Contacts of the helix formed by residues 951 - 958 (chain A) in PDB entry 3W5D
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 ASP 951 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A TYR 2.9 13.0 + - - +
950A VAL* 1.3 68.6 - - - +
952A PRO* 1.4 72.3 - - + +
953A LEU 3.2 0.5 + - - -
954A PRO* 3.3 16.7 - - - +
955A MET* 3.7 9.5 + - - +
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Residues in contact with PRO 952 (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 VAL* 3.1 19.3 - - + +
951A ASP* 1.4 90.4 - - + +
953A LEU* 1.3 64.3 + - + +
955A MET* 3.4 11.4 + - + +
956A ILE* 3.1 36.0 + - + +
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Residues in contact with LEU 953 (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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794A TRP* 5.8 5.4 - - + -
946A LEU* 3.6 40.4 - - + +
947A ILE* 3.6 24.5 - - + -
950A VAL* 2.9 16.3 + - + +
952A PRO* 1.3 78.8 - - + +
954A PRO* 1.4 71.2 - - + +
956A ILE* 3.1 15.0 + - + -
957A PHE* 2.9 45.4 + - + -
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Residues in contact with PRO 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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947A ILE 3.1 21.1 - - - +
948A LEU 3.7 20.6 - - - +
949A TYR 3.9 6.5 - - - +
950A VAL 2.9 28.5 - - - +
951A ASP* 3.3 22.7 - - - +
953A LEU* 1.4 76.5 - - + +
955A MET* 1.3 55.2 + - - +
958A LYS* 3.1 4.9 + - - -
959A LEU* 2.7 49.0 + - + +
960A LYS* 5.6 3.4 - - - -
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Residues in contact with MET 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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85A ILE* 4.1 42.8 - - + +
86A THR* 3.7 19.4 + - + -
951A ASP 3.7 8.1 + - - +
952A PRO* 3.4 19.0 + - + +
953A LEU 3.1 0.6 - - - -
954A PRO* 1.3 76.1 - - - +
956A ILE* 1.3 78.6 + - + +
958A LYS* 3.2 19.0 + - - +
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Residues in contact with ILE 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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85A ILE 5.1 1.1 - - - +
86A THR* 4.5 9.0 + - - -
89A VAL* 3.9 37.4 - - + +
788A ILE* 5.1 2.3 - - - +
790A VAL* 4.6 16.3 - - + +
952A PRO* 3.2 27.1 - - + +
953A LEU* 3.1 19.7 + - + +
955A MET* 1.3 91.9 - - + +
957A PHE* 1.3 72.6 + - + +
958A LYS* 4.1 5.9 - - - +
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Residues in contact with PHE 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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788A ILE* 3.8 3.9 - - - +
790A VAL* 3.6 43.1 - - + -
791A GLN* 2.8 43.0 + - + +
794A TRP* 3.7 38.1 - + + -
947A ILE* 3.5 33.9 - - + -
953A LEU* 2.9 42.3 + - + +
956A ILE* 1.3 80.6 - - + +
958A LYS* 1.3 65.8 + - - +
959A LEU* 3.6 22.2 - - + -
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Residues in contact with LYS 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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83A GLU* 6.0 0.2 + - - -
86A THR* 3.6 34.3 + - - +
788A ILE* 3.9 20.5 - - + +
894A PRO* 3.7 23.2 - - + +
897A MET* 4.2 26.5 - - + +
954A PRO 3.1 8.0 + - - -
955A MET* 3.2 11.5 + - - +
956A ILE 4.1 3.6 - - - +
957A PHE* 1.3 82.8 - - - +
959A LEU* 1.3 67.0 + - - +
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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