Contacts of the strand formed by residues 1328 - 1331 (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 GLY1328 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ALA 3.2 10.5 - - - -
332B GLY 3.5 9.2 + - - -
333B CYS* 4.0 9.9 - - - -
1302G VAL 3.5 3.8 + - - -
1303G VAL* 3.4 13.2 - - - +
1304G GLU 2.9 24.4 + - - -
1326G ALA* 3.5 2.9 - - - +
1327G ASP* 1.3 79.0 - - - +
1329G VAL* 1.3 67.5 + - - +
1344G ARG* 5.8 1.3 - - - +
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Residues in contact with VAL1329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ASN* 3.9 20.0 - - - +
311B HIS* 4.6 9.0 - - + +
329B VAL 3.7 2.0 - - - +
330B VAL* 3.6 1.7 - - - -
331B ALA* 2.7 43.4 + - + +
333B CYS* 4.6 0.4 - - - -
1304G GLU* 3.3 37.7 - - + +
1306G HIS* 4.7 8.1 - - + -
1310G ILE* 6.1 2.0 - - + -
1311G HIS* 6.3 1.6 - - - +
1323G SER* 3.7 21.8 - - - +
1326G ALA* 4.2 2.5 - - + -
1328G GLY* 1.3 79.3 - - - +
1330G VAL* 1.3 69.1 - - - +
1331G ALA* 5.1 4.3 - - + +
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Residues in contact with VAL1330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL 3.6 2.9 - - - -
330B VAL* 4.4 12.1 - - + -
333B CYS* 4.3 19.3 - - - -
340B PHE* 5.0 0.7 - - + -
1303G VAL* 4.4 10.1 - - + -
1304G GLU 2.8 13.4 + - - +
1305G VAL* 3.3 10.0 - - + -
1306G HIS* 2.8 27.2 + - - +
1329G VAL* 1.3 75.6 - - - +
1331G ALA* 1.4 62.7 + - - +
1333G CYS* 4.0 22.4 - - + +
1337G GLY* 3.8 27.4 - - - +
1340G PHE* 4.1 19.1 - - + -
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Residues in contact with ALA1331 (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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328B GLY* 3.3 0.3 - - - -
329B VAL* 2.8 42.6 + - + +
1306G HIS* 3.3 15.5 - - + -
1308G SER 4.0 9.2 - - - +
1309G ASN* 4.4 13.0 - - - +
1310G ILE* 4.4 13.9 - - + -
1311G HIS* 4.7 9.0 - - + +
1329G VAL* 4.2 5.1 - - + -
1330G VAL* 1.4 75.0 - - - +
1332G GLY* 1.3 63.6 + - - +
1333G CYS* 3.3 4.9 + - - -
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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