Contacts of the strand formed by residues 1000 - 1008 (chain A) in PDB entry 3CMM
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 THR1000 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A ASP* 2.7 29.8 + - - -
558A PHE* 2.8 38.9 - - + -
998A VAL* 2.9 20.7 - - - +
999A SER* 1.3 82.3 + - - +
1001A MET* 1.3 70.8 + - - +
1002A ILE* 5.2 0.7 - - + -
1021A THR* 3.6 16.2 - - + -
1022A ILE 3.5 3.8 + - - -
1023A HIS* 4.7 10.6 + - + -
1024A LEU* 5.5 0.4 - - - -
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Residues in contact with MET1001 (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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959A TYR* 4.0 33.4 - - + +
982A ILE* 4.1 23.6 - - + -
983A THR* 4.9 11.9 - - - +
986A VAL* 4.9 12.8 - - + -
995A PRO* 3.4 35.2 - - + -
998A VAL* 4.4 6.7 - - + -
1000A THR* 1.3 82.1 - - - +
1002A ILE* 1.3 63.3 + - - +
1003A LEU* 3.9 5.2 + - + -
1020A ILE 3.5 0.3 - - - +
1021A THR* 3.3 4.3 - - - -
1022A ILE* 2.8 49.6 + - + +
1024A LEU* 4.9 20.0 - - + -
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Residues in contact with ILE1002 (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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554A ARG* 4.2 30.7 - - - +
555A ARG* 6.2 1.8 - - - +
558A PHE* 3.6 45.3 - - + -
959A TYR* 3.3 20.5 - - + -
960A GLY 4.7 2.1 + - - -
1000A THR* 4.8 0.6 - - + +
1001A MET* 1.3 72.3 - - - +
1003A LEU* 1.3 77.9 + - - +
1004A GLU* 4.8 11.9 - - - +
1019A PHE* 4.1 26.0 - - + -
1020A ILE 3.3 3.4 - - - +
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Residues in contact with LEU1003 (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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942A LEU* 4.7 3.6 - - + -
957A LEU* 3.6 35.2 - - + -
958A SER 3.4 5.8 - - - +
959A TYR* 3.6 30.1 - - + -
964A LEU* 4.3 7.2 - - + -
982A ILE* 4.1 23.3 - - + -
1001A MET* 4.8 3.1 - - + +
1002A ILE* 1.3 88.0 - - - +
1004A GLU* 1.3 62.1 + - - +
1019A PHE* 3.6 3.5 - - - +
1020A ILE* 2.8 50.2 + - + +
1022A ILE* 3.5 30.1 - - + -
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Residues in contact with GLU1004 (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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554A ARG* 4.7 12.0 + - - -
957A LEU* 3.5 5.7 - - - +
958A SER* 2.9 46.6 + - - +
960A GLY* 5.3 8.8 - - - +
1002A ILE* 4.8 9.8 - - + +
1003A LEU* 1.3 75.2 - - - +
1005A ILE* 1.3 63.8 + - - +
1019A PHE* 4.6 14.0 - - + +
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Residues in contact with ILE1005 (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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946A PHE* 4.0 9.2 - - + -
952A LEU* 5.9 0.9 - - + -
954A ILE* 3.7 28.9 - - + -
956A MET 3.3 11.7 - - - +
957A LEU* 3.7 11.4 - - + -
1004A GLU* 1.3 81.4 - - - +
1006A CYS* 1.3 79.2 + - - +
1007A ALA* 4.2 7.2 - - + +
1015A VAL 5.4 0.9 - - - +
1017A VAL* 3.6 38.8 + - + +
1018A PRO 4.9 4.0 + - - +
1019A PHE* 5.5 0.4 - - - +
1020A ILE* 3.0 37.2 - - + -
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Residues in contact with CYS1006 (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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954A ILE* 3.4 6.1 - - - +
955A THR* 2.6 42.8 + - + -
956A MET* 2.8 40.5 + - + +
1005A ILE* 1.3 78.9 - - - +
1007A ALA* 1.3 56.4 + - - +
1014A ASP* 4.7 9.2 - - - +
1015A VAL 5.2 2.0 - - - -
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Residues in contact with ALA1007 (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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952A LEU* 3.9 32.5 - - + -
953A GLU 3.0 16.6 - - - +
954A ILE* 4.6 1.8 - - + -
955A THR* 3.9 2.7 + - - -
1005A ILE* 4.2 13.6 - - + +
1006A CYS* 1.3 76.4 - - - +
1008A ASP* 1.3 62.2 + - - +
1014A ASP* 3.2 5.8 + - - +
1015A VAL* 2.9 33.9 + - - +
1017A VAL* 4.7 5.6 - - + -
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Residues in contact with ASP1008 (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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952A LEU* 3.5 6.3 - - - -
953A GLU* 2.9 42.2 + - + +
955A THR* 3.5 10.6 + - - +
1007A ALA* 1.3 73.2 - - - +
1009A ASP* 1.3 65.2 + - - +
1012A GLY* 2.7 29.4 - - - +
1013A GLU 3.2 6.3 - - - +
1014A ASP* 3.3 25.3 - - - +
1015A VAL* 4.2 2.0 - - - -
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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