Contacts of the helix formed by residues 1216 - 1227 (chain A) in PDB entry 5LUQ
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 GLY1216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1214A GLU 2.8 2.6 + - - -
1215A GLU* 1.3 71.4 - - - +
1217A VAL* 1.3 65.4 + - - -
1218A SER* 3.2 3.2 + - - +
1219A PHE* 4.7 5.7 - - - +
1220A LEU* 3.0 44.9 + - - +
1271A ILE* 3.2 20.9 - - - -
1272A GLY* 4.6 1.1 - - - -
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Residues in contact with VAL1217 (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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1214A GLU* 3.1 32.7 + - + +
1215A GLU 3.6 2.8 + - - +
1216A GLY* 1.3 73.9 - - - +
1218A SER* 1.3 59.5 + - - +
1220A LEU* 4.4 1.7 - - - +
1221A ILE* 2.9 38.7 + - + +
1271A ILE 5.5 0.9 - - - +
1272A GLY* 4.4 18.2 - - - -
1273A GLU 5.4 1.3 - - - +
1274A ARG* 4.1 9.5 + - - +
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Residues in contact with SER1218 (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 LYS 3.9 14.0 + - - -
1214A GLU* 2.9 42.3 + - - +
1215A GLU* 4.2 1.6 + - - -
1216A GLY 4.2 1.0 + - - -
1217A VAL* 1.3 76.3 - - - +
1219A PHE* 1.3 69.4 + - - +
1221A ILE* 2.9 34.9 + - - +
1222A ASN* 3.7 8.3 + - - -
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Residues in contact with PHE1219 (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 ARG* 4.2 25.6 - - + -
1155A ARG* 3.7 42.4 - - + -
1173A LEU* 5.9 4.0 - - + -
1216A GLY* 3.6 7.7 + - - +
1218A SER* 1.3 83.8 + - - +
1220A LEU* 1.3 71.6 + - + +
1221A ILE 3.2 0.3 + - - -
1222A ASN* 3.3 15.2 + - + +
1223A THR* 3.1 49.2 + - + +
1231A GLN* 6.2 1.6 - - - -
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Residues in contact with LEU1220 (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 GLY* 3.0 36.7 + - - +
1219A PHE* 1.3 83.9 - - + +
1221A ILE* 1.3 61.2 + - - +
1223A THR* 2.3 26.6 + - - +
1224A PHE* 3.0 23.7 + - + -
1231A GLN* 3.7 27.1 - - - +
1268A ASN* 5.2 6.5 - - + +
1271A ILE* 5.0 6.7 - - + -
1272A GLY 4.6 10.3 - - - +
1274A ARG* 3.4 43.3 - - + +
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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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1214A GLU* 5.9 0.9 - - - +
1217A VAL* 2.9 34.8 - - + +
1218A SER* 2.9 14.7 + - - +
1220A LEU* 1.3 76.1 - - - +
1222A ASN* 1.3 66.1 + - - +
1224A PHE* 3.1 7.1 + - - +
1225A GLU* 2.9 42.3 + - + +
1274A ARG* 3.0 26.0 - - - +
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Residues in contact with ASN1222 (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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1218A SER 3.7 9.0 + - - -
1219A PHE* 3.3 16.1 + - + +
1221A ILE* 1.3 79.7 - - - +
1223A THR* 1.3 59.2 + - + +
1225A GLU* 3.4 20.7 + - - +
1226A GLY* 3.0 22.7 + - - -
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Residues in contact with THR1223 (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 ARG* 5.6 3.4 - - - +
1219A PHE* 3.1 44.3 + - + +
1220A LEU* 2.3 39.6 + - + +
1222A ASN* 1.3 77.7 - - + +
1224A PHE* 1.3 53.8 + - - +
1226A GLY* 2.8 5.2 + - - -
1227A GLY 2.5 41.4 + - - +
1231A GLN* 5.1 6.6 + - - +
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Residues in contact with PHE1224 (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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1220A LEU* 3.0 32.5 + - + +
1221A ILE* 3.9 4.3 - - - +
1223A THR* 1.3 87.0 + - - +
1225A GLU* 1.3 61.5 + - - +
1226A GLY 4.2 0.3 - - - -
1227A GLY* 3.2 13.9 + - - +
1228A GLY* 3.5 37.6 + - - -
1231A GLN* 5.3 10.5 - - - -
1274A ARG* 4.1 22.2 - - + +
1278A ALA* 3.6 41.5 - - + -
1279A LEU* 4.7 3.6 - - + -
1281A VAL 5.2 1.6 - - - -
1282A LEU* 4.3 12.1 - - + -
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Residues in contact with GLU1225 (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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1221A ILE* 2.9 31.7 + - + +
1222A ASN* 3.5 25.9 - - - +
1224A PHE* 1.3 77.5 - - - +
1226A GLY* 1.3 61.6 + - - +
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Residues in contact with GLY1226 (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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1222A ASN 3.0 10.0 + - - -
1223A THR* 2.8 11.5 + - - -
1224A PHE 4.2 0.4 - - - -
1225A GLU* 1.3 76.5 - - - +
1227A GLY* 1.3 54.8 + - - -
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Residues in contact with GLY1227 (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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1223A THR* 2.5 30.6 + - - +
1224A PHE* 3.2 14.8 - - - -
1226A GLY* 1.3 74.8 - - - +
1228A GLY* 1.3 62.2 + - - +
1229A CYS 3.7 4.0 - - - -
1230A GLY* 4.8 7.0 + - - -
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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