Contacts of the strand formed by residues 1269 - 1272 (chain B) in PDB entry 1Y6G
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 ALA1269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B PHE* 3.5 37.5 - - + -
1218B HIS* 3.7 15.1 + - + +
1229B THR* 3.8 9.2 - - + +
1231B MET* 4.1 13.5 - - + -
1249B PRO 4.1 3.7 + - - +
1250B TYR* 3.3 6.7 - - + +
1251B GLU 2.8 26.2 + - - -
1268B PRO* 1.3 75.0 - - - +
1270B GLN* 1.3 61.2 + - - +
1271B ILE* 3.4 2.6 + - + -
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Residues in contact with GLN1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228B SER* 5.3 1.6 - - - +
1229B THR 3.0 15.9 + - - +
1230B VAL* 3.2 7.8 - - + +
1231B MET 2.8 29.6 + - - -
1251B GLU* 3.5 18.3 + - - +
1253B TYR* 2.8 30.3 + - + -
1261B MET* 3.8 22.7 - - + -
1262B ASN* 3.3 43.9 - - - +
1263B LEU* 4.8 4.9 - - + -
1267B GLN* 4.4 2.8 - - - +
1268B PRO* 2.5 33.6 - - - +
1269B ALA* 1.3 73.1 - - - +
1271B ILE* 1.3 57.4 + - - +
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Residues in contact with ILE1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B PHE* 3.8 35.2 - - + -
1231B MET* 3.5 23.1 - - + +
1234B LEU* 4.0 21.5 - - + -
1240B PHE* 4.8 1.8 - - + -
1250B TYR* 3.8 22.7 - - + -
1251B GLU 2.7 20.2 + - - +
1252B TYR* 3.6 30.3 - - + -
1253B TYR* 3.2 27.7 + - - +
1261B MET* 4.1 3.3 - - - +
1269B ALA* 3.7 9.9 - - + +
1270B GLN* 1.3 74.9 - - - +
1272B LEU* 1.3 72.2 + - - +
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Residues in contact with LEU1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230B VAL* 5.4 0.2 - - + -
1231B MET 3.2 3.0 + - - +
1232B GLU* 3.6 39.2 - - + +
1233B GLY 2.7 32.6 + - - -
1234B LEU 3.2 4.2 + - - -
1253B TYR* 3.4 26.7 - - + +
1254B GLY 3.8 13.2 - - - +
1255B ASN* 4.0 16.6 - - - +
1258B ILE* 3.7 28.9 - - + -
1261B MET* 3.8 14.6 - - + -
1271B ILE* 1.3 81.0 - - - +
1273B ASP* 1.3 58.0 + - - +
1274B CYS 4.1 11.4 - - - +
1275B TYR* 4.7 0.4 - - + -
1283B ARG* 3.8 4.7 - - - +
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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