Contacts of the helix formed by residues 1369 - 1374 (chain G) 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 ASN1369 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1365G VAL 4.5 5.3 + - - +
1366G MET* 3.3 8.5 + - - +
1367G GLU 3.3 0.4 - - - -
1368G GLN* 1.3 77.1 - - - +
1370G TRP* 1.3 70.2 + - - +
1371G ASP 3.9 0.5 + - - -
1372G GLU* 3.3 37.1 + - + +
1383G ASP* 3.9 19.9 + - - +
1385G GLU* 5.3 2.8 - - - +
1386G ALA* 4.0 22.1 + - - +
1389G LEU* 5.1 7.1 - - - +
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Residues in contact with TRP1370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G GLN* 5.0 10.1 - - + -
1366G MET 2.9 14.3 + - - +
1367G GLU* 2.6 52.4 + - + +
1368G GLN 4.6 2.5 - - - +
1369G ASN* 1.3 77.7 - - - +
1371G ASP* 1.3 91.6 + - + +
1372G GLU* 2.1 30.6 + - - +
1373G LEU* 3.3 13.8 + - - +
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Residues in contact with ASP1371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369G ASN 3.9 1.0 + - - -
1370G TRP* 1.3 118.1 + - + +
1372G GLU* 1.3 50.8 + - - +
1373G LEU* 2.5 20.6 + - - +
1374G ALA* 3.6 9.9 + - - +
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Residues in contact with GLU1372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249G MET* 5.9 1.6 - - - +
1366G MET* 4.1 21.6 - - - +
1369G ASN* 3.3 45.2 + - + +
1370G TRP 2.1 27.2 + - - +
1371G ASP* 1.3 65.4 - - - +
1373G LEU* 1.3 62.6 + - + +
1374G ALA 3.0 17.0 + - - -
1375G SER* 4.3 11.6 + - - -
1386G ALA* 4.8 8.9 - - - +
1390G CYS* 4.1 22.2 - - - -
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Residues in contact with LEU1373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248G ASN* 3.0 17.2 + - - +
1249G MET* 4.7 2.8 + - - +
1250G LYS* 3.3 26.3 + - + +
1366G MET* 5.6 12.3 - - + +
1370G TRP 3.3 14.0 + - - +
1371G ASP* 2.5 12.7 + - - +
1372G GLU* 1.3 75.9 - - + +
1374G ALA* 1.3 54.3 + - - +
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Residues in contact with ALA1374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248G ASN* 2.8 31.4 - - + +
1249G MET* 6.1 0.2 - - - -
1371G ASP 3.6 7.8 + - - +
1372G GLU* 3.8 8.3 - - - -
1373G LEU* 1.3 74.3 - - - +
1375G SER* 1.3 62.1 + - - +
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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