Contacts of the strand formed by residues 1046 - 1054 (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 SER1046 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999A PRO* 3.4 5.4 + - - +
1000A VAL* 3.4 19.2 + - - +
1001A LEU* 2.8 26.7 + - - +
1044A LYS 4.9 1.6 - - - -
1045A VAL* 1.3 83.0 - - - +
1047A VAL* 1.3 59.8 + - - +
1048A VAL* 4.0 1.2 + - - +
1075A THR* 3.7 15.4 + - - -
1076A THR 3.0 17.3 - - - -
1077A VAL* 4.0 13.0 - - - +
1078A LEU 4.6 0.4 - - - +
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Residues in contact with VAL1047 (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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934A HIS* 4.8 6.1 - - - +
955A PRO* 3.6 31.9 - - + -
963A VAL* 4.4 12.8 - - + -
964A TRP* 5.2 7.0 - - + +
1001A LEU* 3.9 22.9 - - + +
1032A LEU* 4.5 12.1 - - + -
1036A TRP* 4.9 8.7 - - + -
1046A SER* 1.3 72.6 - - - +
1048A VAL* 1.3 64.3 + - - +
1074A THR 4.0 0.5 - - - +
1075A THR* 3.7 0.5 - - - -
1076A THR* 3.0 45.3 + - - -
1078A LEU* 4.3 17.0 - - + +
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Residues in contact with VAL1048 (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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934A HIS* 5.6 0.7 - - - -
953A TRP 4.3 0.5 - - - +
955A PRO* 3.3 24.9 - - - +
1000A VAL* 5.0 10.5 - - + -
1001A LEU 3.4 17.8 + - - +
1002A ASP* 4.8 10.1 - - + +
1003A CYS* 4.9 1.9 - - - -
1046A SER* 4.6 6.3 - - - +
1047A VAL* 1.3 78.0 - - - +
1049A SER* 1.3 67.5 + - - +
1050A VAL* 4.4 8.5 + - + +
1073A GLN* 3.3 44.2 - - + +
1074A THR 3.4 4.0 - - - +
1075A THR* 3.5 31.6 - - - +
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Residues in contact with SER1049 (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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934A HIS* 3.6 29.2 + - - +
936A TYR* 2.9 36.4 + - - -
952A PHE* 6.4 0.4 - - - -
953A TRP 3.3 13.7 - - - -
954A VAL* 4.2 18.4 - - - -
955A PRO* 4.8 1.3 - - - -
964A TRP* 5.5 2.0 - - - -
1028A LEU* 5.2 1.5 - - - +
1047A VAL 4.5 0.2 + - - -
1048A VAL* 1.3 79.7 - - - +
1050A VAL* 1.3 62.1 + - - +
1073A GLN* 3.6 1.6 - - - -
1074A THR 3.1 16.9 + - - -
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Residues in contact with VAL1050 (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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936A TYR* 4.4 0.4 - - - -
952A PHE* 3.5 1.7 - - - -
953A TRP* 2.8 58.5 + - + +
1002A ASP* 5.9 6.3 - - + -
1003A CYS* 5.6 5.4 - - - +
1048A VAL* 4.4 13.0 - - + +
1049A SER* 1.3 77.6 - - - +
1051A ALA* 1.3 63.4 - - - +
1071A ARG* 3.5 45.3 - - + +
1072A ALA 3.9 10.5 - - - +
1073A GLN* 4.7 9.9 - - + +
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Residues in contact with ALA1051 (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* 4.5 7.0 - - + +
936A TYR* 3.6 29.3 + - + -
950A ILE* 5.6 2.0 - - + -
951A ASN 3.6 4.5 - - - -
952A PHE* 3.1 33.2 - - + -
1050A VAL* 1.3 76.3 - - - +
1052A GLU* 1.3 61.2 + - - +
1053A ILE 4.3 0.2 - - - -
1070A MET 4.3 0.2 - - - +
1071A ARG* 3.3 2.1 + - - -
1072A ALA* 2.9 33.9 + - + +
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Residues in contact with GLU1052 (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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950A ILE* 4.9 1.8 - - - +
951A ASN* 3.0 38.8 + - + +
953A TRP* 4.3 23.1 + - - +
1050A VAL 4.2 0.6 + - - -
1051A ALA* 1.3 75.0 - - - +
1053A ILE* 1.3 62.7 + - - +
1054A THR* 4.0 20.1 - - + +
1070A MET 3.4 10.5 - - - +
1071A ARG* 2.8 41.1 + - + +
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Residues in contact with ILE1053 (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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907A THR* 3.3 33.4 - - + +
909A VAL* 4.8 9.4 - - + +
938A VAL* 4.0 17.3 - - + -
948A VAL* 4.3 16.4 - - + -
949A SER 4.2 2.9 - - - +
950A ILE* 3.7 33.8 - - + +
1018A PHE* 5.1 4.3 - - + -
1051A ALA 4.3 0.4 - - - -
1052A GLU* 1.3 71.9 - - - +
1054A THR* 1.3 80.3 + - - +
1055A PHE* 4.6 0.7 - - + -
1070A MET* 3.0 72.5 + - + +
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Residues in contact with THR1054 (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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948A VAL* 3.6 4.2 - - - +
949A SER* 2.9 45.0 + - - -
951A ASN* 3.5 22.9 + - - +
1052A GLU* 4.0 22.0 - - + +
1053A ILE* 1.3 82.8 - - - +
1055A PHE* 1.3 77.4 + - - +
1070A MET* 4.4 2.2 - - + -
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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