Contacts of the strand formed by residues 953 - 959 (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 GLU 953 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A ILE* 5.3 1.8 - - + -
947A GLU* 3.2 32.0 - - + +
951A GLY 4.3 0.4 + - - -
952A LEU* 1.3 73.7 - - - +
954A ILE* 1.3 64.3 - - - +
955A THR* 4.4 0.3 + - - -
1007A ALA* 3.0 6.0 - - - -
1008A ASP* 2.9 44.9 + - + +
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Residues in contact with ILE 954 (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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939A LEU* 6.2 0.2 - - + -
942A LEU* 4.1 14.4 - - + -
943A ILE* 4.1 32.4 - - + +
946A PHE* 3.7 26.5 - - + -
952A LEU* 5.4 0.9 - - + -
953A GLU* 1.3 75.8 - - - +
955A THR* 1.3 56.0 + - - +
956A MET 3.4 31.6 - - - +
957A LEU* 4.2 5.6 - - + +
965A TYR* 3.3 37.9 + - + -
967A SER* 4.0 9.1 - - - -
1005A ILE* 3.7 31.4 - - + -
1006A CYS 3.4 3.6 - - - +
1007A ALA* 5.1 2.0 - - + -
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Residues in contact with THR 955 (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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953A GLU 3.4 1.4 + - - -
954A ILE* 1.3 73.4 - - - +
956A MET* 1.3 68.6 + - + +
966A ALA* 3.2 6.7 - - - +
967A SER* 3.0 37.6 + - - +
968A PHE* 5.5 1.0 - - + -
1006A CYS* 2.6 31.9 + - + -
1007A ALA* 3.9 3.3 - - - -
1008A ASP* 3.5 24.1 + - - -
1014A ASP* 3.9 5.7 + - - +
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Residues in contact with MET 956 (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 10.9 - - - +
955A THR* 1.3 93.1 - - + +
957A LEU* 1.3 63.8 + - - +
958A SER* 4.8 7.2 - - - +
963A LEU* 3.6 25.1 - - + -
965A TYR 3.3 5.6 - - - -
966A ALA* 4.3 12.6 - - + -
968A PHE* 4.5 12.3 - - + -
1004A GLU 4.5 0.4 - - - -
1005A ILE* 3.3 6.2 - - - -
1006A CYS* 2.8 49.5 + - + -
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Residues in contact with LEU 957 (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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939A LEU* 3.9 25.4 - - + -
942A LEU* 4.0 15.5 - - + -
954A ILE* 4.2 7.6 - - + -
956A MET* 1.3 75.4 - - - +
958A SER* 1.3 57.4 + - - +
963A LEU* 4.0 1.7 - - - +
964A LEU* 2.8 55.8 + - + +
965A TYR* 2.8 25.4 + - + +
982A ILE* 4.8 1.1 - - + -
985A LEU* 4.5 4.3 - - + -
1003A LEU* 3.6 33.4 - - + -
1004A GLU 3.5 14.4 - - - +
1005A ILE* 3.7 17.3 - - + -
1020A ILE* 4.5 0.4 - - + -
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Residues in contact with SER 958 (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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956A MET* 4.8 7.1 - - - +
957A LEU* 1.3 79.5 + - - +
959A TYR* 1.3 60.3 + - - +
960A GLY 4.0 12.0 + - - -
961A VAL 5.7 0.2 - - - -
962A SER 3.2 17.9 - - - -
963A LEU* 4.5 6.7 - - - -
964A LEU* 4.3 2.7 - - - +
1003A LEU* 3.4 8.8 - - - +
1004A GLU* 2.9 50.6 + - - +
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Residues in contact with TYR 959 (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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958A SER* 1.3 73.3 - - - +
960A GLY* 1.3 65.9 + - - +
961A VAL 3.3 0.3 + - - -
962A SER* 3.0 29.7 + - - +
964A LEU* 4.0 15.8 - - + +
986A VAL* 3.9 33.2 - - + -
990A THR* 5.5 1.3 - - - -
993A ASP* 4.3 10.4 + - - -
995A PRO* 5.6 2.3 - - - +
998A VAL* 5.6 6.9 - - - +
1001A MET* 4.0 33.5 - - + +
1002A ILE* 3.3 26.5 - - + -
1003A LEU* 3.6 17.0 - - + -
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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