Contacts of the helix formed by residues 70 - 85 (chain C) in PDB entry 2Y4T
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 ASN 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 4.1 7.9 - - - +
41C LEU* 3.5 24.2 - - - +
67C ASP* 2.8 31.7 + - + +
69C ASP* 1.3 74.8 - - - +
71C TYR* 1.3 66.8 + - - +
72C ILE* 3.4 22.9 + - - +
73C ALA* 3.4 32.9 + - + +
74C TYR* 3.0 20.4 + - - -
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Residues in contact with TYR 71 (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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69C ASP 3.3 4.8 + - - +
70C ASN* 1.3 74.6 + - - +
72C ILE* 1.3 89.1 + - + +
74C TYR* 3.4 5.7 + - - +
75C TYR* 3.0 31.1 + - + +
97C VAL* 4.2 20.3 - - + +
100C LEU* 3.8 32.5 - - + -
101C LYS* 3.4 41.7 - - + +
104C PHE* 4.3 22.9 - + - -
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Residues in contact with ILE 72 (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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38C GLU* 6.0 1.8 - - - +
41C LEU* 4.2 12.6 - - + -
70C ASN* 3.3 16.1 - - - +
71C TYR* 1.3 105.3 - - + +
73C ALA* 1.3 56.9 + - - +
75C TYR* 3.2 6.9 + - + +
76C ARG* 2.8 69.5 + - + +
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.8 10.7 - - - +
60C PHE* 4.2 2.8 - - - +
63C ALA* 3.7 37.2 - - + +
64C VAL* 3.8 11.0 - - + +
70C ASN* 3.4 28.0 + - + +
72C ILE* 1.3 79.8 - - - +
74C TYR* 1.3 56.9 + - - +
76C ARG* 3.4 1.9 + - - +
77C ARG* 3.0 31.9 + - - +
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Residues in contact with TYR 74 (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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64C VAL* 3.5 33.9 - - + +
67C ASP 4.2 1.3 - - - -
68C PRO* 2.9 51.1 + - + +
69C ASP 4.2 0.2 - - - -
70C ASN 3.0 25.8 - - - -
71C TYR* 3.4 6.6 + - - +
72C ILE 3.3 0.4 - - - -
73C ALA* 1.3 77.9 - - - +
75C TYR* 1.3 61.8 + - - +
77C ARG* 4.3 12.8 - - - -
78C ALA* 3.2 23.4 + - - +
93C ASP* 3.6 20.9 - - - +
96C LYS* 3.8 39.7 + - + -
97C VAL* 3.7 14.1 - - + +
100C LEU* 4.2 4.5 - - + -
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TYR* 3.0 19.6 + + + +
72C ILE* 3.2 7.2 + - + +
74C TYR* 1.3 74.6 - - - +
76C ARG* 1.3 76.5 + - + +
78C ALA* 3.3 4.9 + - - +
79C THR* 3.2 40.8 + - + +
94C LEU* 4.0 17.3 - - + -
97C VAL* 3.5 26.4 - - + +
104C PHE* 4.1 22.6 - + + -
106C ALA* 4.5 9.9 - - - +
107C ALA* 4.0 20.0 - - + -
110C GLN* 4.0 20.7 + - + +
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Residues in contact with ARG 76 (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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41C LEU* 4.3 6.9 + - + +
45C LYS* 3.6 44.8 - - - +
48C LEU* 5.4 4.5 - - - -
60C PHE* 3.4 39.1 - - + -
72C ILE* 2.8 51.8 + - + +
73C ALA* 3.9 1.8 - - - +
75C TYR* 1.3 80.1 - - + +
77C ARG* 1.3 64.1 + - - +
79C THR* 2.7 23.9 + - - -
80C VAL* 3.3 15.1 - - - +
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Residues in contact with ARG 77 (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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57C LEU* 4.3 8.3 - - + +
60C PHE* 3.7 20.3 - - + -
61C HIS* 3.0 60.1 + - + +
64C VAL* 3.3 41.2 - - - +
65C ASP* 4.9 2.0 + - - -
73C ALA 3.0 18.3 + - - +
74C TYR* 4.0 6.1 - - - +
76C ARG* 1.3 76.3 - - - +
78C ALA* 1.3 58.5 + - - +
80C VAL* 3.1 6.6 + - - +
81C PHE* 2.9 43.6 + - + -
93C ASP* 2.8 34.8 + - - +
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Residues in contact with ALA 78 (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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74C TYR 3.2 17.9 + - - +
