Contacts of the helix formed by residues 80 - 96 (chain B) in PDB entry 4YP9
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL 3.3 6.3 + - - +
79B SER* 1.3 71.5 + - - +
81B TYR* 1.3 67.6 + - - +
82B TRP 3.4 2.5 - - - -
83B VAL* 3.6 12.9 + - + +
84B ARG* 3.0 55.0 + - + +
292B GLY* 3.3 18.0 - - - -
293B SER* 2.9 33.9 + - - -
294B ALA 5.3 0.9 - - - -
312B ASN* 5.1 1.6 - - - +
360B PHE* 5.5 0.2 - - - -
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.3 11.3 + - - +
80B ASP* 1.3 81.0 + - - +
82B TRP* 1.3 74.4 + + + +
84B ARG* 3.7 1.7 - - - +
85B ASN* 2.8 50.6 + - - +
158B GLN* 2.4 34.4 + - + -
159B ASN* 4.5 8.1 + - - -
177B GLY* 4.0 4.5 - - - -
178B PHE* 3.9 24.7 - + - -
310B ARG* 3.4 45.5 - - - +
312B ASN* 3.5 22.4 - - - +
315B THR* 3.5 9.4 + - - -
402B A1B 3.4 22.0 - - + -
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Residues in contact with TRP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.3 48.0 - + + -
74B PRO* 3.5 33.5 - - + +
77B GLN* 3.0 34.5 + - + -
79B SER 4.9 1.5 + - - +
80B ASP 3.4 0.2 - - - -
81B TYR* 1.3 84.1 - + + +
83B VAL* 1.3 67.6 + - + +
85B ASN* 3.0 4.4 + - - +
86B ILE* 2.8 28.1 + - - +
134B THR* 3.6 20.2 - - + -
158B GLN* 3.3 25.1 - - + -
159B ASN* 3.8 23.8 - - + -
402B A1B 3.2 36.2 + - + +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 5.3 9.6 - - - +
364A ASP* 4.2 22.2 - - - +
79B SER 5.6 2.2 + - - +
80B ASP* 3.6 16.0 + - + +
81B TYR 3.5 0.2 - - - -
82B TRP* 1.3 77.4 - - + +
84B ARG* 1.3 64.6 + - + +
86B ILE* 3.4 6.9 + - - +
87B ALA* 2.8 30.6 + - + +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 3.0 46.6 + - + +
81B TYR 3.8 0.7 - - - +
83B VAL* 1.3 78.1 - - + +
85B ASN* 1.3 53.9 + - - +
87B ALA* 3.7 3.2 - - - +
88B SER* 2.7 38.7 + - - -
293B SER* 3.0 21.4 + - - -
312B ASN* 3.4 17.5 - - - +
313B ASP* 3.5 2.3 - - - +
360B PHE* 3.1 47.1 - - - +
363B SER* 2.9 35.0 + - - +
364B ASP 3.4 24.4 + - - -
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.2 13.1 + - - +
81B TYR* 2.8 33.9 + - + +
82B TRP* 3.0 9.6 + - - +
84B ARG* 1.3 74.5 - - - +
86B ILE* 1.3 58.7 - - - +
88B SER* 3.1 5.7 + - - -
89B PHE* 2.8 31.4 + - - +
158B GLN* 2.8 27.9 + - - -
312B ASN* 4.0 7.8 + - - +
315B THR* 2.9 28.1 + - - -
316B GLY* 3.9 10.0 - - - +
319B MET* 4.1 6.9 - - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.0 26.2 - - + -
73B TYR* 3.7 26.0 - - + +
82B TRP 2.8 15.4 + - - +
83B VAL* 3.6 9.9 - - - +
85B ASN* 1.3 73.8 - - - +
87B ALA* 1.3 69.8 + - - +
89B PHE* 3.0 16.3 + - + +
90B GLU* 2.9 47.4 + - + +
102B LEU* 4.5 8.5 - - + -
104B GLN* 4.8 18.2 - - - +
132B ILE* 5.6 0.9 - - + -
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Residues in contact with ALA 87 (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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83B VAL* 2.8 22.3 + - + +
84B ARG* 3.7 9.4 - - + +
85B ASN 3.3 0.2 - - - -
86B ILE* 1.3 80.2 - - - +
88B SER* 1.3 60.7 + - - +
90B GLU* 3.8 4.9 + - - +
91B LYS* 3.3 22.3 + - - +
362B TYR 5.1 0.7 - - - +
363B SER* 4.1 18.6 - - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG 2.7 19.8 + - - -
85B ASN* 3.1 13.5 + - - -
87B ALA* 1.3 74.7 - - - +
89B PHE* 1.3 59.0 + - - +
91B LYS* 3.2 2.1 + - - +
92B ARG* 2.9 31.5 + - - +
313B ASP* 3.2 44.3 + - - -
316B GLY* 3.7 11.1 - - - -
317B ILE* 4.8 1.3 - - - -
362B TYR* 3.7 18.6 - - - -
363B SER* 4.4 1.1 - - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 4.3 8.5 - - + -
