Contacts of the strand formed by residues 1048 - 1052 (chain B) in PDB entry 7CN9
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 HIS1048 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909B ILE* 3.1 29.3 - - - +
1032B CYS* 3.4 18.4 - - + -
1036B GLN* 6.0 0.4 - - - -
1037B SER* 4.4 27.3 + - - +
1038B LYS* 6.0 3.8 - - - +
1039B ARG 5.4 2.8 + - - -
1040B VAL* 5.7 6.2 - - + +
1043B CYS* 2.7 50.7 + - + +
1044B GLY* 4.0 7.4 - - - +
1046B GLY 2.8 10.6 + - - +
1047B TYR* 1.3 70.6 - - - +
1049B LEU* 1.3 84.5 + - - +
1050B MET* 3.1 35.0 + - - -
1065B VAL 4.1 4.7 - - - -
1066B THR* 4.5 3.6 - - - -
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Residues in contact with LEU1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ILE* 5.2 9.6 - - + -
902B MET* 4.2 15.9 - - - -
905B ARG* 3.5 17.7 - - + -
906B PHE* 3.4 38.6 - - + -
909B ILE* 4.1 7.0 - - + -
1036B GLN* 3.0 53.7 + - - +
1047B TYR 3.9 1.2 + - - -
1048B HIS* 1.3 80.0 + - - +
1050B MET* 1.3 64.2 + - + +
1065B VAL* 3.0 34.3 + - + +
1067B TYR* 4.7 13.9 - - + +
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Residues in contact with MET1050 (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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881B THR* 5.0 3.8 - - + +
882B ILE* 4.7 10.5 - - + -
902B MET* 3.9 24.2 - - + -
905B ARG* 4.0 29.6 - - - +
1032B CYS 4.3 4.0 - - - +
1033B VAL* 4.8 11.4 - - + +
1035B GLY 5.2 4.9 - - - +
1048B HIS* 3.1 15.0 + - - -
1049B LEU* 1.3 81.8 - - - +
1051B SER* 1.3 90.1 + - - +
1052B PHE* 3.4 28.7 - - + -
1064B HIS* 3.4 2.1 - - - -
1065B VAL* 2.9 41.1 + - + +
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Residues in contact with SER1051 (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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1032B CYS* 3.4 23.1 + - - -
1033B VAL* 3.3 22.8 - - - +
1048B HIS* 4.6 2.7 - - - -
1050B MET* 1.3 96.1 - - - +
1052B PHE* 1.3 69.4 + - - +
1053B PRO* 4.2 0.3 - - - +
1062B PHE* 3.8 2.9 - - - +
1063B LEU 2.1 28.1 + - - -
1064B HIS* 2.2 28.4 + - - +
1065B VAL* 6.1 0.2 - - - -
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Residues in contact with PHE1052 (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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802B PHE* 3.4 38.4 - + - -
805B ILE* 5.1 17.7 - - + -
806B LEU* 6.3 0.2 - - + -
882B ILE* 3.9 26.0 - - + -
898B PHE* 4.5 6.5 - + - -
902B MET* 6.0 0.2 - - + -
927B PHE* 4.3 18.4 - + - -
931B ILE* 6.5 0.7 - - + -
1033B VAL* 5.0 1.6 - - - -
1050B MET* 3.4 31.2 - - + -
1051B SER* 1.3 80.3 - - - +
1053B PRO* 1.3 74.4 - - + +
1062B PHE* 3.3 8.6 - - - +
1063B LEU* 2.9 43.6 + - + +
1065B VAL* 6.0 3.6 - - + -
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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
------------------------------------------------------------
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