Contacts of the helix formed by residues 1210 - 1226 (chain A) in PDB entry 2XT6
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 SER1210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015A GLY 4.8 2.5 - - - -
1208A SER* 3.4 6.3 + - - +
1209A GLY* 1.4 76.7 - - - +
1211A SER* 1.3 61.6 + - - +
1212A LYS* 3.3 10.7 + - - +
1213A VAL* 2.9 39.6 + - - +
1214A HIS* 3.2 19.4 + - - +
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Residues in contact with SER1211 (chain A).
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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1015A GLY* 2.8 28.0 + - - -
1209A GLY 4.1 1.6 + - - -
1210A SER* 1.3 68.9 + - - +
1212A LYS* 1.4 60.0 + - - +
1214A HIS* 3.2 11.4 + - - +
1215A ALA* 3.0 28.5 + - - +
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Residues in contact with LYS1212 (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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1210A SER* 3.3 6.9 + - - +
1211A SER* 1.4 74.3 - - - +
1213A VAL* 1.3 66.5 + - - +
1215A ALA* 3.4 7.9 + - - +
1216A VAL* 3.3 27.6 + - + +
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Residues in contact with VAL1213 (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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1208A SER* 3.4 24.7 - - - +
1210A SER* 2.9 25.9 + - - +
1212A LYS* 1.3 74.3 - - + +
1214A HIS* 1.3 62.9 + - - +
1216A VAL* 3.0 10.7 + - + +
1217A GLU* 2.9 50.4 + - + +
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Residues in contact with HIS1214 (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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1013A HIS* 3.2 38.1 + - + +
1014A GLU* 3.5 11.6 - - - -
1015A GLY* 3.5 27.0 + - - -
1200A ARG* 2.9 38.8 + - - +
1208A SER* 4.8 4.9 - - - +
1210A SER 3.2 13.8 + - - +
1211A SER* 3.3 10.3 - - - +
1213A VAL* 1.3 76.1 - - - +
1215A ALA* 1.3 59.7 + - + +
1217A GLU* 3.3 8.5 + - - +
1218A GLN* 2.8 46.2 + - - +
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Residues in contact with ALA1215 (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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1211A SER 3.0 13.3 + - - +
1212A LYS* 3.6 11.9 - - - +
1213A VAL 3.3 0.2 - - - -
1214A HIS* 1.3 82.8 - - + +
1216A VAL* 1.3 57.2 + - + +
1218A GLN* 3.5 5.3 + - - +
1219A GLN* 3.1 28.8 + - - +
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Residues in contact with VAL1216 (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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1212A LYS* 3.3 17.5 + - + +
1213A VAL* 3.0 8.9 + - + +
1215A ALA* 1.3 73.7 - - + +
1217A GLU* 1.3 61.4 + - + +
1219A GLN* 3.4 6.0 + - - +
1220A GLU* 3.0 41.3 + - - +
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Residues in contact with GLU1217 (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 ARG* 2.8 46.0 + - + +
1201A ARG* 4.4 11.8 + - - +
1203A MET* 3.6 23.2 - - - +
1207A SER* 6.0 0.2 - - - -
1208A SER* 4.4 7.3 + - - -
1213A VAL* 2.9 38.5 + - + +
1214A HIS* 3.6 9.3 - - - +
1216A VAL* 1.3 76.3 - - + +
1218A GLN* 1.3 62.1 + - - +
1220A GLU* 3.3 18.4 - - - +
1221A ILE* 3.2 27.2 + - - +
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Residues in contact with GLN1218 (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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1118A LYS* 4.1 3.4 - - - +
1119A ILE* 4.4 7.2 - - - +
1122A GLU* 3.1 35.8 + - - +
1169A GLU* 3.0 32.0 + - - +
1200A ARG* 2.8 37.4 + - - +
1214A HIS* 2.8 36.1 + - + +
1215A ALA* 3.7 8.5 - - - +
1217A GLU* 1.3 71.2 - - - +