75C TYR 3.3 5.6 + - - +
77C ARG* 1.3 78.2 - - - +
79C THR* 1.3 51.9 + - - +
81C PHE* 3.2 8.6 + - - +
82C LEU* 2.8 40.3 + - + +
90C ALA* 4.2 4.7 - - - +
93C ASP* 3.9 14.5 + - + -
94C LEU* 3.7 36.1 - - + +
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Residues in contact with THR 79 (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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48C LEU* 3.9 16.6 - - - +
75C TYR* 3.2 35.1 + - + +
76C ARG* 2.7 27.7 + - - -
78C ALA* 1.3 76.6 - - + +
80C VAL* 1.3 55.5 + - - +
82C LEU* 3.6 9.3 - - + +
83C ALA* 2.9 29.7 + - - +
94C LEU* 6.1 0.7 - - + -
110C GLN* 4.5 13.2 - - - +
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Residues in contact with VAL 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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48C LEU* 3.6 19.7 - - + -
53C LEU* 3.3 33.7 - - + +
56C ALA* 4.1 2.9 - - + -
57C LEU* 3.7 21.8 - - + +
60C PHE* 3.4 26.7 - - + -
76C ARG 3.3 15.3 - - - +
77C ARG 3.1 7.5 + - - +
79C THR* 1.3 73.2 - - - +
81C PHE* 1.3 66.8 + - - +
83C ALA* 3.2 6.8 + - - +
84C MET* 2.8 27.8 + - - +
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Residues in contact with PHE 81 (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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57C LEU* 3.5 20.0 - - + -
61C HIS* 3.4 23.8 - + - -
77C ARG* 2.9 54.8 + - + -
78C ALA* 3.6 7.6 - - - +
80C VAL* 1.3 70.6 - - - +
82C LEU* 1.3 56.8 + - - +
84C MET* 3.1 7.1 + - - +
85C GLY 2.9 9.0 + - - -
86C LYS* 2.9 63.5 + - + -
89C ALA* 3.6 31.4 - - + -
90C ALA* 3.9 14.4 - - + -
93C ASP* 3.9 9.9 - - - -
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Residues in contact with LEU 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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78C ALA* 2.8 28.0 + - + +
79C THR* 3.6 9.9 - - + +
81C PHE* 1.3 71.6 - - - +
83C ALA* 1.3 57.6 + - - +
85C GLY* 3.0 19.3 + - - +
86C LYS 4.9 1.3 - - - +
90C ALA* 3.9 9.6 - - + +
94C LEU* 3.9 27.4 - - + -
110C GLN* 4.2 20.9 - - + +
113C HIS* 6.4 0.7 - - + -
114C LEU* 3.8 35.0 - - + +
117C LYS* 5.5 3.8 - - + -
186C TRP* 3.9 22.1 - - + -
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Residues in contact with ALA 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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48C LEU* 5.5 5.4 - - + -
53C LEU* 3.8 27.6 - - + +
79C THR 2.9 19.5 + - - +
80C VAL* 3.7 6.1 - - - +
82C LEU* 1.3 74.4 - - - +
84C MET* 1.3 58.9 + - - +
85C GLY 3.2 0.7 + - - -
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Residues in contact with MET 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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53C LEU* 3.8 37.9 - - + +
54C ALA* 3.6 29.2 - - + +
57C LEU* 4.2 22.4 - - + -
80C VAL* 2.8 22.4 + - - +
81C PHE* 3.5 7.4 - - - +
83C ALA* 1.3 76.3 - - - +
85C GLY* 1.3 59.5 + - - +
86C LYS* 3.5 11.6 + - + +
216C LYS* 6.0 1.6 - - - -
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Residues in contact with GLY 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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81C PHE 2.9 3.2 + - - -
82C LEU 3.0 13.5 + - - -
83C ALA 3.2 1.8 + - - -
84C MET* 1.3 77.6 - - - +
86C LYS* 1.3 56.4 + - - +
87C SER* 2.8 17.4 + - - -
186C TRP* 3.8 24.6 + - - -
217C LEU* 5.2 6.8 - - - +
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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