Contacts of the helix formed by residues 81 - 100 (chain B) in PDB entry 4YYH
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 SER 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ILE* 5.1 3.8 - - - -
29B LEU* 4.7 5.6 - - - -
79B TYR* 3.3 5.3 + - - +
80B LYS* 1.3 83.7 - - - +
82B VAL* 1.3 65.4 + - - +
83B THR* 3.4 14.9 - - - -
84B GLU* 3.1 29.9 + - - +
85B PHE* 3.2 19.4 + - - +
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Residues in contact with VAL 82 (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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25B ILE* 5.5 2.6 - - + +
28B LEU* 3.6 30.5 - - + -
29B LEU* 3.9 18.1 - - + +
32B PHE* 4.0 21.1 - - + -
81B SER* 1.3 73.0 - - - +
83B THR* 1.4 52.6 + - - +
85B PHE* 3.1 1.6 + - + +
86B LYS* 2.7 57.0 + - + +
121B MET* 4.9 6.5 - - + +
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Residues in contact with THR 83 (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 SER* 3.1 13.8 + - - -
82B VAL* 1.4 78.9 - - - +
84B GLU* 1.4 64.8 + - + +
86B LYS* 3.4 13.0 + - - +
87B ALA* 3.1 21.6 + - + +
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Residues in contact with GLU 84 (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 GLU 3.8 5.7 - - - +
79B TYR* 3.7 21.2 - - + -
80B LYS* 2.8 47.2 + - - +
81B SER* 3.1 16.1 + - - +
83B THR* 1.4 78.4 - - + +
85B PHE* 1.3 66.1 + - - +
87B ALA* 3.3 9.4 + - - +
88B ASP* 3.2 18.0 + - - +
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Residues in contact with PHE 85 (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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29B LEU* 3.7 34.1 - - + -
32B PHE* 3.8 11.4 - + + -
33B LEU* 3.9 28.9 - - + -
36B LEU* 3.8 10.3 - - + -
70B MET* 3.4 27.8 - - + +
74B ILE* 3.8 21.8 - - + -
79B TYR* 3.6 32.4 - + + -
81B SER 3.2 7.3 + - - +
82B VAL* 3.1 8.2 + - + +
84B GLU* 1.3 77.4 - - - +
86B LYS* 1.4 64.5 + - - +
88B ASP* 3.1 5.7 + - - +
89B PHE* 3.1 17.6 + - + +
121B MET* 3.7 28.7 - - + -
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Residues in contact with LYS 86 (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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82B VAL* 2.7 43.5 + - + +
83B THR* 3.7 10.3 - - + +
85B PHE* 1.4 74.2 - - - +
87B ALA* 1.4 50.6 + - - +
89B PHE* 3.2 9.1 + - - +
90B LYS* 2.9 34.5 + - - +
118B PHE* 3.5 41.6 - - + -
121B MET* 3.8 39.5 + - + -
122B SER* 4.3 12.1 + - - +
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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 THR* 3.1 14.0 + - + +
84B GLU* 3.5 13.0 - - - +
85B PHE 3.2 0.4 - - - -
86B LYS* 1.4 74.1 - - - +
88B ASP* 1.3 61.9 + - - +
90B LYS* 3.4 6.5 + - - +
91B LEU* 2.9 29.3 + - - +
118B PHE* 5.4 0.7 - - - -
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Residues in contact with ASP 88 (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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65B MET* 3.5 35.4 - - + +
70B MET* 4.2 5.2 - - + -
73B LYS* 2.7 26.3 + - - -
79B TYR* 2.6 33.5 + - - +
84B GLU 3.2 8.1 + - - +
85B PHE 3.1 8.6 + - - +
87B ALA* 1.3 77.5 - - - +
89B PHE* 1.4 65.7 + - - +
91B LEU* 3.3 14.8 + - - +
92B MET* 3.0 19.6 + - - +
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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
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36B LEU* 3.9 22.7 - - + -
67B PHE* 4.0 16.8 - + - -
70B MET* 3.8 15.5 - - + +
85B PHE* 3.1 12.2 + - + +
86B LYS* 3.2 9.4 + - - +
88B ASP* 1.4 75.9 - - - +
90B LYS* 1.3 60.5 + - - +
92B MET* 3.2 32.5 + - + +
