Contacts of the helix formed by residues 63 - 71 (chain A) in PDB entry 4FZY
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 TRP 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.7 1.1 - - - -
38A ARG* 3.5 70.9 - - + -
39A PRO 3.9 14.4 - - - -
40A ASP* 4.6 9.2 - - + -
61A LYS 5.3 1.7 + - - -
62A PRO* 1.3 77.8 - - + +
64A ILE* 1.3 68.6 + - - +
65A GLU* 3.1 19.1 - - + +
66A ASP* 3.0 31.3 + - - +
67A VAL* 3.6 8.7 + - - +
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Residues in contact with ILE 64 (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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16A ILE* 4.1 34.3 - - + -
19A ILE* 4.5 8.1 - - + -
37A VAL* 3.4 17.6 - - + +
38A ARG 4.4 1.4 + - - -
40A ASP* 6.4 1.6 - - + -
63A TRP* 1.3 73.0 - - - +
65A GLU* 1.3 84.7 + - - +
67A VAL* 3.0 17.4 + - + +
68A ILE* 2.9 42.4 + - + +
89A LEU* 4.5 1.6 - - + -
90A PRO* 3.7 32.5 - - + -
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Residues in contact with GLU 65 (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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63A TRP* 3.1 21.3 - - + +
64A ILE* 1.3 94.3 - - + +
66A ASP* 1.3 69.0 + - - +
67A VAL 3.3 0.7 + - - -
68A ILE* 3.9 8.5 - - - +
69A PRO* 3.4 17.8 - - - +
90A PRO* 5.6 3.6 - - + +
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Residues in contact with ASP 66 (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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62A PRO* 4.1 13.9 - - + +
63A TRP* 3.0 41.6 + - - +
65A GLU* 1.3 83.2 - - - +
67A VAL* 1.3 60.7 + - - +
69A PRO* 3.7 8.8 - - - +
70A HIS* 4.4 8.3 + - - -
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Residues in contact with VAL 67 (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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19A ILE* 4.0 26.9 - - + -
35A HIS* 3.9 32.8 - - + +
37A VAL* 4.1 11.0 - - + -
62A PRO* 3.8 27.8 - - + -
63A TRP 3.9 9.0 - - - +
64A ILE* 3.0 8.0 + - + +
66A ASP* 1.3 82.2 - - - +
68A ILE* 1.3 63.6 + - - +
69A PRO* 3.0 6.3 - - - -
70A HIS* 3.2 24.4 + - + +
71A TYR* 3.5 7.7 - - + -
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Residues in contact with ILE 68 (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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19A ILE* 3.8 27.1 - - + -
64A ILE* 2.9 19.6 + - + +
65A GLU* 3.9 8.5 - - - +
67A VAL* 1.3 74.6 - - - +
69A PRO* 1.3 73.9 - - + +
70A HIS 3.2 0.4 - - - -
71A TYR* 3.1 17.6 + - + -
72A TYR* 3.4 45.3 + - + +
89A LEU* 4.2 1.6 - - + -
90A PRO* 4.0 32.3 - - + -
92A MET* 3.8 21.8 - - - -
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Residues in contact with PRO 69 (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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65A GLU 3.4 10.1 - - - +
66A ASP* 3.7 5.6 - - - +
67A VAL* 3.0 16.2 - - - +
68A ILE* 1.3 101.3 - - + +
70A HIS* 1.3 64.4 + - + +
71A TYR 3.3 0.5 + - - -
72A TYR* 3.7 28.3 + - + +
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Residues in contact with HIS 70 (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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3A ARG* 4.2 3.1 + - - -
33A MET* 3.5 24.5 - - - +
35A HIS* 4.1 26.0 + + + -
66A ASP 4.4 8.4 + - - -
67A VAL* 3.2 32.7 + - + +
68A ILE 3.2 1.0 - - - -
69A PRO* 1.3 81.3 - - + +
71A TYR* 1.3 64.6 + - + +
72A TYR 3.6 2.6 - - - +
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Residues in contact with TYR 71 (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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3A ARG* 2.8 24.3 + - - +
5A ILE* 4.0 18.6 - - + -
19A ILE* 3.3 32.0 + - + -
20A ALA* 3.7 5.6 - - - -
21A SER* 3.5 44.4 - - - -
33A MET* 3.9 9.9 - - + -
34A SER* 3.2 21.7 + - - -
35A HIS* 2.7 40.2 + + - -
67A VAL 3.5 16.4 - - - -
68A ILE* 3.1 16.6 + - + +
70A HIS* 1.3 79.1 - - + +
72A TYR* 1.3 60.3 + - - +
77A TYR* 3.0 15.9 + - - -
92A MET* 4.6 2.9 - - + -
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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