Contacts of the strand formed by residues 1085 - 1091 (chain A) in PDB entry 3PT6
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 ARG1085 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A ASN* 3.1 26.6 + - - +
1064A THR* 3.6 12.6 - - - +
1073A GLU* 4.2 7.9 + - - -
1078A TYR* 3.0 65.3 + - + +
1079A SER* 4.6 4.6 - - - +
1081A GLY* 3.3 22.6 + - - -
1082A GLY* 3.2 33.5 + - - +
1083A PRO* 3.3 7.9 + - - +
1084A ASP* 1.3 75.5 - - - +
1086A PHE* 1.3 63.4 + - - +
1365A PHE* 5.2 3.7 - - - -
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Residues in contact with PHE1086 (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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944A TYR* 3.0 35.0 - + - -
997A ILE* 3.7 21.1 - - + -
1026A ARG* 4.3 4.0 - - - -
1042A ILE 4.1 5.2 - - - -
1043A ASN* 3.1 28.3 - - - +
1045A LEU* 3.8 22.0 - - + -
1063A CYS* 4.4 6.3 - - - -
1064A THR 2.7 9.7 + - - +
1065A VAL* 3.6 18.2 - - + -
1066A GLU 3.3 7.8 + - - -
1078A TYR* 2.7 24.0 + - - -
1084A ASP* 3.9 10.5 - - - -
1085A ARG* 1.3 77.5 - - - +
1087A TYR* 1.3 61.7 + - - +
1364A PRO 3.7 15.7 - - - -
1365A PHE* 3.7 29.8 - + - -
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Residues in contact with TYR1087 (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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1041A ASP* 3.2 22.0 + - - -
1043A ASN* 3.1 26.7 + - - -
1044A MET* 3.3 47.6 - - + +
1045A LEU* 2.6 34.4 + - - -
1065A VAL* 4.5 0.7 - - - -
1066A GLU* 3.2 16.4 - - + +
1067A TYR 5.2 0.2 - - - -
1068A GLY* 4.4 6.7 - - - +
1075A ILE* 3.5 42.8 - - + +
1078A TYR* 3.9 12.8 - + + -
1079A SER* 4.6 0.9 - - - -
1086A PHE* 1.3 76.6 - - - +
1088A PHE* 1.3 66.7 + - - +
1089A LEU* 3.8 23.0 - - + +
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Residues in contact with PHE1088 (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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999A ARG* 4.2 13.2 - - - -
1024A PHE* 3.9 10.3 - + + -
1045A LEU* 2.9 28.0 - - + +
1047A TRP* 4.1 17.5 - + + +
1065A VAL* 3.5 24.7 - - + -
1066A GLU* 3.2 5.6 + - - -
1067A TYR* 3.2 48.0 - + + -
1068A GLY 2.7 31.0 + - - -
1087A TYR* 1.3 79.3 - - - +
1089A LEU* 1.3 56.5 + - - +
1090A GLU 4.1 1.3 - - - +
1102A PRO* 3.5 26.5 - - + -
1106A ALA* 4.1 25.1 - - + -
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Residues in contact with LEU1089 (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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1044A MET* 5.1 10.6 - - + +
1045A LEU 4.0 2.6 + - - -
1046A TYR* 5.4 2.4 - - + -
1067A TYR* 3.6 10.0 + - - -
1068A GLY* 3.6 26.7 - - - -
1069A GLU* 4.1 21.2 - - + +
1075A ILE* 4.3 16.4 - - + -
1087A TYR* 3.8 21.2 - - + +
1088A PHE* 1.3 73.9 - - - +
1090A GLU* 1.3 74.3 + - + +
1101A ASP* 4.3 3.1 - - - +
1102A PRO* 2.9 21.0 - - - +
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Residues in contact with GLU1090 (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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1046A TYR* 3.7 39.4 + - + -
1047A TRP* 3.3 17.3 + - - +
1088A PHE* 4.1 2.8 - - - -
1089A LEU* 1.3 89.2 + - + +
1091A ALA* 1.3 63.2 + - - +
1099A PHE* 3.1 31.6 - - + +
1100A GLU 3.5 8.5 - - - +
1101A ASP* 4.2 3.4 - - + +
1102A PRO* 3.3 15.8 - - - +
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Residues in contact with ALA1091 (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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1046A TYR* 5.1 0.7 - - - -
1047A TRP* 3.0 31.4 - - + +
1048A SER* 5.2 0.2 - - - -
1090A GLU* 1.3 74.4 - - - +
1092A TYR* 1.3 62.0 - - - +
1099A PHE* 3.3 21.5 - - - -
1100A GLU* 2.8 32.0 + - + +
1101A ASP 4.1 2.9 - - - +
1102A PRO* 3.6 15.9 - - + +
1103A PRO* 4.3 4.5 - - + -
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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