Contacts of the strand formed by residues 1062 - 1070 (chain A) in PDB entry 3OV6
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 PHE1062 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.7 27.4 - - + -
95A GLU* 3.7 11.2 - - - -
97A GLN* 3.4 35.2 - - + -
1028A SER* 3.2 2.9 - - - -
1029A GLY 3.1 23.6 + - - -
1030A PHE* 3.0 52.2 + + + -
1031A HIS* 3.5 22.2 - + - -
1032A PRO 4.2 0.4 - - - -
1033A SER* 3.6 33.2 - - - -
1054A LEU* 3.8 15.0 - - + -
1055A SER 3.1 15.9 - - - +
1056A PHE* 3.7 7.2 - + + -
1061A SER* 1.3 72.9 - - - +
1063A TYR* 1.3 61.3 + - - +
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Residues in contact with TYR1063 (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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11A HIS* 5.9 0.9 + - - -
31A TRP* 3.9 26.7 - + - -
34A GLU* 4.7 14.6 - - + +
1026A TYR* 3.5 30.5 - + + +
1027A VAL 2.9 5.2 - - - -
1028A SER* 3.4 22.9 - - - -
1030A PHE* 4.1 1.1 - - - -
1052A SER* 5.3 1.3 - - - -
1053A ASP 4.2 0.9 - - - +
1054A LEU* 4.2 1.3 - - - +
1055A SER* 2.8 52.8 + - - -
1056A PHE* 3.4 32.0 + - - -
1057A SER* 4.0 13.9 - - - +
1062A PHE* 1.3 77.3 - - - +
1064A LEU* 1.3 71.2 + - - +
1065A LEU* 5.0 0.9 - - + -
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Residues in contact with LEU1064 (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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1025A CYS 3.8 0.5 - - - +
1026A TYR* 3.5 9.1 - - - -
1027A VAL* 2.7 42.0 + - + +
1030A PHE* 4.6 3.6 - - + -
1035A ILE* 4.2 25.4 - - + -
1037A VAL* 4.6 6.1 - - + -
1051A HIS* 4.6 5.6 - - - +
1052A SER* 3.3 29.6 - - - +
1053A ASP 3.6 17.7 - - - +
1054A LEU* 3.9 17.9 - - + +
1063A TYR* 1.3 77.4 - - - +
1065A LEU* 1.3 58.8 + - - +
1066A TYR* 3.9 30.5 - - + +
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Residues in contact with LEU1065 (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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238A PRO* 3.8 29.6 - - + +
239A ASN 3.9 16.2 - - - +
240A ALA 5.5 0.4 - - - +
1010A TYR* 3.8 20.4 - - - +
1024A ASN* 4.3 5.4 - - + -
1025A CYS 3.4 12.8 - - - +
1026A TYR* 4.3 13.2 - - + -
1051A HIS* 3.1 8.8 - - - +
1052A SER* 3.1 40.1 + - - +
1063A TYR* 5.0 1.7 - - + -
1064A LEU* 1.3 73.9 - - - +
1066A TYR* 1.3 78.5 + - - +
1067A TYR* 4.3 19.9 - - + -
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Residues in contact with TYR1066 (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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1024A ASN* 3.2 1.7 - - - -
1025A CYS* 2.7 54.0 + - + +
1027A VAL* 5.4 0.9 - - + -
1037A VAL* 3.6 54.3 + - + +
1038A ASP* 5.1 1.3 - - - -
1039A LEU* 4.1 15.9 - - + -
1049A VAL* 4.0 27.4 - - + -
1050A GLU 3.3 2.9 - - - -
1051A HIS* 3.6 31.5 + + + -
1064A LEU* 3.9 28.3 - - + +
1065A LEU* 1.3 82.7 - - - +
1067A TYR* 1.3 67.8 + - - +
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Residues in contact with TYR1067 (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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240A ALA* 3.6 47.7 + - + -
241A GLN* 4.3 11.4 + - - -
1022A PHE* 4.6 11.2 - + + -
1023A LEU 3.1 14.4 - - - +
1024A ASN* 3.6 12.1 - - - +
1039A LEU* 3.9 5.1 - - - +
1049A VAL* 3.4 1.9 - - - +
1050A GLU* 2.8 82.3 + - + +
1051A HIS* 5.2 3.4 - - - -
1052A SER 5.9 0.2 - - - -
1065A LEU* 4.3 18.2 - - + -
1066A TYR* 1.3 81.0 - - - +
1068A THR* 1.3 70.9 + - - +
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Residues in contact with THR1068 (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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1022A PHE* 3.4 8.8 - - - -
1023A LEU* 2.8 38.6 + - + -
1039A LEU* 3.8 20.6 - - + -
1046A ILE* 3.8 26.4 - - + +
1048A LYS 2.8 25.3 + - - -
1049A VAL* 4.2 4.0 - - - +
1067A TYR* 1.3 82.6 - - - +
1069A GLU* 1.3 77.7 + - - +
1070A PHE* 4.7 1.6 - - + -
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Residues in contact with GLU1069 (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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1020A SER* 5.2 7.9 - - - +
1021A ASN 3.4 8.3 - - - +
1022A PHE* 4.0 23.7 - - + -
1046A ILE* 5.4 2.3 - - - +
1048A LYS* 4.8 18.6 + - - +
1068A THR* 1.3 93.7 + - - +
1070A PHE* 1.3 63.2 + - - +
1078A TYR* 5.4 0.3 - - - -
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Residues in contact with PHE1070 (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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1011A SER* 4.2 2.7 - - - -
1020A SER* 3.9 1.2 + - - -
1021A ASN* 2.7 61.7 + - + +
1022A PHE 3.9 12.6 - - - -
1023A LEU* 3.6 31.9 - - + -
1068A THR* 4.7 1.6 - - + -
1069A GLU* 1.3 77.3 - - - +
1071A THR* 1.3 62.4 + - - +
1072A PRO* 3.9 13.9 - - + -
1078A TYR* 3.4 51.4 - + + -
1095A TRP* 3.7 52.3 - + - -
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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