Contacts of the helix formed by residues 1307 - 1315 (chain A) in PDB entry 5EPG
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 THR1307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A GLN* 3.6 14.1 - - - +
1216A THR 3.5 11.4 - - - +
1219A GLU* 3.4 37.3 + - + +
1305A PRO* 3.0 21.3 + - + +
1306A LEU* 1.3 74.2 - - - +
1308A PRO* 1.4 75.8 - - - +
1309A GLU* 3.6 12.3 + - - +
1310A LYS* 3.2 22.7 + - - +
1311A ILE* 3.0 21.9 + - - +
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Residues in contact with PRO1308 (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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430A GLN* 4.6 7.0 - - - +
431A ALA 3.8 17.0 - - - +
432A GLN* 3.8 36.8 - - - +
440A ILE* 5.3 0.4 - - + -
514A PHE* 3.6 14.2 - - + -
1177A THR 4.6 1.3 - - - +
1178A GLY* 3.2 30.3 - - - +
1179A ASP* 5.1 2.0 - - - -
1180A HIS* 5.7 5.2 - - + +
1216A THR 5.1 1.1 - - - +
1217A ILE* 5.3 3.1 - - + -
1306A LEU 4.7 0.9 - - - +
1307A THR* 1.4 88.3 - - - +
1309A GLU* 1.3 61.0 + - - +
1311A ILE* 4.2 2.5 - - + -
1312A ARG* 3.1 26.2 + - - +
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Residues in contact with GLU1309 (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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432A GLN* 5.7 0.4 + - - -
511A LYS* 3.6 49.6 + - - +
513A GLU* 6.1 0.2 - - - +
514A PHE* 3.4 35.8 + - + +
1219A GLU* 4.9 4.9 - - - +
1307A THR* 3.2 11.3 + - - +
1308A PRO* 1.3 79.3 - - - +
1310A LYS* 1.3 66.8 + - + +
1312A ARG* 3.8 0.7 - - - +
1313A MET* 3.2 34.1 + - + +
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Residues in contact with LYS1310 (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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1219A GLU* 4.2 13.7 + - - -
1302A LEU* 4.2 8.6 - - + +
1303A ASN* 3.5 39.3 - - + +
1304A SER 4.6 0.4 + - - -
1305A PRO* 2.7 41.9 + - - +
1306A LEU* 4.2 10.1 - - + -
1307A THR* 3.2 16.8 + - - +
1309A GLU* 1.3 81.8 - - + +
1311A ILE* 1.3 67.0 + - - +
1313A MET* 4.2 3.0 - - - +
1314A ALA* 3.3 21.5 + - - +
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Residues in contact with ILE1311 (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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1173A ILE* 4.1 31.9 - - + -
1174A ASP 4.8 0.9 - - - +
1178A GLY* 3.5 32.5 - - - +
1180A HIS* 4.4 21.1 - - + +
1283A ILE* 3.9 17.3 - - + -
1287A VAL* 4.2 7.6 - - + +
1306A LEU* 3.4 29.6 - - + +
1307A THR 3.0 18.7 + - - +
1308A PRO* 4.2 1.1 - - + -
1309A GLU 3.3 0.4 - - - -
1310A LYS* 1.3 75.4 - - - +
1312A ARG* 1.3 64.8 + - - +
1314A ALA* 3.2 15.7 + - - +
1315A CYS* 3.2 15.2 + - - -
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Residues in contact with ARG1312 (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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514A PHE* 3.4 35.0 - - + -
517A THR* 3.2 25.0 - - + +
518A LEU* 5.0 0.2 - - - -
521A SER* 3.0 18.2 + - - -
1175A CYS 3.2 16.7 + - - -
1176A LEU* 2.6 37.6 + - - +
1177A THR 3.7 4.7 - - - +
1178A GLY* 3.8 7.8 - - - +
1308A PRO 3.1 9.9 + - - +
1309A GLU 3.8 1.3 - - - +
1311A ILE* 1.3 77.0 - - - +
1313A MET* 1.3 58.7 + - + +
1315A CYS* 3.1 34.9 + - - +
1317A ASP* 3.3 23.0 + - - -
1319A PHE* 3.7 9.3 - - - +
1320A THR* 3.6 8.3 + - - -
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Residues in contact with MET1313 (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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513A GLU* 3.4 32.1 - - - +
514A PHE* 3.7 17.3 - - + -
517A THR* 3.1 29.4 - - + +
1291A ARG* 4.7 0.2 + - - -
1309A GLU* 3.2 24.1 + - + +
1310A LYS* 4.5 3.1 - - - +
1312A ARG* 1.3 78.8 - - + +
1314A ALA* 1.3 58.9 + - - +
1315A CYS 4.6 0.4 - - - -
1316A GLU* 3.6 18.9 - - - +
1320A THR* 3.6 33.7 - - + +
1323A ILE* 5.7 1.8 - - + -
1325A ARG* 5.6 4.5 - - - +
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Residues in contact with ALA1314 (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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1287A VAL* 3.5 22.0 - - + -
1291A ARG* 2.4 39.7 + - - +
1300A LEU* 4.5 4.3 - - + -
1302A LEU* 3.8 18.6 - - + -
1310A LYS 3.3 18.8 + - - +
1311A ILE* 3.2 6.8 + - - +
1313A MET* 1.3 76.1 - - - +
1315A CYS* 1.3 58.3 + - - +
1316A GLU 3.0 3.8 + - - -
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Residues in contact with CYS1315 (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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1173A ILE* 4.0 17.3 - - - -
1175A CYS* 3.6 47.3 - - + +
1287A VAL* 4.1 10.1 - - - -
1290A ALA* 4.1 12.3 - - - -
1291A ARG* 5.2 1.3 - - - -
1294A ARG* 3.3 13.8 + - - +
1311A ILE* 3.2 12.9 + - - -
1312A ARG* 3.1 32.3 + - - +
1314A ALA* 1.3 70.5 - - - +
1316A GLU* 1.3 64.5 + - - +
1317A ASP* 3.4 0.5 - - - +
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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