 - - + +
1217A ARG* 3.7 27.8 - - + +
1218A ARG* 3.1 35.6 + - - +
1220A GLU* 1.3 78.0 - - + +
1222A VAL* 1.3 61.6 + - - +
1223A SER 3.5 2.8 + - - -
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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