Contacts of the strand formed by residues 1149 - 1151 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061E HIS* 3.9 5.9 - - - +
1087E LEU* 4.0 23.1 - - + -
1090E TYR* 6.4 0.2 - - + -
1115E MET* 4.1 25.8 - - + -
1118E GLU* 3.0 29.4 + - + +
1119E ILE* 3.4 34.1 - - + -
1141E CYS* 3.8 16.8 - - + -
1142E MET 3.2 7.0 - - - +
1143E VAL* 4.0 11.7 - - + -
1147E PHE 4.2 4.7 - - - +
1148E THR* 1.3 76.3 - - - +
1150E LYS* 1.3 70.4 - - - +
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Residues in contact with LYS1150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059E CYS 5.1 0.2 + - - -
1060E HIS* 2.7 43.1 + - - +
1061E HIS* 3.1 13.7 - - - +
1062E VAL 4.2 8.5 + - - +
1063E VAL* 3.8 11.0 - - + +
1080E GLU* 2.7 32.0 + - - +
1082E MET* 3.4 32.3 - - + -
1118E GLU 5.7 0.2 - - - -
1141E CYS* 3.3 3.9 - - - -
1142E MET* 2.9 32.4 + - - +
1144E ALA* 5.1 3.4 - - - -
1148E THR* 4.1 19.3 - - + -
1149E VAL* 1.3 81.9 - - - +
1151E ILE* 1.3 66.3 + - - +
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Residues in contact with ILE1151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061E HIS 2.7 15.8 + - - +
1062E VAL* 3.5 9.0 - - + +
1063E VAL 2.9 24.1 + - - -
1119E ILE* 3.7 47.1 - - + +
1122E GLY* 4.1 12.3 - - - -
1123E MET* 4.2 8.5 - - + +
1126E LEU* 5.6 1.8 - - + -
1133E HIS* 3.4 36.8 - - + +
1136E LEU* 4.2 9.0 - - + -
1140E ASN 4.6 2.0 - - - +
1141E CYS* 4.1 13.0 - - - +
1150E LYS* 1.3 72.5 - - - +
1152E GLY* 1.3 62.2 + - - +
1154E PHE* 3.8 15.9 - - + -
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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
------------------------------------------------------------
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