Contacts of the strand formed by residues 1247 - 1252 (chain A) in PDB entry 6Q6Q
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 GLU1247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A CYS* 3.4 21.3 - - + -
1183A ILE 3.1 11.8 + - - +
1184A ARG* 3.1 32.9 + - + +
1185A THR 2.9 25.6 + - - -
1245A PRO* 4.0 3.3 - - - +
1246A THR* 1.3 78.7 - - - +
1248A LEU* 1.3 61.9 + - - +
1249A HIS* 2.8 35.1 + - + +
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Residues in contact with LEU1248 (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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155A ARG* 4.4 13.0 - - + -
562A CYS 3.0 11.0 + - - +
563A SER* 3.2 8.8 - - - -
564A THR 3.1 23.7 + - - +
565A LEU* 5.3 1.5 - - + +
1185A THR* 3.4 27.4 - - + +
1187A ILE* 4.5 6.7 - - + -
1205A GLU* 3.7 36.8 - - + +
1208A PHE* 5.2 7.0 - - + -
1209A ILE* 6.3 3.4 - - + -
1244A MET* 5.6 7.0 - - + -
1245A PRO* 4.6 18.2 - - + +
1247A GLU* 1.3 74.7 - - - +
1249A HIS* 1.3 72.3 + - - +
1250A ILE* 4.1 19.3 - - + -
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Residues in contact with HIS1249 (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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562A CYS* 5.1 3.4 - - - -
564A THR* 2.3 46.9 + - + +
983A MET* 4.0 15.9 - - + +
1184A ARG* 3.3 22.6 + - + -
1185A THR 2.9 7.2 + - - +
1186A ASP* 3.1 28.2 - - - +
1187A ILE* 2.7 32.8 + - - +
1247A GLU* 2.8 37.4 + - + +
1248A LEU* 1.3 77.9 + - - +
1250A ILE* 1.3 58.4 + - - +
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Residues in contact with ILE1250 (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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564A THR 3.1 7.0 + - - +
565A LEU* 3.3 18.6 - - + +
566A LYS* 2.9 23.7 + - - +
983A MET* 4.9 1.1 - - - -
1187A ILE* 3.2 22.7 - - + +
1201A ILE* 4.5 20.2 - - + +
1204A ILE* 3.7 38.4 - - + -
1205A GLU* 3.5 35.4 - - + +
1248A LEU* 4.1 13.0 - - + -
1249A HIS* 1.3 78.4 - - - +
1251A ALA* 1.3 69.1 + - - +
1252A LEU* 5.0 1.3 - - + -
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Residues in contact with ALA1251 (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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566A LYS* 3.5 21.5 - - + -
979A GLU* 4.2 16.2 - - - +
983A MET* 3.6 24.9 - - - -
1187A ILE 2.9 6.5 + - - +
1188A VAL* 3.2 10.3 - - + +
1189A MET 3.1 22.9 + - - -
1250A ILE* 1.3 77.6 - - - +
1252A LEU* 1.3 67.6 + - - +
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Residues in contact with LEU1252 (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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566A LYS* 2.9 18.6 + - - +
567A TYR* 4.0 27.0 - - + -
568A GLN* 5.4 3.3 + - - +
979A GLU* 5.6 1.1 - - - +
1189A MET* 3.6 9.6 - - + +
1191A VAL* 4.2 28.3 - - + -
1194A SER* 4.6 14.1 - - - +
1197A PRO* 4.7 4.7 - - + -
1200A ASP* 5.4 3.1 - - + -
1201A ILE* 4.0 22.0 - - + -
1204A ILE* 3.8 29.8 - - + -
1250A ILE* 5.0 1.6 - - + -
1251A ALA* 1.3 79.4 - - - +
1253A LEU* 1.3 68.7 + - - +
1254A PRO* 3.4 6.8 - - - +
1268A LEU* 5.4 0.4 - - + -
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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