Contacts of the strand formed by residues 972 - 978 (chain A) in PDB entry 6BM0
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 VAL 972 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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944A PHE* 4.0 17.0 - - + -
946A CYS* 3.7 2.4 - - - +
947A GLY* 3.4 27.4 + - - +
950A PRO* 3.7 23.6 - - + +
966A MET* 3.8 17.9 - - + -
968A ILE 5.7 0.7 - - - +
969A ASP 4.9 3.1 - - - +
970A GLY 4.0 5.2 - - - +
971A PRO* 1.3 80.5 - - - +
973A ASP* 1.3 62.9 + - - +
974A SER 3.3 26.0 - - - +
989A TYR* 4.0 24.0 - - + -
990A PHE 3.4 12.6 - - - +
991A ASN* 5.6 0.2 - - - -
992A ARG* 5.0 0.7 + - - -
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Residues in contact with ASP 973 (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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533A TYR* 4.8 11.3 - - + +
928A VAL* 4.2 16.1 - - + +
929A ALA 4.7 0.9 - - - +
930A ARG* 5.9 0.5 - - - +
946A CYS* 3.7 13.9 - - - +
971A PRO 4.2 0.4 + - - -
972A VAL* 1.3 75.2 - - - +
974A SER* 1.3 61.9 + - - +
990A PHE* 3.7 15.4 + - + +
991A ASN 3.8 4.2 - - - +
992A ARG* 2.7 57.1 + - - +
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Residues in contact with SER 974 (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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533A TYR 3.1 25.1 + - - -
534A ASP* 5.0 0.2 - - - -
535A MET* 3.1 23.8 - - - +
928A VAL* 5.3 0.4 - - - -
932A ARG* 3.3 24.2 - - - +
946A CYS* 4.1 3.4 - - - -
972A VAL* 3.3 13.5 - - - +
973A ASP* 1.3 79.5 - - - +
975A PHE* 1.3 62.1 + - - +
989A TYR* 3.3 1.2 - - - +
990A PHE* 3.2 29.5 + - - +
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Residues in contact with PHE 975 (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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535A MET* 3.7 4.6 - - - +
932A ARG* 2.8 39.3 + - + +
934A PHE* 4.4 15.0 - + + -
937A ILE* 4.3 4.9 - - + -
944A PHE* 3.5 49.8 - + + -
946A CYS* 3.9 5.8 - - - -
952A TRP* 3.7 23.8 - + - -
974A SER* 1.3 80.6 + - - +
976A ALA* 1.3 82.9 + - - +
977A PRO* 4.5 2.2 - - + -
987A PHE* 3.5 44.6 - + + -
988A LEU 3.4 7.0 - - - -
989A TYR* 3.8 17.7 - + + -
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Residues in contact with ALA 976 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A MET* 3.9 18.6 - - + -
536A TRP* 4.5 3.8 - - - -
537A THR* 3.7 33.4 - - + +
932A ARG* 6.1 0.2 - - - -
975A PHE* 1.3 83.8 - - - +
977A PRO* 1.3 72.2 - - + +
987A PHE* 3.6 1.9 - - - +
988A LEU* 2.7 35.4 + - + +
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Residues in contact with PRO 977 (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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537A THR* 2.4 35.8 + - - +
572A HIS* 3.8 17.3 + - + +
932A ARG* 6.3 1.8 - - + -
933A TYR 4.4 6.7 - - - +
934A PHE* 3.7 31.0 - - + -
935A GLU 4.9 7.0 - - - +
937A ILE* 4.0 18.2 - - + -
975A PHE* 4.8 3.6 - - + -
976A ALA* 1.3 86.2 - - + +
978A PHE* 1.3 58.8 + - - +
986A GLY 4.0 5.4 - - - +
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Residues in contact with PHE 978 (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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537A THR* 4.2 10.5 - - + -
572A HIS* 3.8 8.4 - - + -
575A LEU* 5.7 3.8 - - + -
588A THR* 3.9 23.8 - - + -
592A ILE* 4.6 3.8 - - + -
977A PRO* 1.3 76.0 - - - +
979A HIS* 1.3 63.5 + - - +
980A ASN* 3.3 42.2 - - + -
983A CYS* 3.9 15.5 - - + -
984A PRO 3.5 2.3 - - - +
986A GLY* 2.9 35.7 + - - +
987A PHE 4.1 8.3 - - - -
988A LEU* 3.8 35.0 - - + -
998A ILE* 3.8 36.3 - - + -
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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