Contacts of the strand formed by residues 1071 - 1077 (chain A) in PDB entry 3K72
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 ARG1071 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909A VAL* 3.6 0.6 - - - +
953A TRP* 4.8 4.2 - - - +
1050A VAL* 3.5 34.0 - - + +
1051A ALA 3.3 7.4 - - - +
1052A GLU* 2.8 33.9 + - + -
1068A ALA* 3.1 23.0 + - + +
1069A PHE 3.3 3.0 + - - -
1070A MET* 1.3 81.1 - - + +
1072A ALA* 1.3 62.1 + - - +
1073A GLN* 5.3 0.9 - - - +
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Residues in contact with ALA1072 (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 VAL* 3.6 28.0 - - + +
910A SER* 4.0 9.9 - - - -
911A SER* 4.1 2.7 - - - +
936A TYR* 3.6 27.1 - - + -
1050A VAL* 3.9 5.9 - - - +
1051A ALA 2.9 27.5 + - - +
1071A ARG* 1.3 77.2 - - - +
1073A GLN* 1.3 65.7 + - - +
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Residues in contact with GLN1073 (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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911A SER* 3.3 14.1 + - - -
936A TYR* 3.4 6.2 - - - -
1000A VAL* 6.3 0.2 - - - +
1048A VAL* 3.3 39.4 - - + +
1049A SER 3.6 3.6 - - - +
1050A VAL* 4.7 9.3 - - + +
1071A ARG 5.3 0.9 - - - +
1072A ALA* 1.3 80.5 - - - +
1074A THR* 1.3 69.8 + - - +
1075A THR* 5.0 4.5 - - + +
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Residues in contact with THR1074 (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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911A SER* 2.6 22.1 + - - +
915A PHE* 3.0 42.4 - - + -
934A HIS* 2.8 40.3 + - + +
935A ARG 4.9 1.4 + - - -
936A TYR* 3.0 24.6 + - - -
1048A VAL* 3.4 4.1 - - - -
1049A SER 3.1 25.9 + - - -
1073A GLN* 1.3 72.3 - - - +
1075A THR* 1.3 59.7 + - - +
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Residues in contact with THR1075 (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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915A PHE* 2.9 27.7 - - + -
917A LYS* 4.2 14.2 - - - +
1000A VAL* 5.8 1.0 - - - +
1046A SER* 3.7 19.6 + - - -
1047A VAL 3.7 3.8 - - - -
1048A VAL* 3.5 22.4 - - - +
1073A GLN* 5.1 4.3 - - + +
1074A THR* 1.3 72.7 - - - +
1076A THR* 1.3 59.3 + - - +
1077A VAL* 5.0 1.4 - - - +
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Residues in contact with THR1076 (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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915A PHE* 3.4 10.4 - - - -
916A THR* 2.8 27.7 + - - +
918A TYR* 4.1 15.3 - - + -
932A ALA* 4.6 9.1 - - + +
934A HIS* 3.2 27.3 + - - -
1032A LEU* 4.9 0.9 - - + -
1046A SER* 3.0 8.3 - - - -
1047A VAL* 3.0 40.5 + - + -
1074A THR 3.9 1.2 + - - -
1075A THR* 1.3 71.9 - - - +
1077A VAL* 1.3 75.0 + - - +
1078A LEU* 4.2 7.6 - - + -
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Residues in contact with VAL1077 (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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917A LYS* 3.2 41.8 - - + +
918A TYR* 3.9 9.4 - - - -
919A LEU* 3.2 49.2 + - + +
1044A LYS* 4.4 10.3 - - + +
1045A VAL 3.3 14.4 - - - +
1046A SER* 4.0 9.0 - - - -
1075A THR* 4.5 2.7 - - - +
1076A THR* 1.3 82.0 - - - +
1078A LEU* 1.3 69.8 + - - +
1079A GLU* 3.6 9.2 - - + +
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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