Contacts of the strand formed by residues 1260 - 1266 (chain A) in PDB entry 2Y23
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 VAL1260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1252A VAL* 4.1 16.8 - - + -
1253A GLU 3.6 5.4 - - - +
1254A ILE* 3.7 22.0 - - + -
1258A GLY 4.4 2.0 - - - +
1259A GLN* 1.3 70.7 - - - +
1261A ARG* 1.3 60.0 + - - +
1262A PHE* 3.9 26.0 - - + -
1303A MET 3.9 0.9 - - - +
1304A PHE* 3.4 9.5 - - - -
1305A MET* 3.0 50.3 + - + +
1307A LYS* 4.7 7.6 - - - -
1308A LEU* 4.1 23.8 - - + -
1341A LEU* 5.7 0.2 - - + -
1345A ALA* 4.1 14.4 - - + -
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Residues in contact with ARG1261 (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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1251A ALA 3.9 0.5 - - - +
1252A VAL* 3.5 4.8 - - - -
1253A GLU* 2.8 65.0 + - + +
1255A LEU* 4.1 23.5 - - + +
1259A GLN 3.8 1.4 + - - -
1260A VAL* 1.3 71.3 - - - +
1262A PHE* 1.3 71.1 + - - +
1263A TRP* 3.6 46.4 + - - +
1300A ILE* 4.2 12.5 - - - +
1302A GLU* 2.9 28.3 + - + +
1303A MET 3.8 2.0 - - - -
1304A PHE* 3.7 23.1 - - + -
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Residues in contact with PHE1262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1250A LEU* 4.4 6.1 - - + -
1251A ALA 3.7 3.1 - - - -
1252A VAL* 3.4 28.0 - - + -
1260A VAL* 3.9 15.0 - - + -
1261A ARG* 1.3 73.3 - - - +
1263A TRP* 1.3 63.3 + - - +
1302A GLU* 3.3 5.7 - - - +
1303A MET* 2.8 55.6 + - + +
1305A MET* 2.6 39.5 - - + -
1308A LEU* 5.2 0.2 - - + -
1316A TYR* 3.6 49.4 - + + -
1318A PHE* 4.0 17.6 - + + -
1331A VAL* 4.6 4.9 - - + -
1333A LEU* 4.1 11.7 - - + -
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Residues in contact with TRP1263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1248A SER* 4.0 21.3 - - - -
1249A GLU 3.8 2.1 - - - +
1250A LEU* 3.4 7.0 - - - +
1251A ALA* 2.8 67.2 + - + +
1252A VAL 4.8 0.2 - - - +
1253A GLU* 4.0 15.3 + - + +
1261A ARG* 3.6 62.1 - - - +
1262A PHE* 1.3 75.3 - - - +
1264A MET* 1.3 81.1 + - - +
1265A GLN* 4.7 11.0 - - + -
1300A ILE* 5.1 8.7 - - + -
1301A ILE 3.3 11.0 - - - +
1302A GLU* 4.1 2.7 - - + -
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Residues in contact with MET1264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A VAL* 3.7 26.5 - - + -
1248A SER* 3.5 10.1 - - - +
1249A GLU 4.4 1.6 - - - -
1250A LEU* 3.7 11.7 - - + +
1263A TRP* 1.3 88.5 - - - +
1265A GLN* 1.3 64.0 + - - +
1266A ALA 5.1 0.7 - - - +
1299A GLY 3.7 0.7 - - - +
1300A ILE* 3.7 3.1 - - - +
1301A ILE* 3.1 35.7 + - + -
1318A PHE* 3.8 35.9 - - + -
1320A LEU* 3.7 31.4 - - + -
1329A SER* 3.5 31.4 - - - +
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Residues in contact with GLN1265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A VAL* 3.6 4.0 - - - +
1247A LYS* 2.9 56.5 + - + +
1248A SER* 3.1 28.3 + - - +
1263A TRP* 4.7 8.8 - - + -
1264A MET* 1.3 77.6 - - - +
1266A ALA* 1.3 72.5 + - - +
1298A THR* 3.0 26.1 + - - +
1299A GLY 3.3 5.2 - - - +
1300A ILE* 4.0 23.2 - - + +
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Residues in contact with ALA1266 (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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1244A VAL* 5.2 4.7 - - + -
1245A PRO 3.7 11.7 - - - +
1246A VAL* 4.3 8.3 - - + +
1247A LYS* 4.3 1.2 - - - +
1264A MET* 4.2 1.6 - - - +
1265A GLN* 1.3 88.5 + - - +
1267A GLU* 1.3 63.5 + - - +
1268A LYS 3.3 2.6 + - - +
1269A LEU* 3.2 30.7 - - + -
1298A THR 3.8 9.2 - - - +
1299A GLY* 2.9 10.4 + - - +
1301A ILE* 4.8 11.0 - - + +
1320A LEU* 5.0 7.9 - - + -
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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