Contacts of the strand formed by residues 986 - 991 (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 GLY 986 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936A ASP 5.4 0.2 + - - -
937A ILE* 3.3 25.1 - - - +
978A PHE 2.9 31.4 + - - +
983A CYS* 4.7 1.1 - - - -
984A PRO 3.0 4.2 + - - -
985A ARG* 1.3 74.6 - - - +
987A PHE* 1.3 65.3 + - - -
999A SER 3.5 11.4 - - - -
1000A VAL* 4.5 4.9 - - - -
1001A LEU 5.3 0.2 - - - -
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Residues in contact with PHE 987 (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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521A PRO* 3.5 27.1 - - + -
937A ILE* 3.7 15.3 - - + -
952A TRP* 3.6 26.2 - + - -
966A MET* 5.2 1.8 - - + -
975A PHE* 3.5 34.5 - + + -
976A ALA 3.6 6.5 - - - -
978A PHE* 3.9 7.4 + - - +
986A GLY* 1.3 79.5 - - - +
988A LEU* 1.3 65.5 + - - +
989A TYR* 3.9 20.2 - + - -
998A ILE* 4.1 0.5 - - - -
999A SER* 3.0 48.2 + - - +
1000A VAL 3.8 2.5 - - - -
1001A LEU* 3.5 37.2 - - + -
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Residues in contact with LEU 988 (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* 3.5 14.8 - - + +
537A THR* 4.0 4.3 - - + -
575A LEU* 3.8 38.1 - - + -
975A PHE* 3.4 2.4 - - - -
976A ALA 2.7 43.1 + - - +
978A PHE* 3.8 29.4 - - + -
987A PHE* 1.3 80.3 - - - +
989A TYR* 1.3 59.8 + - - +
996A LEU* 3.7 15.7 - - + -
997A ARG 3.4 20.4 - - - +
998A ILE* 3.6 27.8 - - + -
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Residues in contact with TYR 989 (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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490A PHE* 3.4 28.4 - - - -
521A PRO* 4.0 9.3 - - + +
523A VAL* 4.5 0.5 - - - +
535A MET* 4.1 1.1 - - - -
966A MET* 4.9 11.3 - - + +
969A ASP* 3.8 22.1 + - + +
972A VAL* 4.0 22.7 - - + -
974A SER 3.3 15.9 - - - +
975A PHE* 3.8 13.5 - + + +
987A PHE* 3.9 27.1 - + - -
988A LEU* 1.3 75.6 - - - +
990A PHE* 1.3 81.1 + - - +
991A ASN* 4.8 0.4 - - - -
995A GLU 3.7 1.2 - - - +
996A LEU* 3.5 8.9 - - - +
997A ARG* 3.3 46.9 + - + -
999A SER* 3.9 18.8 - - - -
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Residues in contact with PHE 990 (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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529A LEU* 4.7 8.7 - - + -
532A CYS* 3.2 47.8 - - - -
533A TYR* 3.5 16.6 - - - -
534A ASP 4.0 7.9 - - - -
535A MET* 4.0 3.1 - - + -
577A LEU* 3.6 17.0 - - + -
972A VAL* 3.4 16.5 - - - +
973A ASP* 3.7 8.5 + - + +
974A SER* 3.2 33.0 + - - +
989A TYR* 1.3 89.3 - - - +
991A ASN* 1.3 67.9 + - - +
994A GLY* 5.3 3.1 - - - -
995A GLU 3.8 4.3 - - - -
996A LEU* 3.6 46.7 - - + -
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Residues in contact with ASN 991 (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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969A ASP* 3.1 52.8 + - - +
970A GLY* 4.9 0.9 - - - -
971A PRO 3.8 4.8 - - - +
972A VAL* 5.6 0.2 - - - -
973A ASP* 3.8 10.3 - - - +
989A TYR* 4.4 1.1 - - + -
990A PHE* 1.3 80.1 - - - +
992A ARG* 1.3 82.2 + - - +
993A GLN* 2.9 27.5 + - - +
994A GLY* 3.2 11.1 + - - -
995A GLU* 3.2 31.8 + - + +
997A ARG* 3.5 12.1 - - - +
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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