Contacts of the helix formed by residues 1277 - 1290 (chain A) in PDB entry 3PTA
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 SER1277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1272A VAL 3.2 20.3 + - - -
1273A SER* 2.8 22.2 + - - +
1274A PHE 2.7 13.9 + - - -
1276A ARG* 1.3 74.5 - - - +
1278A MET* 1.3 63.0 + - - +
1279A VAL 3.5 1.8 - - - -
1280A LEU* 3.2 7.9 + - - +
1281A LYS* 3.1 23.2 + - - +
1344A VAL 4.1 13.5 + - - -
1345A VAL* 3.9 25.7 - - - +
1346A ASP 5.4 0.4 + - - -
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Residues in contact with MET1278 (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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807A ALA* 5.7 6.1 - - + -
808A THR* 3.7 26.7 - - + +
1235A PHE* 3.8 25.6 - - + -
1240A TYR* 6.5 0.2 - - + -
1274A PHE 3.2 0.4 + - - -
1275A LYS 2.9 18.2 + - - +
1276A ARG* 2.9 6.3 + - + +
1277A SER* 1.3 74.8 - - - +
1279A VAL* 1.3 67.3 + - - +
1281A LYS* 2.9 31.4 + - - +
1282A LEU* 2.9 39.2 + - + +
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Residues in contact with VAL1279 (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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1229A PHE* 4.2 22.2 - - + -
1235A PHE* 4.5 3.5 - - + -
1243A PHE* 4.5 16.7 - - + -
1248A VAL* 5.8 0.2 - - + -
1271A PHE* 3.4 40.8 - - + +
1274A PHE* 3.1 42.6 - - + +
1275A LYS* 3.8 11.9 - - + -
1278A MET* 1.3 73.9 - - - +
1280A LEU* 1.3 60.6 + - - +
1282A LEU* 3.6 4.3 + - - +
1283A THR* 3.0 33.5 + - + +
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Residues in contact with LEU1280 (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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804A VAL* 5.5 2.0 - - + -
1271A PHE* 3.8 36.1 + - + +
1272A VAL* 3.6 39.5 - - + +
1277A SER 3.2 9.7 + - - +
1278A MET 3.0 0.8 - - - -
1279A VAL* 1.3 82.5 - - - +
1281A LYS* 1.3 67.3 + - + +
1283A THR* 2.8 20.5 + - - +
1284A LEU* 3.1 25.1 + - + +
1296A PHE* 4.3 28.7 - - + -
1315A ILE* 4.4 15.5 - - + -
1345A VAL* 4.8 9.6 - - + -
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Residues in contact with LYS1281 (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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804A VAL* 3.2 32.3 - - + +
805A LEU* 3.6 14.5 + - - +
806A GLY* 5.1 1.3 - - - +
807A ALA* 5.5 6.9 - - - +
808A THR* 4.1 15.4 - - + +
1276A ARG 4.3 6.5 + - - -
1277A SER 3.1 16.1 + - - +
1278A MET* 2.9 36.4 + - - +
1280A LEU* 1.3 80.1 - - + +
1282A LEU* 1.3 56.5 + - - +
1284A LEU* 3.3 8.1 + - - -
1285A ARG* 2.9 30.1 + - - +
1345A VAL* 3.9 18.6 - - + -
1346A ASP* 3.2 22.4 + - - +
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Residues in contact with LEU1282 (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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808A THR* 3.4 31.2 - - + -
1235A PHE* 4.7 3.8 - - + -
1240A TYR* 4.6 17.3 - - + -
1243A PHE* 3.5 34.8 - - + -
1244A LYS* 5.0 7.0 - - - +
1252A LEU* 5.5 0.2 - - - -
1278A MET* 2.9 38.1 + - + +
1279A VAL 3.9 4.0 - - - +
1281A LYS* 1.3 73.0 - - - +
1283A THR* 1.3 57.3 + - - +
1284A LEU 3.0 4.7 - - - -
1285A ARG* 3.3 6.0 + - + +
1286A CYS* 2.8 32.7 + - - +
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Residues in contact with THR1283 (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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1243A PHE* 4.8 6.5 - - + -
1248A VAL* 3.6 31.6 - - + -
1252A LEU* 4.1 17.9 - - + +
1265A LEU* 5.0 6.3 - - + -
1271A PHE* 4.1 17.0 - - + -
1279A VAL* 3.0 15.8 + - + +
1280A LEU* 2.8 21.9 + - - +
1282A LEU* 1.3 75.6 - - - +
1284A LEU* 1.3 61.4 + - - +
1286A CYS* 3.7 8.5 - - - +
1287A LEU* 3.2 31.4 + - - +
1315A ILE* 4.9 5.6 - - - +
