Contacts of the helix formed by residues 1309 - 1313 (chain G) in PDB entry 2BT4
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 ASN1309 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B SER 3.1 18.7 + - - -
326B ALA 2.8 27.9 + - - -
327B ASP 3.7 16.7 + - - +
329B VAL* 3.9 13.7 - - - +
1308G SER* 1.4 71.2 - - - +
1310G ILE* 1.3 65.0 + - - +
1311G HIS* 2.9 30.0 + - - +
1312G GLN* 2.9 30.4 + - + +
1313G ARG* 3.5 8.0 - - - +
1331G ALA* 4.4 2.4 - - - +
1332G GLY* 3.5 10.6 - - - +
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Residues in contact with ILE1310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285G HIS* 4.5 6.5 - - + -
1306G HIS* 4.0 28.7 - - + +
1308G SER* 3.2 11.3 + - - +
1309G ASN* 1.3 72.8 + - - +
1311G HIS* 1.3 85.5 + - + +
1312G GLN 3.1 0.9 - - - -
1313G ARG* 3.2 19.0 + - - +
1317G ARG* 3.3 26.9 - - + +
1318G HIS* 3.2 28.3 - - - +
1320G SER* 5.0 6.3 - - - -
1323G SER* 6.0 0.2 - - - +
1329G VAL* 6.1 2.2 - - + -
1331G ALA* 4.4 8.3 - - + -
1360G CA2 3.9 33.7 - - + +
2417G GOL 4.7 4.0 - - - +
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Residues in contact with HIS1311 (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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311B HIS* 4.1 18.0 + + - -
323B SER* 3.9 32.1 - - - +
324B GLN* 4.6 11.8 - - - +
329B VAL* 4.7 12.4 - - + +
2414B GOL 2.6 35.8 + - - -
1309G ASN* 2.9 22.7 + - - +
1310G ILE* 1.3 95.3 - - + +
1312G GLN* 1.3 57.2 - - - +
1313G ARG 3.4 1.1 - - - -
1318G HIS* 3.4 39.4 + - - -
1329G VAL* 6.3 1.4 - - - +
1331G ALA* 4.7 8.0 - - + +
2417G GOL 3.9 10.1 - - - -
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Residues in contact with GLN1312 (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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323B SER 3.2 11.4 + - - +
324B GLN* 3.1 30.6 + - - +
325B ARG* 3.2 12.9 + - - +
326B ALA 2.8 27.5 + - - +
327B ASP* 4.8 2.8 - - - +
1309G ASN* 2.9 24.2 + - + +
1311G HIS* 1.3 76.6 - - - +
1313G ARG* 1.3 64.4 + - + +
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Residues in contact with ARG1313 (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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1224G GLN* 4.4 16.4 + - - +
1227G ILE* 4.5 14.8 - - - +
1228G TYR* 2.8 35.2 + - - -
1308G SER* 3.0 31.2 + - - -
1309G ASN 3.5 13.5 - - - +
1310G ILE* 3.2 13.1 + - - +
1312G GLN* 1.3 86.4 - - + +
1314G GLU* 1.3 73.9 + - - +
1315G PRO* 3.5 1.2 - - - +
1317G ARG* 4.0 30.1 - - - +
1318G HIS* 2.7 22.9 + - - -
1360G CA2 4.2 9.5 + - - +
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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