Contacts of the helix formed by residues 1198 - 1208 (chain A) in PDB entry 5J67
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 ASP1198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1186A GLN* 5.4 1.2 + - - -
1190A ASN* 3.2 23.8 + - - +
1194A GLU* 3.9 22.1 + - + +
1197A GLY* 1.3 72.8 - - - -
1199A PHE* 1.3 65.2 + - - +
1200A VAL* 3.7 11.8 + - - +
1201A TRP* 3.6 26.9 + - + +
1202A ARG* 2.7 34.3 + - - +
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Residues in contact with PHE1199 (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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1151A ALA* 6.5 0.4 - - - -
1154A ILE* 4.4 13.7 - - + -
1158A TYR* 4.8 1.0 - + - -
1174A LEU* 3.8 37.2 - - + -
1182A LEU* 4.4 7.4 - - + -
1185A VAL* 4.3 9.2 - - + -
1186A GLN* 3.6 40.4 - - + -
1189A TYR* 3.6 37.6 - + + -
1190A ASN* 3.0 18.9 + - - +
1198A ASP* 1.3 78.3 + - - +
1200A VAL* 1.3 61.9 + - + +
1202A ARG* 4.0 0.7 - - - +
1203A SER* 2.8 45.4 + - - -
1215A ILE* 3.9 21.1 - - + -
1219A LEU* 4.7 3.4 - - + -
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Residues in contact with VAL1200 (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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1186A GLN* 3.6 24.2 - - - +
1198A ASP* 3.4 10.1 + - - +
1199A PHE* 1.3 79.1 - - + +
1201A TRP* 1.3 62.9 + - - +
1203A SER* 3.2 6.9 + - - -
1204A GLU* 2.9 35.2 + - - +
1212A ALA* 4.5 7.8 - - + +
1215A ILE* 5.8 3.4 - - + -
1216A LEU* 3.6 49.8 - - + -
1219A LEU* 4.6 3.4 - - + -
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Residues in contact with TRP1201 (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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1196A PHE 5.0 1.6 - - - -
1197A GLY* 4.1 20.9 - - - -
1198A ASP* 3.3 23.4 + - + +
1200A VAL* 1.3 80.6 - - - +
1202A ARG* 1.3 68.8 + - - +
1204A GLU* 3.4 11.3 + - - +
1205A ASP* 2.9 62.9 + - - +
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Residues in contact with ARG1202 (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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1155A TYR* 4.0 15.8 - - - -
1158A TYR* 3.1 45.7 + - + +
1159A ASN* 4.0 10.5 + - - +
1161A TYR* 3.6 18.3 + - - -
1189A TYR* 3.5 27.4 + - + +
1196A PHE* 3.3 28.7 + - - +
1197A GLY* 4.1 7.0 - - - +
1198A ASP 2.7 22.8 + - - +
1199A PHE 4.3 1.6 - - - +
1201A TRP* 1.3 82.9 - - - +
1203A SER* 1.3 64.2 + - - +
1205A ASP* 3.4 7.0 + - - +
1206A GLU* 3.2 39.7 + - - +
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Residues in contact with SER1203 (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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1158A TYR* 2.8 30.7 + - - -
1199A PHE* 2.8 39.7 + - - -
1200A VAL* 3.2 7.8 + - - -
1202A ARG* 1.3 76.6 - - - +
1204A GLU* 1.3 56.6 + - - +
1207A LEU* 2.9 35.9 + - - +
1212A ALA* 4.1 7.4 - - - +
1215A ILE* 4.4 20.4 - - - +
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Residues in contact with GLU1204 (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* 2.9 18.3 + - - +
1201A TRP* 3.6 16.3 - - + +
1203A SER* 1.3 74.3 - - - +
1205A ASP* 1.3 62.4 + - - +
1208A GLY* 3.0 27.3 + - - -
1209A PRO* 3.9 26.8 - - + +
1212A ALA* 3.5 14.8 - - + +
1213A HIS* 3.7 26.2 - - - -
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Residues in contact with ASP1205 (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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1201A TRP* 2.9 56.6 + - - +
1202A ARG* 3.6 14.1 - - - +
1203A SER 3.4 0.2 - - - -
1204A GLU* 1.3 81.2 - - - +
1206A GLU* 1.3 67.0 + - + +
1208A GLY* 4.7 1.0 + - - -
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Residues in contact with GLU1206 (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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1158A TYR* 3.3 47.7 - - + +
1161A TYR* 2.9 58.1 - - - +
1167A GLN* 2.8 37.9 + - + +
1202A ARG* 3.2 28.6 + - - +
1203A SER 4.5 0.2 - - - +
1205A ASP* 1.3 83.2 - - + +
1207A LEU* 1.3 61.4 + - + +
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Residues in contact with LEU1207 (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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1158A TYR* 3.4 36.1 - - + +
1167A GLN* 3.2 43.3 - - + +
1170A ALA* 4.3 2.2 - - + -
1171A TYR* 4.4 19.3 - - + +
1174A LEU* 4.9 0.7 - - + -
1203A SER* 2.9 15.8 + - - +
1206A GLU* 1.3 81.0 - - + +
1208A GLY* 1.3 62.1 + - - +
1211A LYS* 3.7 33.9 - - + +
1212A ALA 5.1 0.2 - - - +
1215A ILE* 4.0 24.2 - - + -
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Residues in contact with GLY1208 (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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1203A SER 3.7 0.6 + - - -
1204A GLU* 3.0 20.7 + - - -
1205A ASP 4.6 0.8 + - - -
1206A GLU 3.8 1.0 - - - -
1207A LEU* 1.3 78.7 - - - +
1209A PRO* 1.4 75.8 - - - +
1210A ARG 3.3 3.6 + - - -
1211A LYS 3.6 1.1 + - - -
1212A ALA* 3.3 21.0 + - - +
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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