Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 4YYH
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.5 10.8 - - - +
46A ALA 3.4 5.0 - - - +
47A PHE* 3.6 18.7 - - - +
48A PRO* 3.2 30.5 - - + +
49A VAL* 6.4 0.2 - - + -
65A MET* 1.3 80.0 - - - +
67A PHE* 1.3 65.6 + - - +
68A GLY* 2.7 27.0 + - - -
69A THR* 2.5 30.3 + - - -
70A MET* 3.1 23.3 + - - +
92A MET* 3.7 14.6 - - - -
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Residues in contact with PHE 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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33A LEU* 3.4 24.2 - - + +
36A LEU* 3.8 39.0 - - + -
37A GLN* 3.2 46.6 - - + +
40A ASP* 3.9 14.4 - - + -
45A PHE* 2.8 45.2 + + + +
46A ALA 4.3 0.4 - - - +
66A ASP* 1.3 74.0 - - - +
68A GLY* 1.3 58.8 + - - +
70A MET* 3.3 9.4 + - - +
71A LYS* 2.9 28.6 + - - +
89A PHE* 4.0 12.1 - + - -
92A MET* 3.5 25.1 - - + -
113A ILE* 4.5 3.8 - - + -
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Residues in contact with GLY 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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37A GLN* 5.3 0.6 - - - +
46A ALA 3.1 14.3 + - - -
47A PHE* 4.9 8.5 - - - -
66A ASP* 2.7 13.0 + - - -
67A PHE* 1.3 73.6 - - - +
69A THR* 1.4 62.2 + - - +
71A LYS* 3.3 7.0 + - - +
72A ASP* 3.0 31.0 + - - +
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Residues in contact with THR 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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48A PRO* 4.2 6.8 - - - +
64A PRO 5.7 0.2 - - - +
65A MET* 3.7 27.1 - - + -
66A ASP* 2.5 34.0 + - - -
68A GLY* 1.4 73.1 - - - +
70A MET* 1.3 64.8 + - - +
72A ASP* 3.3 10.6 + - + +
73A LYS* 3.0 31.4 + - + +
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Residues in contact with MET 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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33A LEU* 4.4 9.9 - - + -
36A LEU* 5.3 0.2 - - + -
65A MET* 3.6 15.7 - - + -
66A ASP 3.1 16.3 + - - +
67A PHE* 3.5 23.3 - - - +
68A GLY 3.3 0.2 - - - -
69A THR* 1.3 77.9 - - - +
71A LYS* 1.3 56.0 + - - +
73A LYS* 3.1 3.5 + - - +
74A ILE* 2.9 32.6 + - - +
79A TYR* 3.5 18.5 - - + +
85A PHE* 3.5 41.5 - - + +
88A ASP* 4.1 6.7 - - + +
89A PHE* 3.7 40.6 - - + +
92A MET* 4.5 4.9 - - - +
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Residues in contact with LYS 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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30A GLU* 3.2 33.9 + - - +
33A LEU* 3.6 19.7 - - + +
34A ARG* 6.3 3.1 - - - +
37A GLN* 5.7 2.9 - - - +
67A PHE 2.9 14.0 + - - +
68A GLY* 3.5 10.5 - - - +
70A MET* 1.3 73.3 - - - +
72A ASP* 1.3 72.5 + - - +
74A ILE* 3.1 6.0 + - - +
75A VAL* 3.0 32.7 + - + +
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Residues in contact with ASP 72 (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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68A GLY 3.0 16.1 + - - +
69A THR* 3.7 11.1 - - + +
70A MET 3.3 0.2 - - - -
71A LYS* 1.3 82.2 - - - +
73A LYS* 1.4 52.3 + - + +
75A VAL* 3.3 9.4 + - - +
76A ALA* 2.8 34.9 + - - +
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Residues in contact with LYS 73 (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 MET* 4.5 5.6 - - + +
69A THR* 3.0 31.3 + - + +
70A MET 3.1 2.9 + - - +
72A ASP* 1.4 72.8 - - + +
74A ILE* 1.3 64.9 + - - +
76A ALA* 3.4 0.7 + - - -
77A ASN 3.1 3.1 + - - -
78A GLU* 2.8 63.6 + - + +
79A TYR* 3.5 31.2 + - + +
88A ASP* 2.7 34.2 + - - +
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Residues in contact with ILE 74 (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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26A GLN* 2.9 52.8 + - + +
29A LEU* 3.7 36.1 - - + +
30A GLU* 3.6 28.3 - - + +
33A LEU* 3.9 19.7 - - + -
70A MET 2.9 17.8 + - - +
71A LYS* 3.1 4.9 + - - +
73A LYS* 1.3 76.2 - - - +
75A VAL* 1.3 51.0 - - - +
77A ASN* 2.9 21.7 + - - -
78A GLU 5.0 0.4 - - - +
79A TYR* 3.8 20.6 - - + +
85A PHE* 3.9 7.4 - - + -
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Residues in contact with VAL 75 (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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26A GLN* 3.5 11.2 + - - +
30A GLU* 3.7 16.6 - - - +
71A LYS* 3.0 30.4 + - + +
72A ASP* 3.6 11.7 - - - +
74A ILE* 1.3 75.4 - - - +
76A ALA* 1.3 58.5 + - - +
77A ASN* 3.2 4.3 + - - +
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Residues in contact with ALA 76 (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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72A ASP 2.8 17.7 + - - +
73A LYS 3.9 1.3 - - - +
74A ILE 3.2 0.6 - - - -
75A VAL* 1.3 73.6 - - - +
77A ASN* 1.3 69.1 + - - +
78A GLU* 3.3 34.0 + - + +
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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