Contacts of the helix formed by residues 1309 - 1315 (chain D) in PDB entry 5TJ4
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 PRO1309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1270D ASP* 4.6 28.1 - - - +
1274D SER* 3.6 17.5 - - - +
1306D PRO 5.6 0.2 - - - +
1307D ASP 4.4 2.7 - - - +
1308D LYS* 1.3 101.4 - - + +
1310D LEU* 1.3 75.2 + - + +
1311D LEU* 3.2 4.5 - - + -
1312D SER* 2.9 23.3 + - - +
1313D SER* 3.3 3.5 + - - -
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Residues in contact with LEU1310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270D ASP 4.5 6.2 + - - -
1271D VAL* 3.6 44.6 - - + +
1274D SER* 3.6 20.6 + - - +
1275D LEU* 4.7 3.6 - - + -
1288D LEU* 3.2 47.3 - - + -
1292D VAL* 4.7 6.1 - - + -
1309D PRO* 1.3 79.4 - - + +
1311D LEU* 1.3 58.7 + - + +
1313D SER* 2.8 33.9 + - - +
1314D LEU* 3.5 7.8 + - + +
1329D ILE* 4.5 24.0 - - + -
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Residues in contact with LEU1311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288D LEU* 5.3 6.3 - - + -
1291D ARG* 4.3 35.4 - - + +
1292D VAL* 5.0 5.2 - - + +
1295D VAL* 3.5 30.5 - - + -
1303D MET* 4.4 24.2 - - + -
1308D LYS* 4.1 29.6 - - + -
1309D PRO* 3.2 3.8 - - + -
1310D LEU* 1.3 81.7 - - + +
1312D SER* 1.3 62.8 + - - +
1314D LEU* 3.2 34.2 + - + +
1315D PHE* 3.5 14.1 - - - -
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Residues in contact with SER1312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267D LYS* 4.4 5.9 + - - +
1270D ASP* 5.9 1.6 - - - -
1301D LEU* 6.3 0.7 - - - -
1303D MET* 5.5 4.9 - - - -
1305D ASP* 3.0 24.5 + - - -
1306D PRO* 4.8 1.0 - - - +
1308D LYS 2.1 31.5 + - - -
1309D PRO* 2.9 15.0 + - - -
1311D LEU* 1.3 73.1 - - - +
1313D SER* 1.3 58.7 + - - -
1315D PHE* 3.2 31.0 + - - +
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Residues in contact with SER1313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263D LEU* 3.3 22.9 - - - +
1267D LYS* 3.6 26.4 - - - +
1270D ASP* 5.3 2.0 - - - -
1271D VAL* 3.7 25.7 - - - +
1309D PRO 3.3 2.5 + - - -
1310D LEU* 2.8 19.7 + - - -
1312D SER* 1.3 69.8 - - - +
1314D LEU* 1.3 57.6 + - - +
1315D PHE 3.1 2.2 - - - -
1325D ARG* 2.7 29.1 + - - -
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Residues in contact with LEU1314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292D VAL* 4.5 17.9 - - + -
1295D VAL* 4.4 24.9 - - + -
1310D LEU* 4.0 10.1 - - + +
1311D LEU* 3.4 26.7 - - + +
1312D SER 3.2 1.0 - - - -
1313D SER* 1.3 78.0 - - - +
1315D PHE* 1.3 60.9 + - + +
1321D LEU* 4.0 13.2 - - + -
1322D VAL* 3.1 31.8 + - - +
1325D ARG* 3.6 15.7 - - + +
1326D ALA* 3.5 37.7 - - + +
1329D ILE* 4.1 14.1 - - + -
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Residues in contact with PHE1315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267D LYS* 2.6 28.6 + - - -
1295D VAL* 4.2 14.1 - - + -
1299D GLY 4.8 12.3 - - - -
1300D GLU 5.0 2.2 - - - -
1301D LEU* 3.3 35.9 - - + -
1303D MET* 4.5 6.3 - - + -
1311D LEU* 3.5 25.1 - - + -
1312D SER* 3.2 16.4 + - - +
1313D SER 3.1 0.4 - - - -
1314D LEU* 1.3 78.6 - - - +
1316D ASN* 1.3 57.8 + - - +
1319D GLY* 4.3 15.5 - - - -
1320D VAL 3.4 5.2 - - - +
1321D LEU* 3.4 49.8 - - + -
1325D ARG* 2.9 7.7 + - - -
325J GLN* 5.6 4.5 - - - -
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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