Contacts of the strand formed by residues 872 - 878 (chain A) in PDB entry 4B87
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 ALA 872 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865A ALA* 4.4 12.6 - - + +
866A VAL* 4.2 19.1 - - + +
869A ASN* 3.0 19.7 + - + +
870A PRO 4.5 3.5 - - - +
871A HIS* 1.3 80.5 - - - +
873A LEU* 1.3 62.4 + - - +
874A VAL* 4.3 0.6 + - + -
928A LEU* 4.5 9.7 - - - +
953A TYR* 4.1 5.6 - - - -
955A GLN* 3.5 36.6 - - + +
957A LEU* 5.6 3.6 - - + +
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Residues in contact with LEU 873 (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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872A ALA* 1.3 75.0 - - - +
874A VAL* 1.3 62.9 + - - +
875A VAL* 3.9 14.0 + - + -
928A LEU 3.5 19.5 - - - +
930A HIS* 3.6 38.6 - - + +
945A HIS* 3.5 32.3 - - + +
946A LEU* 5.1 1.3 - - + -
953A TYR* 3.7 36.1 - - + -
955A GLN 2.7 16.0 + - - +
956A ILE* 3.3 12.4 - - + +
957A LEU* 2.8 28.9 + - - +
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Residues in contact with VAL 874 (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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862A ALA* 4.0 15.7 - - + -
865A ALA* 5.7 0.9 - - + -
866A VAL* 4.5 11.7 - - + -
872A ALA* 4.2 0.9 - - + -
873A LEU* 1.3 76.9 - - - +
875A VAL* 1.3 60.6 + - - +
890A ILE* 3.9 18.2 - - + -
894A LEU* 3.8 27.4 - - + -
928A LEU 3.1 11.8 + - - +
929A VAL* 3.1 11.1 - - + -
930A HIS 2.8 31.2 + - - +
957A LEU* 3.3 17.3 - - + +
959A PHE* 3.9 26.7 - - + -
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Residues in contact with VAL 875 (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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873A LEU* 3.9 24.9 - - + -
874A VAL* 1.3 80.5 - - - +
876A CYS* 1.3 72.6 + - - +
929A VAL* 5.5 0.2 - - - -
930A HIS* 3.3 14.6 - - + +
932A LEU* 3.7 22.7 - - + -
937A ILE* 3.6 27.6 - - + -
942A LEU* 4.0 5.4 - - + -
945A HIS* 4.4 2.0 - - + -
956A ILE* 4.1 20.4 - - + -
957A LEU 2.8 10.1 + - - +
958A ALA* 3.2 4.5 - - + -
959A PHE* 2.9 28.2 + - - -
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Residues in contact with CYS 876 (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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874A VAL* 5.3 0.7 - - - -
875A VAL* 1.3 83.8 - - - +
877A GLY* 1.3 56.0 + - - +
886A VAL* 4.7 0.7 - - - -
887A PHE* 3.9 26.2 - - + -
890A ILE* 4.0 24.0 - - - -
929A VAL* 4.8 7.0 - - - -
930A HIS 2.9 7.2 + - - +
931A LEU* 3.3 20.5 - - + +
932A LEU 2.8 31.0 + - - -
937A ILE* 4.1 0.4 - - - -
959A PHE* 3.8 11.0 - - - -
2042A EDO 3.9 18.8 - - - +
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Residues in contact with GLY 877 (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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876A CYS* 1.3 77.9 - - - +
878A THR* 1.3 62.8 + - - -
883A LYS* 6.0 0.9 - - - +
887A PHE* 5.6 1.7 - - - -
931A LEU* 4.3 3.5 - - - +
932A LEU 3.1 7.9 - - - -
934A MET* 3.4 23.8 - - - +
937A ILE* 3.6 22.3 - - - +
959A PHE 3.8 9.3 + - - -
2042A EDO 4.4 7.9 + - - -
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Residues in contact with THR 878 (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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877A GLY* 1.3 75.2 - - - -
879A TYR* 1.3 60.7 + - - +
880A SER 3.0 11.3 + - - -
882A GLY 5.1 2.6 + - - -
887A PHE* 5.2 4.4 - - - -
904A LYS* 2.9 46.2 + - + +
931A LEU* 3.8 22.2 - - + -
932A LEU 2.8 17.5 + - - +
933A PRO* 3.4 6.4 - - + +
934A MET* 2.9 23.3 + - - +
2044A EDO 3.4 3.3 + - - +
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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