Contacts of the strand formed by residues 1209 - 1213 (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 ILE1209 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204G LEU* 4.3 19.7 - - + -
1208G PRO* 1.3 71.6 - - - +
1210G MET* 1.3 74.6 + - - +
1211G ILE* 3.5 7.0 + - + +
1244G ALA* 4.4 6.1 - - + -
1250G THR 2.9 16.9 + - - +
1251G VAL* 3.3 7.1 - - + -
1252G ASP 2.9 22.5 + - - -
1273G HIS* 4.2 0.7 - - - -
1274G CYS* 3.6 20.2 - - - -
1275G GLY 3.7 13.0 - - - +
1277G VAL* 4.1 21.3 - - + -
1342G VAL* 4.1 26.7 - - + +
1345G ILE* 4.0 19.7 - - + -
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Residues in contact with MET1210 (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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1208G PRO 3.8 2.6 + - - -
1209G ILE* 1.3 74.6 - - - +
1211G ILE* 1.3 59.7 + - - +
1212G LEU* 3.6 22.0 - - + -
1252G ASP* 3.5 14.6 - - - +
1254G ARG* 3.5 40.8 - - - +
1265G TRP 3.5 23.6 - - - +
1268G GLU* 4.4 1.8 - - + -
1269G ALA* 3.9 14.8 - - + +
1273G HIS* 3.4 45.3 - - + +
1275G GLY 2.9 14.2 + - - +
1276G ILE* 3.3 5.8 - - + +
1277G VAL 2.9 24.9 + - - +
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Residues in contact with ILE1211 (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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1209G ILE* 3.7 17.5 - - + +
1210G MET* 1.3 75.7 - - - +
1212G LEU* 1.3 63.7 + - - +
1213G ASN* 4.0 3.0 + - - +
1240G CYS* 3.9 26.9 - - + -
1251G VAL* 4.0 16.8 - - + -
1252G ASP 2.9 9.1 + - - +
1253G PHE* 3.5 29.6 - - + -
1254G ARG 2.9 26.9 + - - +
1277G VAL* 3.2 16.4 - - + +
1338G TYR* 4.1 20.2 - - + -
1342G VAL* 4.1 17.7 - - + -
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Residues in contact with LEU1212 (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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1210G MET* 3.6 32.3 - - + -
1211G ILE* 1.3 74.5 - - - +
1213G ASN* 1.3 61.9 - - - +
1214G GLY 4.3 0.2 - - - -
1254G ARG* 3.7 11.7 - - + -
1262G LEU* 4.5 12.1 - - + +
1265G TRP* 3.8 32.3 - - + -
1266G ILE* 3.6 39.5 - - + +
1276G ILE* 4.3 15.5 - - + -
1277G VAL 2.9 8.1 + - - +
1278G ILE* 3.4 19.1 - - + +
1279G ASN 2.9 26.4 + - - -
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Residues in contact with ASN1213 (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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1211G ILE* 4.0 4.4 + - - +
1212G LEU* 1.3 79.4 - - - +
1214G GLY* 1.3 61.1 + - - +
1217G LEU* 3.8 9.2 - - + -
1233G LEU* 3.9 8.0 - - - +
1253G PHE* 3.1 35.4 - - - -
1254G ARG 3.0 24.3 + - - +
1255G GLN* 3.2 15.2 - - + -
1256G SER 2.9 27.2 + - - +
1262G LEU* 3.9 6.9 - - - +
1279G ASN* 3.4 3.7 - - - +
1338G TYR* 2.7 37.4 + - - -
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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