Contacts of the strand formed by residues 770 - 775 (chain A) in PDB entry 4BL8
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 TRP 770 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A THR* 3.6 18.4 - - + -
738A LYS* 3.9 23.6 - - + -
743A ASP 5.0 7.5 + - - -
745A ALA* 3.4 27.6 - - + -
747A THR* 3.2 27.6 - - - -
757A PHE* 4.3 5.3 - - + -
766A ALA* 3.3 3.5 - - - +
767A HIS* 2.8 51.5 + + + +
768A GLY* 2.9 3.6 - - - -
769A PRO* 1.3 81.4 - - + +
771A LEU* 1.3 63.8 + - - +
772A GLN* 4.1 6.7 + - + -
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Residues in contact with LEU 771 (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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615A TRP* 3.5 38.6 - - + -
706A LEU* 4.7 2.5 - - + -
709A VAL* 3.8 15.0 - - + -
711A LEU* 3.5 31.2 - - + -
745A ALA 3.0 16.9 + - - +
746A ILE* 3.5 8.0 - - + -
747A THR* 2.8 28.4 + - - -
765A ALA 3.4 21.5 - - - +
766A ALA* 3.9 12.3 - - + -
769A PRO 3.3 0.4 + - - -
770A TRP* 1.3 75.5 - - - +
772A GLN* 1.3 61.6 + - - +
773A ILE* 3.6 23.1 - - + -
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Residues in contact with GLN 772 (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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747A THR* 3.4 32.7 + - + +
749A VAL* 4.4 4.5 - - + -
755A GLY 5.3 1.0 + - - -
756A ALA* 3.4 19.0 - - - +
757A PHE* 2.9 58.2 + - + -
758A ALA* 3.8 9.0 + - + +
763A PRO 3.5 2.2 - - - +
765A ALA 2.8 40.2 + - - +
770A TRP* 4.1 7.2 + - + -
771A LEU* 1.3 73.0 - - - +
773A ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 773 (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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709A VAL* 4.7 4.3 - - + -
711A LEU* 3.5 22.4 - - + -
746A ILE* 4.6 4.5 - - + -
747A THR 3.1 10.4 + - - +
748A PHE* 3.5 36.9 - - + -
749A VAL* 3.0 23.0 + - - -
758A ALA* 4.7 0.2 - - - -
763A PRO 3.3 3.1 - - - -
764A TYR* 3.8 25.1 - - + -
771A LEU* 3.6 31.4 - - + -
772A GLN* 1.3 80.3 - - - +
774A LEU* 1.3 59.7 + - - +
775A LEU* 4.0 9.5 + - + +
807A LYS* 4.7 10.8 - - + +
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Residues in contact with LEU 774 (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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749A VAL* 3.2 21.8 - - + +
750A SER 4.0 12.6 - - - +
751A THR* 4.4 9.6 - - - +
752A GLY 5.2 1.8 - - - +
758A ALA* 3.5 29.6 - - + +
759A THR 4.1 2.2 - - - +
760A GLU* 3.8 41.1 - - + +
763A PRO* 2.9 35.6 + - + +
764A TYR* 4.5 0.5 - - - -
773A ILE* 1.3 73.1 - - - +
775A LEU* 1.3 82.4 + - - +
776A THR* 4.2 5.5 + - + +
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Residues in contact with LEU 775 (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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725A LEU* 4.0 10.5 - - + -
729A LEU* 4.0 16.2 - - + +
748A PHE* 3.8 27.6 - - + -
749A VAL 3.2 8.2 + - - +
750A SER* 4.2 3.6 - - - -
751A THR* 3.9 16.1 + - - +
764A TYR* 4.7 10.8 - - + +
773A ILE* 4.5 16.6 - - + +
774A LEU* 1.3 86.1 - - - +
776A THR* 1.3 64.1 + - - +
777A GLU 3.9 0.5 + - - -
779A PHE* 4.1 26.5 - - + -
780A VAL* 3.6 18.2 - - + +
783A MET* 3.9 20.6 - - + -
807A LYS* 4.5 6.7 - - + +
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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