Contacts of the strand formed by residues 1067 - 1072 (chain A) in PDB entry 6TPN
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 MET1067 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033A VAL* 3.6 10.8 - - + -
1035A PHE* 3.8 15.3 - - + -
1058A LEU* 4.4 11.4 - - + -
1063A GLU 3.5 20.9 - - - +
1064A PHE* 3.0 14.6 + - - +
1066A GLU* 1.3 80.9 - - + +
1068A ARG* 1.3 76.4 + - - +
1069A PHE* 3.7 20.6 - - + -
1092A ASN* 2.9 21.6 + - - +
1170A ILE* 3.6 42.0 - - + +
1171A LEU* 4.1 18.8 - - + -
1174A LEU* 3.8 18.4 - - + -
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Residues in contact with ARG1068 (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 LEU* 3.8 24.0 - - + -
1029A MET* 4.0 20.7 - - - +
1030A ASP* 3.0 44.6 + - - -
1031A GLU 3.2 18.9 + - - -
1032A GLY* 4.2 18.1 - - - -
1033A VAL 3.0 7.5 + - - +
1034A THR* 4.1 6.3 - - + -
1035A PHE* 2.6 37.6 + - - -
1065A GLN* 3.1 26.3 + - - +
1066A GLU* 4.0 2.6 + - - +
1067A MET* 1.3 91.5 + - - +
1069A PHE* 1.3 59.6 + - - +
1092A ASN* 3.6 22.4 - - - +
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Residues in contact with PHE1069 (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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1029A MET* 4.3 0.9 - - - +
1035A PHE* 3.3 38.8 - + + -
1051A LEU* 4.8 4.5 - - + -
1055A ILE* 4.2 26.9 - - + -
1058A LEU* 4.2 9.0 - - + -
1064A PHE* 3.7 28.5 - + - -
1067A MET* 3.7 29.8 - - + -
1068A ARG* 1.3 75.8 - - - +
1070A ILE* 1.3 67.1 + - - +
1071A ILE* 4.0 7.2 - - + -
1092A ASN* 2.9 17.8 + - - +
1093A VAL* 4.4 14.6 - - + -
1094A LYS* 3.0 26.9 + - - +
1116A ILE* 4.4 11.2 - - + -
1170A ILE* 4.1 13.7 - - + -
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Residues in contact with ILE1070 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023A LEU* 5.5 2.5 - - + -
1024A LEU* 5.4 1.8 - - + -
1027A PHE* 3.8 31.2 - - + -
1029A MET* 4.7 8.7 - - - -
1034A THR* 4.1 18.4 - - + -
1035A PHE 2.7 15.9 + - - +
1036A MET* 3.3 7.6 - - + -
1037A PHE* 2.7 34.8 + - - +
1069A PHE* 1.3 79.9 - - - +
1071A ILE* 1.3 58.0 + - - +
1072A ILE* 3.7 28.3 - - + -
1094A LYS* 3.5 16.2 - - + +
1096A ILE* 4.0 15.5 - - + -
1108A LEU* 4.9 6.7 - - + -
1112A VAL* 5.0 5.2 - - + -
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Residues in contact with ILE1071 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A PHE* 3.7 21.1 - - + -
1041A PHE* 4.0 20.4 - - + -
1048A VAL* 4.1 9.9 - - + -
1051A LEU* 4.1 13.9 - - + -
1052A LEU* 4.4 15.3 - - + -
1055A ILE* 3.9 25.8 - - + -
1069A PHE* 4.8 4.5 - - + -
1070A ILE* 1.3 77.4 - - - +
1072A ILE* 1.3 61.3 + - - +
1083A ALA* 5.0 4.0 - - + -
1086A LEU* 6.0 0.9 - - + -
1093A VAL* 4.1 22.7 - - + -
1094A LYS 2.9 10.6 + - - +
1095A VAL* 3.2 18.2 - - + +
1096A ILE 2.9 23.9 + - - -
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Residues in contact with ILE1072 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036A MET* 3.8 20.2 - - + -
1037A PHE* 2.7 17.8 + - - +
1038A ILE* 3.3 16.1 - - + -
1039A GLY 3.0 26.7 + - - +
1041A PHE* 4.3 2.2 - - - -
1070A ILE* 3.7 23.3 - - + -
1071A ILE* 1.3 77.3 - - - +
1073A GLY* 1.3 62.1 + - - +
1096A ILE* 3.4 19.7 - - + +
1098A GLU 5.2 2.0 - - - +
1100A LEU* 3.6 28.0 - - + -
1108A LEU* 3.6 31.6 - - + -
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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