Contacts of the strand formed by residues 1149 - 1151 (chain B) in PDB entry 3F5P
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 VAL1149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061B HIS* 4.0 3.3 - - - -
1087B LEU* 4.0 15.3 - - + -
1115B MET* 4.1 27.6 - - + +
1118B GLU* 3.0 29.7 + - - +
1119B ILE* 3.4 36.1 - - + -
1141B CYS* 3.9 14.6 - - + -
1142B MET 3.1 7.0 - - - +
1143B VAL* 3.7 22.4 - - + -
1147B PHE 4.1 5.4 - - - +
1148B THR* 1.3 77.5 - - - +
1150B LYS* 1.3 69.4 + - - +
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Residues in contact with LYS1150 (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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1059B CYS 5.1 0.2 + - - -
1060B HIS* 2.8 46.5 + - - +
1061B HIS* 3.3 12.3 - - - +
1062B VAL 4.2 0.8 + - - -
1063B VAL* 3.7 22.8 - - + +
1080B GLU* 3.1 33.1 + - - +
1082B MET* 3.7 24.9 - - + -
1141B CYS* 3.3 5.6 - - - -
1142B MET 2.7 37.3 + - - -
1144B ALA* 5.1 3.1 - - - -
1148B THR* 4.2 17.5 - - + -
1149B VAL* 1.3 81.8 - - - +
1151B ILE* 1.3 67.4 + - - +
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Residues in contact with ILE1151 (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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1061B HIS 2.9 16.4 + - - +
1062B VAL* 3.3 12.4 - - + +
1063B VAL 2.9 23.2 + - - -
1118B GLU 4.5 0.2 - - - +
1119B ILE* 3.2 49.1 - - + +
1122B GLY* 4.4 1.6 - - - -
1123B MET* 4.0 25.1 - - + +
1126B LEU* 5.5 1.6 - - + -
1133B HIS* 3.3 31.6 - - + +
1136B LEU* 4.3 11.9 - - + -
1140B ASN 4.5 2.9 - - - +
1141B CYS* 4.6 2.7 - - - -
1150B LYS* 1.3 72.3 - - - +
1152B GLY* 1.3 62.8 + - - +
1154B PHE* 3.4 18.6 - - + -
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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
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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