Contacts of the strand formed by residues 940 - 945 (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 TYR 940 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934A PHE* 3.3 10.3 - - + -
936A ASP 3.3 4.2 + - - -
937A ILE 3.0 30.0 + - - +
938A TYR* 3.9 28.3 - + - -
939A GLY* 1.3 83.5 - - - +
941A SER* 1.3 59.6 + - - +
954A LEU* 3.8 26.0 - - + -
956A THR* 4.0 27.6 - - + -
1001A LEU* 4.7 7.0 - - + -
1006A SER* 4.3 7.6 + - - -
1007A TYR* 3.5 56.0 + + + -
1008A ASP* 4.2 7.2 + - + +
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Residues in contact with SER 941 (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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854A LEU* 4.5 4.2 - - - +
855A GLY 4.2 15.6 + - - -
858A GLN* 4.6 16.5 + - - -
933A TYR* 4.6 5.2 - - - -
934A PHE* 3.6 11.4 - - - -
935A GLU* 4.4 10.1 - - - -
936A ASP* 4.2 2.5 - - - +
939A GLY 4.0 2.7 + - - -
940A TYR* 1.3 75.1 - - - +
942A GLY* 1.3 59.4 + - - +
954A LEU* 4.0 5.9 - - - +
955A VAL 3.7 34.5 + - - +
956A THR* 6.3 0.4 - - - +
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Residues in contact with GLY 942 (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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854A LEU* 3.7 17.3 - - - -
933A TYR* 3.3 9.2 - - - -
934A PHE* 2.7 50.2 + - - +
941A SER* 1.3 76.7 - - - +
943A VAL* 1.3 58.1 + - - -
953A LEU 3.3 11.0 - - - -
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Residues in contact with VAL 943 (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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850A LEU* 4.9 2.0 - - + -
852A VAL* 3.7 29.8 - - + -
854A LEU* 4.4 4.7 - - + -
864A LEU* 3.8 23.3 - - + -
931A PHE* 4.4 5.6 - - + -
932A ARG 3.8 14.1 - - - +
933A TYR* 4.3 7.6 - - + +
934A PHE* 3.4 6.6 - - - -
942A GLY* 1.3 77.6 - - - +
944A PHE* 1.3 75.2 + - - +
945A ILE* 3.9 5.8 - - + -
952A TRP 3.7 0.2 - - - -
953A LEU* 2.7 59.3 + - + +
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Residues in contact with PHE 944 (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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930A ARG 3.4 2.8 - - - +
932A ARG* 2.9 35.1 + - - +
934A PHE* 3.6 5.2 - - + -
943A VAL* 1.3 75.6 - - - +
945A ILE* 1.3 66.4 + - - +
946A CYS* 3.6 28.0 - - - -
950A PRO* 3.6 25.6 - - + -
951A HIS 4.0 4.3 - - - -
952A TRP* 3.6 49.4 - + - -
966A MET* 3.7 15.7 - - + -
972A VAL* 4.0 11.2 - - + -
975A PHE* 3.5 50.5 - + + -
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Residues in contact with ILE 945 (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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864A LEU* 4.0 16.4 - - + -
871A LEU* 3.8 21.8 - - + -
873A ILE* 5.5 0.7 - - + -
899A ILE* 4.2 12.6 - - + -
901A PHE* 4.0 21.3 - - + -
930A ARG 3.4 2.7 - - - -
931A PHE* 3.7 26.2 - - + -
943A VAL* 3.9 13.9 - - + +
944A PHE* 1.3 79.9 - - - +
946A CYS* 1.3 63.8 + - - +
949A SER 4.3 0.8 - - - +
950A PRO* 3.5 7.6 - - - +
951A HIS* 3.1 40.2 + - + +
953A LEU* 4.5 16.8 - - + -
963A LEU* 5.9 2.9 - - + -
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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