85B ASN 2.8 20.4 + - - +
86B ILE* 3.0 18.4 + - + +
88B SER* 1.3 78.2 + - - +
90B GLU* 1.3 63.3 + - + +
92B ARG* 3.3 1.4 + - - +
93B LEU* 2.8 49.3 + - + +
102B LEU* 4.7 8.5 - - + -
132B ILE* 3.7 28.7 - - + -
316B GLY* 3.3 26.8 - - - +
319B MET* 3.5 17.0 - - + -
320B ALA* 3.3 28.3 - - + -
323B ILE* 3.5 23.8 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LYS* 5.2 10.0 + - - -
86B ILE* 2.9 42.6 + - + +
87B ALA* 4.2 4.0 - - - +
89B PHE* 1.3 76.8 - - + +
91B LYS* 1.3 59.5 + - - +
93B LEU* 3.2 7.0 + - + +
94B TYR* 2.9 28.2 + - - +
100B TYR* 2.5 46.0 + - + +
102B LEU* 4.1 20.4 - - + +
104B GLN* 5.4 1.9 + - - -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 3.3 15.5 + - - +
88B SER* 3.2 1.8 + - - -
90B GLU* 1.3 76.0 - - - +
92B ARG* 1.3 61.0 + - - +
94B TYR* 3.4 9.9 + - + +
95B LYS* 2.9 50.4 + - + +
361B ARG 5.5 1.6 + - - -
362B TYR* 3.7 45.4 + - + +
364B ASP* 4.9 9.5 + - - -
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Residues in contact with ARG 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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51B ALA 2.8 28.1 + - - -
52B VAL 3.8 3.8 + - - -
54B ALA 3.2 19.4 + - - -
55B GLN 3.9 1.4 + - - -
56B PRO* 3.9 24.4 - - - +
57B VAL 5.2 0.2 - - - +
88B SER 2.9 16.4 + - - +
91B LYS* 1.3 73.4 - - - +
93B LEU* 1.3 66.1 + - - +
95B LYS* 3.3 1.9 + - - +
96B LEU* 3.0 37.9 + - + +
317B ILE* 3.5 35.8 - - + +
320B ALA* 3.5 24.7 - - + -
321B GLU* 3.1 20.8 + - - -
361B ARG* 4.3 6.1 - - - +
362B TYR* 3.1 35.2 + - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 4.1 8.5 - - + -
89B PHE* 2.8 49.4 + - + +
90B GLU* 3.4 9.6 - - - +
92B ARG* 1.3 76.7 - - - +
94B TYR* 1.3 63.1 + - - +
96B LEU* 3.1 13.8 + - - +
97B ASN 3.1 8.5 + - - -
98B ILE* 3.4 47.4 + - + +
100B TYR* 3.7 38.4 - - + -
320B ALA* 4.0 16.6 - - + +
323B ILE* 4.8 9.4 - - + -
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Residues in contact with TYR 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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90B GLU 2.9 13.5 + - - +
91B LYS* 3.4 15.3 - - + +
93B LEU* 1.3 74.6 - - - +
95B LYS* 1.3 59.9 + - + +
97B ASN* 2.6 42.9 + - - +
98B ILE 5.0 2.7 - - - +
100B TYR* 4.8 5.0 - - + +
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Residues in contact with LYS 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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55B GLN* 5.7 1.8 + - - -
56B PRO* 3.6 36.2 - - + +
58B PRO* 4.3 9.0 - - - +
91B LYS* 2.9 37.0 + - + +
92B ARG* 3.3 6.7 + - - +
94B TYR* 1.3 81.5 - - + +
96B LEU* 1.3 58.4 + - - +
97B ASN* 3.3 3.6 + - - +
362B TYR* 3.2 39.3 + - + +
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Residues in contact with LEU 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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56B PRO* 4.2 7.4 - - + -
57B VAL 3.8 19.5 - - - +
58B PRO* 3.5 6.0 - - + +
59B LEU* 3.0 23.9 + - - +
92B ARG* 3.0 27.8 + - + +
93B LEU 3.5 4.7 - - - +
95B LYS* 1.3 77.7 - - - +
97B ASN* 1.3 72.1 + - - +
98B ILE* 3.8 12.3 - - + -
320B ALA* 3.6 30.1 - - + +
321B GLU* 3.4 27.6 - - - +
324B LYS* 3.6 32.5 - - + +
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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
------------------------------------------------------------
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