Contacts of the strand formed by residues 1047 - 1054 (chain A) in PDB entry 6VSB
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 TYR1047 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909A ILE* 4.2 30.3 - - + -
1040A VAL* 5.4 9.4 - - + -
1046A GLY* 1.3 72.7 - - - -
1048A HIS* 1.3 66.3 + - - +
1049A LEU* 3.8 1.9 - - - +
1066A THR* 3.2 3.3 - - - -
1067A TYR* 2.9 62.2 + + - +
1069A PRO* 4.3 20.4 - - + -
1108A ASN* 4.0 25.7 + - - -
886B TRP* 3.2 35.3 + + - -
887B THR* 3.6 16.3 - - + +
890B ALA* 4.1 19.3 - - + +
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Residues in contact with HIS1048 (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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909A ILE* 3.8 14.1 - - - +
1032A CYS* 3.3 44.6 + - - +
1035A GLY 4.5 2.5 - - - -
1036A GLN* 3.7 13.8 + - - +
1037A SER* 3.8 34.3 + - - +
1039A ARG 5.6 3.1 - - - +
1043A CYS* 3.2 39.7 - - + +
1046A GLY 3.6 4.6 + - - +
1047A TYR* 1.3 73.3 - - - +
1049A LEU* 1.3 62.6 + - - +
1050A MET* 3.4 24.2 + - - -
1051A SER* 3.8 8.9 + - - -
1064A HIS* 4.4 1.6 - - + -
1066A THR* 3.9 9.2 - - + -
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Residues in contact with LEU1049 (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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720A ILE* 3.8 23.6 - - + -
902A MET* 4.5 9.0 - - + -
905A ARG* 2.9 46.0 + - + +
906A PHE* 3.5 43.5 - - + -
909A ILE* 3.7 25.8 - - + -
1036A GLN* 3.7 7.5 - - - +
1048A HIS* 1.3 76.9 + - - +
1050A MET* 1.3 65.7 + - + +
1065A VAL* 3.0 11.5 + - + +
1066A THR* 3.9 1.6 - - - -
1067A TYR* 3.6 30.7 - - + +
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Residues in contact with MET1050 (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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881A THR* 4.5 14.4 - - - +
898A PHE* 3.9 26.9 - - + -
901A GLN* 4.8 5.8 - - - +
902A MET* 3.4 34.1 - - + +
905A ARG* 4.3 12.3 - - - +
927A PHE* 4.7 4.7 - - - -
1032A CYS 4.7 0.2 - - - -
1048A HIS* 3.4 10.7 + - - -
1049A LEU* 1.3 80.2 - - + +
1051A SER* 1.3 59.1 + - - +
1052A PHE* 3.3 34.1 - - + -
1064A HIS* 3.8 0.3 - - - -
1065A VAL* 2.7 57.9 + - + +
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Residues in contact with SER1051 (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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881A THR* 4.2 7.0 + - - +
1032A CYS* 2.5 36.8 + - - +
1033A VAL* 3.2 25.4 + - - +
1048A HIS* 3.8 2.7 - - - -
1050A MET* 1.3 77.5 - - - +
1052A PHE* 1.3 75.4 + - - +
1062A PHE* 5.3 0.4 - - - -
1063A LEU 3.2 9.6 - - - -
1064A HIS* 3.4 29.3 - - - -
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Residues in contact with PHE1052 (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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802A PHE* 3.7 20.2 - + - -
805A ILE* 4.1 25.1 - - + -
878A LEU* 3.7 17.9 - - + -
881A THR* 3.5 31.6 - - + -
882A ILE* 3.9 15.3 - - + -
927A PHE* 4.3 5.8 - + - -
931A ILE* 5.8 1.8 - - + -
1050A MET* 3.3 41.1 - - + -
1051A SER* 1.3 76.7 - - - +
1053A PRO* 1.3 72.7 - - + +
1054A GLN* 3.8 0.4 + - - +
1062A PHE* 3.4 5.3 - - - -
1063A LEU* 2.9 49.4 + - + +
1065A VAL* 4.2 10.8 - - + -
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Residues in contact with PRO1053 (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 THR* 4.4 15.3 - - + +
877A LEU* 3.9 30.1 - - + -
878A LEU* 3.2 21.2 - - + +
1029A MET* 3.9 11.9 - - + -
1033A VAL* 3.6 24.5 - - + -
1052A PHE* 1.3 86.9 - - + +
1054A GLN* 1.3 76.1 + - - +
1060A VAL* 4.4 4.9 - - + -
1061A VAL 3.6 4.9 - - - +
1062A PHE* 3.7 21.4 - - + -
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Residues in contact with GLN1054 (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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805A ILE* 3.4 19.7 + - + +
816A SER* 3.2 17.5 + - - -
818A ILE* 3.5 21.1 - - + +
819A GLU* 3.3 16.4 + - + +
822A LEU* 4.1 17.7 - - + -
874A THR* 4.6 5.3 - - - -
878A LEU* 3.2 20.6 - - - +
1052A PHE* 4.4 1.1 - - + +
1053A PRO* 1.3 90.6 + - - +
1055A SER* 1.3 62.6 + - - +
1060A VAL* 3.8 5.0 - - - +
1061A VAL* 2.5 46.8 + - + +
1063A LEU* 4.1 24.2 - - + -
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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