Contacts of the helix formed by residues 86 - 101 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.7 7.4 - - + -
81B PHE* 2.9 41.8 + - + +
82B LEU* 5.4 0.7 - - - -
84B MET* 4.1 31.2 - - + +
85B GLY* 1.3 73.8 - - - +
87B SER* 1.3 64.1 - - - +
88B LYS* 3.3 3.1 - - - -
89B ALA* 3.1 18.5 + - + +
90B ALA* 3.2 13.0 + - - +
217B LEU 6.1 0.4 - - - -
219B ASN* 4.3 21.9 - - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 2.9 8.3 + - - -
86B LYS* 1.3 72.2 - - - +
88B LYS* 1.3 62.5 + - - +
89B ALA 3.5 0.2 + - - -
90B ALA* 3.6 7.0 + - - +
91B LEU 3.7 3.1 + - - -
114B LEU* 3.6 11.0 - - - +
118B GLN* 3.4 39.7 + - - +
186B TRP* 3.3 42.7 + - - +
217B LEU* 4.2 16.6 + - - +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS 3.3 0.8 - - - -
87B SER* 1.3 81.0 + - - +
89B ALA* 1.3 57.9 + - - +
91B LEU* 4.1 2.1 - - - +
92B PRO* 3.1 26.3 - - - +
118B GLN* 4.6 5.2 - - - +
217B LEU 3.7 15.6 + - - +
218B LYS* 4.3 23.4 + - + +
219B ASN* 5.2 5.2 - - - +
220B ASP* 2.9 42.0 + - + +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.4 47.1 - - + -
86B LYS* 3.1 15.0 + - + +
88B LYS* 1.3 76.9 - - - +
90B ALA* 1.3 65.2 + - - +
91B LEU 3.4 0.4 + - - -
92B PRO* 3.7 14.6 - - - +
93B ASP* 4.1 5.0 - - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 3.9 8.5 - - + +
81B PHE* 3.7 24.8 - - + +
82B LEU* 3.8 29.4 - - + +
86B LYS 3.2 11.7 + - - +
87B SER 3.9 2.2 - - - +
88B LYS 3.4 0.4 - - - -
89B ALA* 1.3 77.8 - - - +
91B LEU* 1.3 63.7 + - - +
93B ASP* 3.2 9.2 + - - +
94B LEU* 3.2 17.3 + - + +
114B LEU* 3.8 13.0 - - + -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER 3.7 0.6 + - - -
88B LYS 3.7 3.9 + - - +
90B ALA* 1.3 76.8 - - - +
92B PRO* 1.4 77.2 - - + +
94B LEU* 2.8 16.3 + - - +
95B THR* 3.1 34.9 + - + +
111B ARG* 4.9 4.7 - - + -
114B LEU* 3.6 17.7 - - + +
115B LEU* 3.7 28.0 - - + -
118B GLN* 3.3 37.2 - - - +
120B LYS* 4.5 5.8 - - - +
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Residues in contact with PRO 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LYS 3.1 22.4 - - - +
89B ALA* 3.7 12.8 - - - +
91B LEU* 1.4 93.0 - - + +
93B ASP* 1.3 64.0 + - - +
95B THR* 3.3 18.9 + - - +
96B LYS* 3.4 12.3 + - - +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 3.7 32.2 - - + +
77B ARG* 2.7 52.2 + - - +
78B ALA* 3.8 5.6 + - + -
81B PHE* 3.3 16.7 - - - -
89B ALA 4.1 7.5 - - - +
90B ALA 3.2 8.7 + - - +
91B LEU 3.1 0.6 - - - -
92B PRO* 1.3 80.3 - - - +
94B LEU* 1.3 59.2 + - - +
96B LYS* 3.2 3.8 + - - +
97B VAL* 2.9 33.4 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 4.2 20.2 - - + -
78B ALA* 4.0 12.3 - - + -
82B LEU* 4.4 13.5 - - + -
90B ALA 3.2 9.4 + - - +
91B LEU 2.8 13.6 + - - +
93B ASP* 1.3 74.8 - - - +
95B THR* 1.3 60.1 + - - +
97B VAL* 3.4 6.5 + - + +
98B ILE* 3.2 28.9 + - - +
107B ALA* 3.6 21.1 - - + +
110B GLN* 3.9 22.2 - - + +
111B ARG* 3.7 28.3 - - + -
114B LEU* 3.7 28.5 - - + -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.1 28.7 + - + +
92B PRO* 3.3 12.0 + - + +
94B LEU* 1.3 71.9 - - - +
96B LYS* 1.3 68.6 + - - +
98B ILE* 3.3 6.1 + - - +
99B GLN* 3.0 38.6 + - - +
111B ARG* 3.2 39.9 - - - +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO 4.3 5.4 + - - -
74B TYR* 3.4 49.5 + - + -
92B PRO 3.4 12.2 + - - +
93B ASP 3.2 10.4 + - - +
95B THR* 1.3 78.4 + - - +
97B VAL* 1.3 65.2 + - - +
99B GLN* 3.1 21.2 + - + +
100B LEU* 3.0 46.1 + - + +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 3.4 39.7 - - + +
74B TYR* 3.3 23.3 - - + -
75B TYR* 3.4 18.2 - - + +
93B ASP 2.9 21.3 + - - +
94B LEU* 3.6 9.6 - - - +
96B LYS* 1.3 73.6 - - - +
98B ILE* 1.3 52.7 + - - +
100B LEU* 3.3 3.4 + - - +
101B LYS* 2.7 34.9 + - + +
104B PHE* 4.1 7.0 - - + -
107B ALA* 3.8 23.6 - - + -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU 3.2 17.4 + - - +
95B THR* 3.6 6.3 - - - +
96B LYS 3.2 0.4 - - - -
97B VAL* 1.3 74.8 - - - +
99B GLN* 1.3 59.1 + - + +
101B LYS 4.1 5.2 - - - -
102B MET* 2.9 46.5 + - + +
104B PHE 5.0 2.2 - - - +
107B ALA* 4.0 9.0 - - + +
108B ARG* 3.3 64.4 - - + +
111B ARG* 3.5 39.5 - - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 3.0 30.4 + - - +
96B LYS* 3.1 26.6 + - + +
98B ILE* 1.3 76.9 - - + +
100B LEU* 1.3 60.0 + - + +
102B MET* 3.2 27.0 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO 5.0 0.2 - - - +
69B ASP* 3.5 30.3 - - + +
71B TYR* 3.7 27.8 - - + -
74B TYR* 3.6 32.5 - - + -
96B LYS* 3.0 40.2 + - + +
97B VAL 3.7 2.7 - - - +
99B GLN* 1.3 78.8 - - + +
101B LYS* 1.3 63.4 + - - +
102B MET 4.0 0.6 + - - -
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.8 47.5 + - + -
97B VAL 2.7 17.7 + - - +
98B ILE* 3.2 7.2 - - - +
100B LEU* 1.3 77.5 - - - +
102B MET* 1.3 56.4 + - - +
103B ASP* 3.0 27.3 + - + +
104B PHE* 2.9 41.4 + - + +
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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