Contacts of the helix formed by residues 970 - 978 (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 PRO 970 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968A PHE* 3.6 5.1 - - + +
969A PHE* 1.3 97.8 - - + +
971A PRO* 1.3 69.9 - - + +
972A LYS* 3.1 12.5 + - + +
973A LYS* 3.4 24.1 + - + +
974A LEU* 3.0 25.6 + - - +
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Residues in contact with PRO 971 (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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969A PHE 4.7 0.2 - - - +
970A PRO* 1.3 84.9 - - + +
972A LYS* 1.4 65.7 - - + +
974A LEU* 3.9 14.3 - - + +
975A LYS* 3.5 26.3 + - + +
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Residues in contact with LYS 972 (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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970A PRO* 4.6 11.0 - - + -
971A PRO* 1.4 84.5 - - + +
973A LYS* 1.3 65.8 + - + +
974A LEU 3.4 0.3 + - - -
975A LYS* 4.5 0.7 - - - +
976A GLU* 3.7 18.7 + - - +
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Residues in contact with LYS 973 (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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969A PHE* 4.6 30.2 - - + -
970A PRO* 3.4 23.2 + - + +
972A LYS* 1.3 80.3 - - + +
974A LEU* 1.3 67.3 + - - +
976A GLU* 3.7 11.6 + - - +
977A ARG* 3.3 61.9 + - - +
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Residues in contact with LEU 974 (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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965A TYR* 3.6 37.0 - - + +
966A ALA 4.5 1.8 - - - +
967A SER 5.7 3.4 - - - +
969A PHE* 3.8 26.7 - - + +
970A PRO 3.0 20.9 + - - +
971A PRO* 4.0 13.2 - - + +
972A LYS 3.2 0.6 - - - -
973A LYS* 1.3 75.9 - - - +
975A LYS* 1.3 54.9 + - + +
977A ARG* 3.0 5.0 + - - +
978A LEU* 2.7 55.5 + - + +
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Residues in contact with LYS 975 (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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971A PRO* 3.5 17.7 + - + +
972A LYS 4.9 0.7 - - - +
974A LEU* 1.3 77.7 - - + +
976A GLU* 1.3 61.7 + - - +
977A ARG 3.3 0.2 - - - -
978A LEU* 4.2 19.2 + - + +
979A ASN* 4.4 13.0 + - - +
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Residues in contact with GLU 976 (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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972A LYS 3.7 16.7 + - - +
973A LYS* 4.0 11.0 - - - +
974A LEU 3.2 0.4 - - - -
975A LYS* 1.3 77.9 - - - +
977A ARG* 1.3 68.3 + - - +
979A ASN* 4.7 2.8 + - - +
980A LEU* 3.4 21.4 - - + +
988A LEU* 3.6 30.4 - - + +
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Residues in contact with ARG 977 (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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939A LEU* 3.4 21.2 - - + +
963A LEU 3.9 4.0 + - - -
964A LEU 2.7 38.6 + - - -
965A TYR* 5.9 1.8 - - + -
969A PHE* 3.5 21.5 - - - -
973A LYS* 3.3 52.6 + - - +
974A LEU* 3.0 3.4 + - - +
976A GLU* 1.3 88.3 + - - +
978A LEU* 1.3 64.5 + - - +
979A ASN 3.1 3.1 - - - -
980A LEU* 3.1 19.4 + - - +
985A LEU* 3.6 20.1 - - + +
988A LEU* 4.3 19.0 - - + +
989A VAL* 3.7 24.1 - - - +
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Residues in contact with LEU 978 (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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938A LYS* 4.4 0.3 - - - +
939A LEU* 3.6 8.7 + - + +
940A SER* 2.8 49.4 + - - -
943A ILE* 3.6 30.7 - - + -
965A TYR* 4.6 8.7 - - + +
974A LEU* 2.7 52.5 + - + +
975A LYS* 4.2 17.9 - - + +
976A GLU 3.8 0.2 - - - -
977A ARG* 1.3 72.3 - - - +
979A ASN* 1.3 60.1 + - - +
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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