1219A GLN* 1.3 63.1 + - - +
1221A ILE* 3.5 8.3 + - - +
1222A LEU* 3.4 23.9 + - + +
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Residues in contact with GLN1219 (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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1126A ARG* 3.7 10.4 + - - -
1215A ALA 3.1 16.6 + - - +
1216A VAL* 3.9 6.3 - - - +
1218A GLN* 1.3 73.3 - - - +
1220A GLU* 1.4 59.2 - - - +
1222A LEU* 3.3 19.5 + - - +
1223A ASP* 2.9 61.8 + - - +
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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 VAL* 3.0 24.1 + - - +
1217A GLU* 3.3 25.9 + - - +
1219A GLN* 1.4 76.5 - - - +
1221A ILE* 1.4 53.1 + - + +
1223A ASP* 3.5 8.0 + - - +
1224A THR* 2.7 41.1 + - - +
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Residues in contact with ILE1221 (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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1119A ILE* 3.7 25.1 - - + -
1167A VAL* 3.7 18.8 - - + -
1168A GLN 3.5 21.8 - - - +
1169A GLU* 3.8 6.7 - - - +
1198A ILE* 3.7 14.1 - - + +
1199A SER 4.2 15.0 - - - +
1200A ARG* 3.5 36.8 - - + +
1217A GLU 3.2 13.6 + - - +
1218A GLN* 3.7 11.2 - - - +
1219A GLN 3.3 0.2 - - - -
1220A GLU* 1.4 71.6 - - + +
1222A LEU* 1.3 60.6 + - + +
1224A THR* 3.3 3.9 + - - -
1225A ALA* 3.0 28.3 + - - +
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Residues in contact with LEU1222 (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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1119A ILE* 4.6 10.5 - - + -
1122A GLU* 3.7 50.3 - - + +
1123A LEU* 3.8 24.9 - - + +
1126A ARG* 3.9 21.5 - - + +
1218A GLN* 3.4 16.8 - - + +
1219A GLN* 3.3 26.7 + - - +
1221A ILE* 1.3 73.9 - - - +
1223A ASP* 1.3 63.1 + - - +
1225A ALA* 3.3 5.5 + - - -
1226A PHE* 3.1 29.8 + - - +
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Residues in contact with ASP1223 (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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1126A ARG* 2.9 31.0 + - - +
1219A GLN* 2.9 42.8 + - - +
1220A GLU* 3.7 8.1 + - - +
1222A LEU* 1.3 73.9 - - - +
1224A THR* 1.3 57.3 + - - +
1226A PHE 3.4 2.9 + - - -
1227A GLY* 2.9 27.4 + - - -
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Residues in contact with THR1224 (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 ARG* 3.4 9.2 + - - -
1165A PHE* 6.1 0.4 - - + -
1198A ILE* 4.0 28.7 - - + +
1220A GLU* 2.7 25.4 + - - +
1221A ILE* 3.6 4.2 - - - -
1223A ASP* 1.3 72.7 - - - +
1225A ALA* 1.3 65.2 + - - +
1227A GLY* 3.2 12.6 + - - +
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Residues in contact with ALA1225 (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 ARG* 2.7 32.2 + - - -
1113A LEU* 3.8 17.4 - - + +
1123A LEU* 3.7 26.7 - - + -
1167A VAL* 4.6 4.9 - - + -
1198A ILE* 3.7 16.8 - - + +
1221A ILE 3.0 17.2 + - - +
1222A LEU 3.3 6.3 + - - +
1224A THR* 1.3 74.8 - - - +
1226A PHE* 1.4 60.6 + - + +
1227A GLY 3.5 0.2 - - - -
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Residues in contact with PHE1226 (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 ARG* 4.3 1.8 - - - +
1113A LEU* 4.1 12.1 - - + -
1123A LEU* 3.2 50.0 - - + -
1126A ARG* 3.4 31.6 + - + +
1127A LYS* 3.8 24.2 - - + -
1130A GLU* 3.8 14.6 - - - +
1132A ARG* 2.6 46.9 + - + +
1135A VAL* 3.7 27.6 - - + -
1137A ILE* 4.7 2.0 - - + -
1222A LEU* 3.1 20.1 + - - +
1223A ASP 3.4 3.4 - - - -
1225A ALA* 1.4 77.3 - - + +
1227A GLY* 1.3 58.0 + - - +
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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