Contacts of the helix formed by residues 79 - 90 (chain C) in PDB entry 4H7Y
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 ALA 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C LYS* 3.9 4.5 - - + +
72C ALA* 3.6 42.2 - - + +
75C GLU 3.5 6.5 + - - +
76C PRO 3.4 8.8 + - - +
77C ASP 3.7 0.2 - - - -
78C ASP* 1.3 76.8 - - - +
80C ARG* 1.3 64.6 + - - +
81C ASP 3.2 3.1 - - - -
82C TYR* 3.1 28.0 + - + -
83C PHE* 3.5 13.9 - - + -
103C PHE* 4.1 3.6 - - + -
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ASP 5.4 6.6 + - - +
78C ASP 3.5 2.2 - - - -
79C ALA* 1.3 78.1 - - - +
81C ASP* 1.3 66.5 + - - +
82C TYR 3.2 0.2 + - - -
83C PHE* 3.3 6.0 + - - +
84C GLN* 3.0 46.1 + - + +
100C PHE* 4.2 8.7 - - + -
103C PHE* 4.0 25.0 - - + -
104C GLU* 2.6 42.3 + - - +
107C GLN* 4.9 3.0 - - - +
109C ASN* 3.5 12.9 - - - +
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.0 13.1 - - + +
49B LEU 4.8 1.2 - - - +
51B PRO* 3.1 27.7 - - + +
60B PHE* 4.5 0.7 - - - -
64B GLN* 3.1 23.1 + - - -
85B MET* 3.4 18.4 - - - +
89B ASN* 3.0 21.9 + - - +
78C ASP 4.8 0.8 + - - +
79C ALA 3.1 1.2 + - - -
80C ARG* 1.3 79.0 - - - +
82C TYR* 1.3 71.5 + - + +
84C GLN* 3.2 9.0 + - - +
85C MET* 2.9 33.2 + - - +
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE 3.9 12.8 - - - -
47B GLU* 3.4 45.0 + - - +
48B ALA 5.9 0.2 - - - -
49B LEU 5.1 1.1 - - - -
50B PRO* 3.4 32.4 - - - +
51B PRO* 3.9 5.8 - - + +
64C GLN 4.5 1.0 - - - +
67C PHE* 3.7 15.3 - + + -
68C ALA* 3.7 22.8 - - + +
71C LYS* 3.5 44.5 - - + -
78C ASP* 3.6 20.2 + - - -
79C ALA* 3.1 20.1 + - - +
81C ASP* 1.3 80.3 - - + +
83C PHE* 1.3 60.4 + - - +
85C MET* 3.6 2.3 + - - +
86C ALA* 3.1 26.2 + - - +
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL* 6.1 1.1 - - + -
68C ALA* 3.5 41.7 - - + -
69C GLU* 3.9 9.9 - - + -
72C ALA* 3.9 5.6 - - + -
79C ALA 3.5 16.8 - - - -
80C ARG* 3.3 5.3 + - - +
81C ASP 3.3 0.2 - - - -
82C TYR* 1.3 77.3 - - - +
84C GLN* 1.3 64.3 + - - +
86C ALA* 3.3 6.4 + - + +
87C ARG* 3.0 25.6 + - - +
96C VAL* 5.4 1.0 - - - +
99C SER* 3.5 31.4 - - - -
100C PHE* 3.5 44.9 - + + +
103C PHE* 3.5 42.6 - + + -
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Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASP* 3.9 27.8 + - - +
82B TYR* 4.0 13.4 + - + -
85B MET* 4.0 21.3 - - + +
80C ARG* 3.0 36.8 + - + +
81C ASP* 3.2 10.3 + - - +
83C PHE* 1.3 78.8 - - - +
85C MET* 1.3 69.7 + - + +
87C ARG* 3.5 16.7 + - - +
88C ALA* 2.9 28.9 + - - +
100C PHE* 3.5 24.0 - - + -
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Residues in contact with MET 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER* 3.7 35.0 - - - +
46B ILE* 3.7 24.9 - - + -
47B GLU* 3.5 29.8 - - + +
67B PHE* 3.7 30.3 - - + -
82B TYR* 4.4 1.3 - - + -
85B MET* 4.1 15.5 - - - -
64C GLN* 3.8 1.8 - - - -
81C ASP 2.9 16.9 + - - +
82C TYR 3.9 0.4 - - - +
83C PHE 3.2 0.2 - - - -
84C GLN* 1.3 92.8 - - + +
86C ALA* 1.3 60.1 + - - +
88C ALA* 3.2 2.3 + - - +
89C ASN* 2.8 39.5 + - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 5.7 0.2 - - - +
64C GLN* 3.5 40.6 + - + +
65C VAL* 4.2 7.2 - - + +
68C ALA* 5.2 0.9 - - + -
82C TYR 3.1 18.3 + - - +
83C PHE* 3.3 8.5 + - + +
85C MET* 1.3 75.6 - - - +
87C ARG* 1.3 57.3 + - - +
90C CYS* 2.9 35.9 + - - +
96C VAL* 3.6 14.5 - - + +
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASP 5.9 0.2 + - - -
81B ASP* 2.7 34.4 + - - +
82B TYR* 5.1 10.6 + - - +
83C PHE 3.0 16.7 + - - +
84C GLN* 3.9 15.6 + - - +
86C ALA* 1.3 78.5 - - - +
88C ALA* 1.3 62.2 + - - +
91C LYS* 3.4 25.1 + - + +
96C VAL* 3.7 14.9 - - + +
97C HIS* 3.5 41.1 + - + +
100C PHE* 3.8 19.8 - - + -
116C LEU* 3.8 24.3 + - - +
119C LYS* 4.3 24.4 - - - +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 6.2 0.7 - - + -
67B PHE* 4.0 21.5 - - + -
71B LYS* 4.1 17.9 + - - +
82B TYR* 3.2 29.1 + - + +
84C GLN 2.9 15.4 + - - +
85C MET* 3.2 6.7 + - - +
87C ARG* 1.3 78.5 - - - +
89C ASN* 1.3 65.5 + - - +
91C LYS* 4.6 7.8 + - - +
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 5.2 4.9 - - - +
40B GLY* 4.7 2.8 - - - -
43B SER* 3.1 32.3 + - - -
47B GLU* 5.6 0.4 - - - +
67B PHE* 5.6 0.3 - - - -
51C PRO* 3.6 22.7 - - + +
55C GLY* 3.3 25.6 - - - -
60C PHE* 4.1 6.7 - - + -
64C GLN* 3.0 33.2 + - - +
85C MET* 2.8 17.9 + - - +
88C ALA* 1.3 82.4 - - - +
90C CYS* 1.3 64.0 + - - +
91C LYS 3.7 1.1 - - - -
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Residues in contact with CYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR 5.2 0.2 - - - -
55C GLY 3.9 11.7 - - - +
60C PHE* 3.6 31.6 - - - -
61C ALA* 3.7 31.9 - - + -
64C GLN* 4.0 9.4 - - - -
86C ALA 2.9 18.5 + - - +
87C ARG 4.0 0.4 - - - -
89C ASN* 1.3 86.8 - - - +
91C LYS* 1.3 64.7 + - - +
92C LYS 3.0 5.5 + - - -
93C PHE* 3.3 11.8 + - + -
96C VAL* 3.7 17.6 - - + +
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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