Contacts of the helix formed by residues 86 - 101 (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 LYS 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C LEU* 6.0 3.1 - - + -
81C PHE* 2.9 45.5 + - + +
82C LEU* 5.5 0.2 - - - -
84C MET* 3.3 14.6 - - + +
85C GLY* 1.3 72.2 - - - +
87C SER* 1.3 64.6 + - - +
88C LYS* 3.4 4.5 - - + +
89C ALA* 3.2 14.4 + - + +
90C ALA* 3.0 24.0 + - - +
186C TRP* 5.5 0.4 - - - -
219C ASN* 4.6 29.9 - - + +
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Residues in contact with SER 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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85C GLY 2.8 10.2 + - - -
86C LYS* 1.3 70.4 - - - +
88C LYS* 1.3 65.0 + - - +
89C ALA 3.4 0.2 + - - -
90C ALA* 3.5 8.9 + - - +
91C LEU 3.7 4.5 + - - -
114C LEU* 4.0 3.9 - - - +
118C GLN* 2.9 45.1 + - - +
186C TRP* 3.3 44.7 + - - +
217C LEU* 4.9 13.6 + - - +
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS* 3.4 2.6 - - + -
87C SER* 1.3 80.0 + - - +
89C ALA* 1.3 57.8 + - + +
91C LEU* 3.9 3.5 + - - +
92C PRO* 3.2 22.3 - - - +
118C GLN* 4.7 3.8 - - - +
217C LEU 3.3 19.2 + - - +
218C LYS* 3.3 29.0 - - + +
219C ASN* 3.8 18.2 - - - +
220C ASP* 3.1 29.1 + - - -
221C ASN* 5.2 0.8 - - - +
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Residues in contact with ALA 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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81C PHE* 3.6 40.0 - - + -
86C LYS* 3.2 16.3 + - + +
88C LYS* 1.3 78.9 - - + +
90C ALA* 1.3 66.8 + - - +
92C PRO* 3.2 18.1 - - - +
93C ASP* 4.0 11.8 - - - +
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Residues in contact with ALA 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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78C ALA* 4.2 5.7 - - + +
81C PHE* 3.9 17.0 - - + +
82C LEU* 3.9 26.2 - - + +
86C LYS 3.0 16.2 + - - +
87C SER* 3.9 2.2 - - - +
88C LYS 3.4 0.4 - - - -
89C ALA* 1.3 76.8 - - - +
91C LEU* 1.3 64.4 + - - +
93C ASP* 3.2 7.2 + - - +
94C LEU* 3.1 22.7 + - - +
114C LEU* 3.8 18.4 - - + -
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Residues in contact with LEU 91 (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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87C SER 3.7 1.4 + - - -
88C LYS 4.2 3.8 - - - +
90C ALA* 1.3 77.3 - - - +
92C PRO* 1.4 71.5 - - + +
93C ASP 3.2 0.2 + - - -
94C LEU* 3.2 5.1 + - - +
95C THR* 2.8 42.6 + - - +
111C ARG* 4.8 5.5 - - + -
114C LEU* 3.4 19.5 - - + +
115C LEU* 3.6 37.7 - - + -
118C GLN* 3.7 23.6 - - - +
120C LYS* 4.2 10.1 - - - +
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Residues in contact with PRO 92 (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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88C LYS 3.2 19.1 - - - +
89C ALA* 3.2 18.2 - - - +
91C LEU* 1.4 100.1 - - + +
93C ASP* 1.3 60.7 + - - +
95C THR* 3.5 8.4 + - - +
96C LYS* 2.9 27.7 + - - +
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Residues in contact with ASP 93 (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* 3.6 25.0 - - - +
77C ARG* 2.8 53.9 + - - +
78C ALA* 3.9 6.7 - - + -
81C PHE* 3.9 6.6 - - - -
89C ALA 4.0 12.2 - - - +
90C ALA 3.2 9.0 + - - +
92C PRO* 1.3 80.3 - - - +
94C LEU* 1.3 61.0 + - - +
96C LYS* 3.2 7.5 + - - +
97C VAL* 2.9 33.4 + - - +
