Contacts of the helix formed by residues 960 - 965 (chain A) in PDB entry 3F2B
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 PHE 960 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856A ARG* 3.2 9.2 - - - +
859A LYS* 3.8 26.8 - - + +
860A GLU* 3.0 53.2 - - + +
863A SER* 3.8 23.1 - - - -
864A ILE* 3.9 13.5 - - + -
898A SER* 3.2 10.2 - - - -
899A SER* 3.9 20.4 - - - -
959A PRO* 1.3 71.4 - - - +
961A GLU* 1.3 70.6 + - + +
963A PHE* 2.9 37.1 + + + +
964A LEU* 3.8 29.7 + - + -
965A GLY 5.2 2.7 - - - -
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Residues in contact with GLU 961 (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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859A LYS* 3.3 30.1 + - - -
959A PRO* 3.2 10.8 - - - +
960A PHE* 1.3 85.8 + - + +
962A THR* 1.3 61.8 + - - +
963A PHE 2.9 2.5 - - - -
964A LEU 4.5 0.2 - - - +
965A GLY* 2.6 51.6 + - - +
966A PHE* 3.4 52.8 - - + -
1217A MET* 3.9 9.8 - - + +
1231A PHE* 3.4 8.1 - - - -
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Residues in contact with THR 962 (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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895A SER* 4.3 4.9 - - - -
898A SER* 3.8 10.1 - - - +
959A PRO* 3.4 19.5 + - - +
960A PHE 3.1 0.6 + - - -
961A GLU* 1.3 76.5 - - - +
963A PHE* 1.3 56.6 + - - +
970A LYS* 3.0 20.8 + - - -
1213A ARG* 3.9 29.6 + - + +
1214A ASP* 2.8 33.6 + - - +
1217A MET* 4.7 2.6 - - - -
1231A PHE* 4.6 1.7 - - - -
1234A MET* 4.1 17.7 - - + +
1235A GLU* 4.9 0.5 - - - +
1272A PRO* 4.0 13.5 - - + -
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Residues in contact with PHE 963 (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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869A PHE* 4.5 10.5 - + - -
873A TYR* 3.5 32.8 - + - -
895A SER* 3.5 34.8 - - - +
896A VAL* 3.6 25.4 - - + -
898A SER* 4.2 5.3 - - - -
899A SER* 5.1 0.7 - - - -
960A PHE* 2.9 20.9 + + + +
962A THR* 1.3 78.4 - - - +
964A LEU* 1.3 92.3 + - + +
965A GLY 3.6 0.2 - - - -
970A LYS* 2.8 31.5 + - - +
972A PRO* 3.5 22.7 - - + +
973A ASP 3.2 26.0 - - - -
974A ILE* 4.6 3.1 - - + -
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Residues in contact with LEU 964 (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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863A SER* 3.7 24.2 - - - +
864A ILE* 4.2 19.1 - - + -
867A HIS* 4.5 9.4 - - + -
869A PHE* 3.8 31.4 - - + -
960A PHE* 3.8 25.4 + - + -
961A GLU 3.5 0.6 + - - -
963A PHE* 1.3 99.4 - - + +
965A GLY* 1.3 65.2 + - - +
968A GLY* 3.4 26.6 + - - -
969A ASP 4.4 0.2 + - - -
970A LYS* 4.1 19.1 - - - +
972A PRO* 4.0 12.1 - - + -
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Residues in contact with GLY 965 (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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863A SER* 5.3 1.9 + - - -
960A PHE* 5.2 4.2 - - - -
961A GLU* 2.6 44.6 + - - +
963A PHE 3.6 0.8 + - - -
964A LEU* 1.3 81.8 - - - +
966A PHE* 1.3 62.0 + - - +
967A LYS 4.6 0.2 - - - -
968A GLY 4.4 0.7 + - - -
1231A PHE* 3.5 26.1 - - - -
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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