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Residues in contact with LEU1284 (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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804A VAL* 4.1 17.9 - - + -
805A LEU* 3.8 11.0 - - + -
876A PHE* 5.6 7.9 - - + -
1280A LEU* 3.1 25.6 + - + +
1281A LYS* 3.6 6.7 - - - +
1282A LEU 3.0 0.6 - - - -
1283A THR* 1.3 79.8 - - - +
1285A ARG* 1.3 53.0 + - - +
1286A CYS 2.9 4.5 - - - -
1287A LEU* 2.9 4.9 + - + +
1288A VAL* 2.7 36.6 + - - +
1294A CYS* 4.1 22.5 - - - -
1295A THR* 4.5 11.2 - - - +
1296A PHE* 3.6 35.0 - - + -
1315A ILE* 4.4 23.1 - - + -
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Residues in contact with ARG1285 (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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805A LEU* 3.3 12.6 - - + +
808A THR* 3.1 35.3 + - - +
809A SER* 4.4 3.9 + - - +
810A ASP* 3.4 37.3 + - - +
813A GLU* 3.2 25.5 + - - -
1281A LYS 2.9 17.9 + - - +
1282A LEU* 3.8 6.3 - - + +
1284A LEU* 1.3 76.2 - - - +
1286A CYS* 1.3 57.1 + - - +
1288A VAL* 3.0 19.0 - - - +
1289A ARG* 2.9 49.6 + - + +
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Residues in contact with CYS1286 (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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851A PRO 5.9 0.7 - - - -
1252A LEU* 3.4 32.8 - - + -
1282A LEU 2.8 18.7 + - - +
1283A THR 3.7 7.2 - - - +
1285A ARG* 1.3 78.4 - - - +
1287A LEU* 1.3 61.4 + - - +
1289A ARG* 2.9 54.6 + - - +
1290A MET* 3.2 17.2 + - - +
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Residues in contact with LEU1287 (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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1252A LEU* 4.0 11.9 - - + -
1255A CYS* 3.8 21.3 - - - -
1263A PHE* 3.8 24.5 - - + -
1283A THR* 3.2 15.4 + - - +
1284A LEU* 2.9 8.1 + - + +
1286A CYS* 1.3 75.5 - - - +
1288A VAL* 1.3 64.9 + - - +
1290A MET* 3.1 28.3 + - + +
1292A TYR* 3.0 38.6 + - + +
1294A CYS* 3.9 17.7 - - + -
1315A ILE* 3.8 18.6 - - + -
1317A ALA* 3.9 14.8 - - + -
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Residues in contact with VAL1288 (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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805A LEU* 3.8 10.8 - - + -
813A GLU* 4.5 3.3 - - - +
815A PHE* 4.2 12.3 - - + -
866A GLN* 3.1 23.3 - - - +
867A LEU* 3.6 24.7 - - + -
876A PHE* 4.2 19.3 - - + -
1284A LEU 2.7 13.2 + - - +
1285A ARG* 3.0 44.6 - - - +
1287A LEU* 1.3 70.7 - - - +
1289A ARG* 1.3 65.6 + - - +
1291A GLY* 2.8 17.0 + - - -
1292A TYR 4.2 7.6 - - - -
1294A CYS* 4.5 5.7 - - - -
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Residues in contact with ARG1289 (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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813A GLU* 5.8 0.2 - - - -
837A LYS* 4.9 11.3 + - - +
849A MET* 2.9 36.3 - - + +
851A PRO 3.5 21.6 + - - -
866A GLN* 5.2 0.2 - - - -
1256A ASP* 5.0 0.8 + - - -
1285A ARG* 2.9 44.2 + - - +
1286A CYS* 2.9 47.4 + - - +
1288A VAL* 1.3 80.3 - - - +
1290A MET* 1.3 88.7 + - - +
1291A GLY* 3.0 4.2 + - - -
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Residues in contact with MET1290 (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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843A TRP* 3.3 26.2 + - - -
1252A LEU* 4.3 13.5 - - + +
1255A CYS* 4.1 7.2 - - - +
1256A ASP* 3.4 39.7 - - - +
1259A ARG* 4.5 12.9 + - - +
1286A CYS* 3.2 27.5 + - - +
1287A LEU* 3.1 35.1 + - + +
1288A VAL 3.1 1.4 - - - -
1289A ARG* 1.3 106.4 - - - +
1291A GLY* 1.3 62.3 + - - +
1292A TYR* 3.2 15.3 + - + -
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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