Contacts of the strand formed by residues 1269 - 1272 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215A PHE* 4.1 31.4 - - + -
1218A HIS* 3.1 26.6 + - + +
1229A THR* 3.6 8.7 - - + -
1231A MET* 4.2 14.4 - - + -
1249A PRO 3.9 5.3 + - - +
1250A TYR* 3.3 4.9 - - - +
1251A GLU 3.1 23.4 + - - -
1268A PRO* 1.3 73.3 - - - +
1270A GLN* 1.3 61.4 + - - +
1271A ILE* 3.6 2.2 + - + -
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Residues in contact with GLN1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228A SER* 6.4 1.3 - - - -
1229A THR 2.7 19.3 + - - +
1230A VAL* 3.1 20.7 - - + +
1231A MET 2.8 27.0 + - - -
1251A GLU* 3.0 32.7 - - - +
1253A TYR* 2.3 32.1 + - + -
1261A MET* 3.5 17.3 - - + +
1262A ASN* 2.9 41.2 + - - +
1263A LEU* 5.6 0.4 - - - -
1267A GLN* 5.2 2.5 - - + -
1268A PRO* 3.8 11.3 - - - +
1269A ALA* 1.3 72.3 - - - +
1271A ILE* 1.3 60.9 + - - +
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Residues in contact with ILE1271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215A PHE* 3.7 23.3 - - + -
1231A MET* 3.4 19.5 - - + +
1234A LEU* 3.4 44.6 - - + +
1240A PHE* 4.9 2.0 - - + -
1250A TYR* 3.6 29.2 - - + -
1251A GLU 2.7 11.0 + - - +
1252A TYR* 3.2 33.4 - - + -
1253A TYR* 3.0 31.8 + - - +
1269A ALA* 4.5 2.0 - - + +
1270A GLN* 1.3 76.5 - - - +
1272A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200A ARG* 5.6 0.2 - - - +
1230A VAL* 4.9 0.7 - - + -
1231A MET 2.9 7.7 + - - +
1232A GLU* 2.9 44.5 - - + +
1233A GLY 2.5 33.8 + - - -
1234A LEU 3.5 3.8 + - - -
1253A TYR 3.0 15.3 - - - +
1254A GLY 2.8 34.3 - - - +
1255A ASN* 4.0 14.1 - - - +
1258A ILE* 3.8 25.4 - - + -
1261A MET* 4.1 16.6 - - + -
1271A ILE* 1.3 75.6 - - - +
1273A ASP* 1.3 61.5 + - - +
1275A TYR* 4.3 0.9 - - + -
1283A ARG* 3.9 1.8 - - - +
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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