Contacts of the strand formed by residues 740 - 746 (chain B) in PDB entry 4BIC
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 TYR 740 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726B ILE* 3.9 20.8 - - + +
729B HIS* 3.4 45.0 - + + +
730B LYS* 3.7 40.3 - - + +
732B LEU 5.3 0.4 + - - -
738B VAL 3.5 3.6 + - - -
739B GLN* 1.3 96.5 + - - +
741B LEU* 1.3 62.8 + - - +
742B GLY* 3.3 34.0 - - - -
743B SER* 2.7 28.8 + - - -
752B ILE* 4.0 20.6 - - + -
753B PHE 3.8 2.7 - - - -
754B MET* 4.3 3.1 - - - -
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Residues in contact with LEU 741 (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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671B LEU* 6.0 5.8 - - + -
706B ILE* 3.9 22.0 - - + -
739B GLN* 4.0 18.2 - - + +
740B TYR* 1.3 83.6 - - - +
742B GLY* 1.3 55.6 + - - +
753B PHE* 2.6 24.0 + - + +
754B MET* 3.6 31.4 - - - +
755B GLU* 3.8 7.6 - - + +
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Residues in contact with GLY 742 (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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740B TYR* 3.3 23.6 - - - -
741B LEU* 1.3 79.4 - - - +
743B SER* 1.3 60.4 + - - -
753B PHE* 2.7 36.7 + - - +
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Residues in contact with SER 743 (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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726B ILE* 3.5 19.0 - - - +
740B TYR* 2.7 22.5 + - - -
742B GLY* 1.3 73.7 - - - -
744B PHE* 1.4 69.7 - - - +
750B ILE* 5.2 3.1 - - - -
751B LYS 3.0 16.6 - - - -
752B ILE* 3.9 17.9 - - - -
753B PHE* 4.2 3.1 - - - -
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Residues in contact with PHE 744 (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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671B LEU* 4.7 20.2 - - + -
673B TYR* 3.6 15.5 - + - -
743B SER* 1.4 77.7 - - - +
745B SER* 1.3 71.1 + - - +
746B GLU* 3.7 28.3 - - + -
750B ILE* 3.6 5.7 - - - +
751B LYS* 2.7 39.4 + - + +
753B PHE* 3.4 40.2 - + - -
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Residues in contact with SER 745 (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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713B GLU* 3.1 32.6 + - - -
744B PHE* 1.3 79.0 - - - +
746B GLU* 1.3 64.3 + - - +
749B PHE 3.3 6.4 + - - -
750B ILE* 3.9 12.3 - - - +
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Residues in contact with GLU 746 (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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673B TYR* 2.6 36.1 + - - -
713B GLU* 4.6 0.4 + - - -
744B PHE* 3.7 19.1 + - + -
745B SER* 1.3 75.1 - - - +
747B ASN* 1.4 77.5 + - + +
748B GLY 3.2 2.5 - - - -
749B PHE* 2.9 29.8 + - - +
751B LYS* 3.1 9.7 + - - +
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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