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Residues in contact with LEU 94 (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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75C TYR* 4.0 29.4 - - + -
78C ALA* 3.7 23.3 - - + -
79C THR* 6.1 0.7 - - + -
82C LEU* 3.9 25.1 - - + -
90C ALA 3.1 8.0 + - - +
91C LEU 3.7 6.3 - - - +
93C ASP* 1.3 76.2 - - - +
95C THR* 1.3 57.6 + - - +
97C VAL* 3.0 7.3 + - + +
98C ILE* 2.8 34.1 + - - +
107C ALA* 4.5 6.7 - - + +
110C GLN* 4.0 14.6 - - + +
111C ARG* 3.9 35.7 - - + +
114C LEU* 4.0 15.5 - - + -
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Residues in contact with THR 95 (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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91C LEU* 2.8 31.8 + - - +
92C PRO* 3.6 8.3 - - - -
94C LEU* 1.3 71.6 - - - +
96C LYS* 1.3 61.9 + - - +
98C ILE* 3.5 2.3 + - - +
99C GLN* 2.9 49.7 + - + +
111C ARG* 3.3 36.1 + - - +
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Residues in contact with LYS 96 (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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68C PRO* 3.7 24.3 + - - +
69C ASP* 5.5 2.9 + - - +
74C TYR* 3.8 39.9 + - + -
92C PRO 2.9 15.8 + - - +
93C ASP 3.2 8.7 + - - +
95C THR* 1.3 73.4 - - - +
97C VAL* 1.3 64.9 + - - +
99C GLN* 3.0 21.3 + - + +
100C LEU* 2.9 39.2 + - + +
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Residues in contact with VAL 97 (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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71C TYR* 4.2 13.4 - - + +
74C TYR* 3.7 6.7 - - + +
75C TYR* 3.5 48.9 - - + +
93C ASP 2.9 30.3 + - - +
94C LEU* 3.0 10.5 + - - +
96C LYS* 1.3 74.7 - - - +
98C ILE* 1.3 62.3 + - - +
100C LEU* 3.4 4.5 + - - +
101C LYS* 3.1 24.8 + - - +
104C PHE* 3.9 13.5 - - + -
107C ALA* 3.7 24.7 - - + -
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Residues in contact with ILE 98 (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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94C LEU 2.8 17.9 + - - +
95C THR* 3.7 5.8 - - - +
96C LYS 3.3 0.2 - - - -
97C VAL* 1.3 74.1 - - - +
99C GLN* 1.3 63.1 + - + +
101C LYS 3.5 16.8 - - - -
102C MET* 3.3 18.0 - - - +
104C PHE 5.0 3.1 - - - +
107C ALA* 3.6 11.4 - - + +
108C ARG* 3.5 70.0 - - + +
111C ARG* 3.4 45.8 - - - +
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Residues in contact with GLN 99 (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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95C THR* 2.9 36.1 + - + +
96C LYS* 3.0 27.4 + - + +
98C ILE* 1.3 80.7 - - + +
100C LEU* 1.3 62.0 + - + +
102C MET* 4.4 14.1 - - - +
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Residues in contact with LEU 100 (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* 3.4 45.1 - - + +
71C TYR* 3.8 30.5 - - + +
74C TYR* 4.2 3.8 - - + -
96C LYS* 2.9 44.8 + - + +
97C VAL 4.0 0.7 - - - +
99C GLN* 1.3 78.1 - - + +
101C LYS* 1.3 73.1 + - + +
102C MET 4.1 0.6 + - - -
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Residues in contact with LYS 101 (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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71C TYR* 3.4 51.7 - - + +
97C VAL 3.1 13.6 + - - +
98C ILE* 3.5 9.0 - - - +
100C LEU* 1.3 85.2 + - - +
102C MET* 1.3 63.1 + - - +
103C ASP 3.2 2.5 - - - -
104C PHE* 3.2 33.8 + - + +
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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