Contacts of the helix formed by residues 1268 - 1279 (chain A) in PDB entry 2J5P
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 LEU1268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1266A ASP* 2.7 9.4 + - - +
1267A PRO* 1.3 82.2 - - + +
1269A PHE* 1.3 53.5 + - - +
1270A ASP 3.3 2.7 - - - -
1271A GLN* 3.0 34.7 + - - +
1272A ALA* 2.7 34.3 + - - +
1291A PHE* 3.4 32.2 - - + +
1293A ILE* 3.2 37.2 - - + -
1297A ARG* 4.1 10.3 - - - +
1301A ILE* 3.8 4.5 - - + -
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Residues in contact with PHE1269 (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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1265A LEU* 3.1 27.8 - - + -
1266A ASP* 2.7 26.3 + - - +
1268A LEU* 1.3 77.4 - - - +
1270A ASP* 1.3 58.1 + - - +
1272A ALA* 2.9 2.1 + - - +
1273A VAL* 2.7 58.0 + - + +
1301A ILE* 3.1 42.6 - - + -
1304A GLN* 3.2 22.9 - - + -
1305A MET* 3.2 7.0 - - + -
1308A GLN* 3.4 29.4 - - + -
1310A ILE* 3.3 24.2 - - + -
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Residues in contact with ASP1270 (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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1265A LEU* 4.8 7.1 - - - +
1266A ASP 4.7 3.5 - - - +
1267A PRO 5.0 4.1 + - - +
1268A LEU 3.3 0.8 - - - -
1269A PHE* 1.3 82.2 - - - +
1271A GLN* 1.3 66.6 + - + +
1273A VAL* 3.4 9.8 + - - +
1274A GLN* 3.1 22.9 + - - +
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Residues in contact with GLN1271 (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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1267A PRO 4.9 3.1 - - - +
1268A LEU* 3.0 37.5 + - - +
1270A ASP* 1.3 80.4 - - + +
1272A ALA* 1.3 52.4 + - - +
1274A GLN* 3.3 9.7 + - - +
1275A PHE* 2.7 35.0 + - - +
1291A PHE* 3.2 14.0 - - + -
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Residues in contact with ALA1272 (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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1268A LEU 2.7 13.8 + - - +
1269A PHE 3.3 2.2 - - - +
1271A GLN* 1.3 70.6 - - - +
1273A VAL* 1.3 59.1 + - - +
1275A PHE* 3.3 1.2 - - - +
1276A VAL* 2.8 36.4 + - - +
1287A VAL* 4.3 9.6 - - + -
1291A PHE* 3.0 19.6 - - + -
1301A ILE* 3.1 36.1 - - + -
1305A MET* 3.8 8.7 - - + -
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Residues in contact with VAL1273 (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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1269A PHE* 2.7 60.5 + - + +
1270A ASP* 3.6 7.6 - - - +
1272A ALA* 1.3 72.9 - - - +
1274A GLN* 1.3 51.1 + - - +
1276A VAL* 2.9 7.2 - - - +
1277A THR* 2.6 51.4 + - + +
1305A MET* 4.1 3.6 - - + -
1310A ILE* 3.3 31.4 - - + -
1324A ALA* 4.9 2.2 - - + -
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Residues in contact with GLN1274 (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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1270A ASP 3.1 14.0 + - - +
1271A GLN* 3.6 8.5 + - - +
1273A VAL* 1.3 79.5 - - - +
1275A PHE* 1.3 55.7 + - - +
1277A THR* 3.0 7.0 - - - -
1278A GLU* 2.7 65.0 + - + +
1327A PRO* 3.7 30.1 - - + +
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Residues in contact with PHE1275 (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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1271A GLN 2.7 18.4 + - - +
1272A ALA 3.3 4.5 - - - +
1274A GLN* 1.3 77.6 - - - +
1276A VAL* 1.3 60.8 + - + +
1278A GLU* 4.0 3.7 - - - +
1279A LYS* 3.0 53.6 + - + +
1281A LYS 5.2 4.7 - - - -
1283A SER* 4.9 4.9 - - - -
1286A GLY* 3.6 11.4 - - - -
1287A VAL* 3.5 40.8 - - + -
1290A GLN* 3.5 35.9 - - + -
1291A PHE* 3.1 26.5 - + + -
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Residues in contact with VAL1276 (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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1272A ALA 2.8 22.5 + - - +
1273A VAL* 2.9 22.9 - - - +
1275A PHE* 1.3 80.4 - - + +
1277A THR* 1.3 54.1 + - - +
1280A ARG* 2.5 30.5 + - - -
1281A LYS 2.8 21.6 + - - +
1282A ALA* 3.3 34.5 - - + -
1283A SER 4.6 1.8 - - - +
1287A VAL* 4.7 2.9 - - + -
1305A MET* 3.5 31.0 - - + -
1310A ILE* 3.9 11.4 - - + -
1322A VAL* 3.4 9.0 - - + +
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Residues in contact with THR1277 (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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1273A VAL* 2.6 50.6 + - + +
1274A GLN* 3.0 13.2 + - - -
1276A VAL* 1.3 75.2 - - + +
1278A GLU* 1.3 71.5 + - - +
1280A ARG* 2.9 26.7 + - - -
1322A VAL* 4.0 1.8 - - - -
1324A ALA* 2.8 31.9 - - + +
1325A PRO 3.4 10.3 - - - +
1326A PRO* 3.2 31.0 - - - +
1327A PRO* 3.8 0.9 - - - +
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Residues in contact with GLU1278 (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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1274A GLN* 2.7 59.6 + - + +
1275A PHE* 4.1 4.3 - - - +
1277A THR* 1.3 74.3 + - - +
1279A LYS* 1.3 62.2 + - + +
1280A ARG* 3.7 5.0 + - - +
1326A PRO* 3.8 20.3 - - + +
1327A PRO* 4.4 3.5 - - + +
1328A PHE* 6.0 1.7 - - - +
1329A ASP* 5.5 2.7 - - - +
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Residues in contact with LYS1279 (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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1275A PHE* 3.0 48.9 + - + +
1278A GLU* 1.3 80.0 - - + +
1280A ARG* 1.3 64.1 + - - +
1281A LYS* 2.9 29.5 + - + +
1290A GLN* 3.9 14.0 - - - +
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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