Contacts of the helix formed by residues 1216 - 1225 (chain J) in PDB entry 6XAV
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 ALA1216 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149J ARG* 5.2 7.9 - - + -
1150J PRO* 4.9 11.0 - - + -
1153J PRO* 5.2 8.7 - - + -
1154J ALA 4.3 8.3 + - - +
1156J LEU* 5.5 0.8 - - - +
1214J PRO 3.3 6.3 + - - +
1215J GLU* 1.3 69.4 - - - +
1217J PRO* 1.3 73.6 - - + +
1218J HIS* 4.4 5.4 - - + +
1219J ASP* 3.4 38.4 + - - +
1220J ILE* 3.3 18.5 + - - +
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Residues in contact with PRO1217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144J LEU 5.9 1.8 - - - +
1147J ALA* 4.3 14.8 - - - +
1148J ARG 4.8 10.5 - - - +
1149J ARG* 5.4 1.6 - - + -
1150J PRO* 5.4 4.0 - - + -
1215J GLU 3.4 6.7 - - - +
1216J ALA* 1.3 85.1 - - + +
1218J HIS* 1.3 82.6 + - + +
1220J ILE* 3.3 4.5 + - + -
1221J LEU* 3.1 19.8 + - - +
1229J VAL* 3.4 19.9 - - + +
1232J TYR* 4.6 15.3 - - + +
1233J ILE* 5.3 5.2 - - + -
1306J LEU* 3.7 19.7 - - + -
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Residues in contact with HIS1218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147J ALA* 3.1 40.5 + - + +
1149J ARG* 4.5 19.2 - - + +
1216J ALA* 3.3 2.5 - - + +
1217J PRO* 1.3 86.7 - - + +
1219J ASP* 1.3 63.5 + - - +
1221J LEU* 3.4 7.8 + - - +
1222J ARG* 3.0 30.3 + - - +
1306J LEU* 3.9 33.3 + - + -
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Residues in contact with ASP1219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154J ALA 4.0 12.0 - - - +
1155J ILE* 4.8 2.9 - - - +
1156J LEU* 4.5 18.6 + - + +
1158J GLU* 5.2 1.3 - - - +
1216J ALA* 3.4 27.7 + - + +
1217J PRO 3.2 0.6 - - - -
1218J HIS* 1.3 83.4 - - - +
1220J ILE* 1.3 58.7 + - + +
1222J ARG* 3.3 28.6 + - - +
1223J LEU* 2.9 45.5 + - + +
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Residues in contact with ILE1220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156J LEU* 4.6 13.7 - - + -
1215J GLU* 3.5 34.1 - - + +
1216J ALA 3.3 17.5 - - - +
1217J PRO* 3.3 8.0 + - + +
1218J HIS 3.3 0.2 - - - -
1219J ASP* 1.3 78.5 - - + +
1221J LEU* 1.3 62.7 + - - +
1224J ARG* 3.0 47.1 + - + +
1225J GLY 3.3 6.4 + - - +
1228J ALA* 3.8 14.1 - - + +
1229J VAL* 3.6 29.8 - - + +
1232J TYR* 4.8 11.4 - - + -
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Residues in contact with LEU1221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217J PRO 3.1 13.4 + - - +
1218J HIS* 3.7 8.1 - - - +
1219J ASP 3.3 0.2 - - - -
1220J ILE* 1.3 78.3 - - - +
1222J ARG* 1.3 63.5 + - - +
1225J GLY* 3.2 35.0 + - - +
1226J VAL* 3.8 22.4 - - + -
1229J VAL* 3.7 20.8 - - + +
1261J LEU* 4.4 15.0 - - + -
1304J ARG* 4.7 9.2 - - + +
1305J ASP* 3.6 17.9 - - - +
1306J LEU* 3.5 38.1 - - + +
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Residues in contact with ARG1222 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1158J GLU* 2.4 44.4 + - - -
1206J ARG* 5.2 3.7 + - - +
1218J HIS 3.0 16.3 + - - +
1219J ASP* 3.6 30.0 + - - +
1221J LEU* 1.3 81.0 - - - +
1223J LEU* 1.3 69.3 + - + +
1225J GLY* 4.7 0.9 + - - -
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Residues in contact with LEU1223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156J LEU* 4.0 21.8 - - + -
1157J ALA 3.9 8.3 - - - +
1158J GLU* 3.4 29.8 - - - +
1206J ARG* 3.4 35.3 + - + +
1207J GLY* 3.8 28.0 - - - +
1219J ASP* 2.9 24.4 + - + +
1220J ILE* 5.1 0.2 - - - -
1222J ARG* 1.3 90.2 - - + +
1224J ARG* 1.3 68.8 + - + +
1225J GLY 3.4 0.6 + - - -
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Residues in contact with ARG1224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156J LEU* 4.5 8.1 - - - +
1207J GLY* 3.6 25.0 + - - -
1209J VAL* 5.8 3.4 - - - +
1215J GLU* 4.5 18.6 + - - -
1220J ILE* 3.0 34.0 + - + +
1223J LEU* 1.3 83.2 - - + +
1225J GLY* 1.3 59.9 + - - +
1227J HIS 5.4 0.2 + - - -
1228J ALA* 3.6 25.9 + - + +
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Residues in contact with GLY1225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220J ILE 3.3 2.8 - - - +
1221J LEU* 3.2 35.9 + - - +
1222J ARG 4.6 0.6 - - - -
1223J LEU 3.4 2.4 + - - -
1224J ARG* 1.3 80.0 - - - +
1226J VAL* 1.3 66.1 + - - -
1227J HIS 3.6 1.6 - - - -
1228J ALA 4.2 0.9 - - - -
1229J VAL* 3.8 5.7 + - - +
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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