93B CYS* 3.1 28.9 + - - -
113B ILE* 3.2 45.1 - - + -
114B LEU* 3.8 14.4 - - + -
117B GLY* 4.0 13.7 - - - -
118B PHE* 3.9 17.5 - + - -
121B MET* 4.0 9.6 - - + -
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Residues in contact with LYS 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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86B LYS 2.9 19.3 + - - +
87B ALA* 3.7 7.4 - - - +
89B PHE* 1.3 69.4 - - - +
91B LEU* 1.3 56.9 + - - +
93B CYS* 3.2 1.7 + - - +
94B ASP* 2.7 70.9 + - - +
114B LEU* 3.9 26.2 - - + -
118B PHE* 3.7 23.3 - - + -
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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
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63B HIS* 3.4 42.6 - - + +
64B PRO 4.3 2.9 - - - +
65B MET* 3.8 18.4 - - + -
87B ALA 2.9 18.7 + - - +
88B ASP* 3.4 18.8 - - - +
90B LYS* 1.3 74.8 - - - +
92B MET* 1.3 54.1 + - - +
94B ASP* 4.4 6.5 - - + -
95B ASN* 2.8 50.9 + - - +
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Residues in contact with MET 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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45B PHE* 3.3 45.9 - - + -
65B MET* 3.5 29.8 - - + +
66B ASP* 3.6 21.1 - - - -
67B PHE* 3.5 43.7 - - + -
70B MET* 4.6 3.4 - - - +
88B ASP 3.0 13.3 + - - +
89B PHE* 3.2 26.9 + - + +
91B LEU* 1.3 77.0 - - - +
93B CYS* 1.3 64.1 + - - +
95B ASN* 3.5 6.3 + - - +
96B ALA* 3.3 16.1 + - - +
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Residues in contact with CYS 93 (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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45B PHE* 4.4 4.5 - - - -
89B PHE* 3.1 39.1 + - - +
90B LYS 3.7 5.8 - - - +
92B MET* 1.3 82.2 - - - +
94B ASP* 1.3 61.6 - - - +
96B ALA 3.2 1.2 + - - -
97B MET* 3.0 33.3 + - + +
110B ALA* 3.5 26.8 - - + +
113B ILE* 4.0 8.7 - - - -
114B LEU* 3.8 30.7 - - + -
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Residues in contact with ASP 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 LYS* 2.7 58.6 + - - +
91B LEU* 3.7 7.3 + - + +
93B CYS* 1.3 71.1 - - - +
95B ASN* 1.3 67.2 + - - +
97B MET* 3.2 23.3 + - - +
98B THR* 2.9 29.2 + - - +
114B LEU* 3.9 8.8 - - - +
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Residues in contact with ASN 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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57B TYR* 3.6 18.1 + - - +
61B ILE* 3.5 32.1 - - + +
62B LYS 5.6 0.2 + - - -
63B HIS 2.8 26.1 + - - +
64B PRO* 3.6 8.7 - - - +
65B MET 3.6 9.0 - - - +
91B LEU* 2.8 37.7 + - - +
92B MET* 3.6 5.8 - - - +
94B ASP* 1.3 73.6 - - - +
96B ALA* 1.3 56.8 + - - +
98B THR* 3.2 2.2 + - - -
99B TYR* 2.9 33.1 + - - +
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Residues in contact with ALA 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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45B PHE* 4.0 4.3 - - + -
57B TYR* 4.8 1.5 + - - -
92B MET 3.3 9.2 + - - +
93B CYS 3.2 3.0 + - - +
94B ASP 3.2 0.4 - - - -
95B ASN* 1.3 79.2 - - - +
97B MET* 1.3 59.0 + - - +
99B TYR* 5.0 0.4 - - - -
100B ASN* 3.0 40.8 + - - +
106B TYR 4.4 2.2 - - - +
107B TYR* 4.5 2.1 - - - -
110B ALA* 3.6 23.8 - - + -
8Y KCR 3.8 30.1 - - + +
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Residues in contact with MET 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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93B CYS* 3.0 19.9 + - + +
94B ASP* 3.2 29.1 + - - +
96B ALA* 1.3 77.6 - - - +
98B THR* 1.3 62.3 + - - +
100B ASN 3.4 10.8 - - - +
107B TYR* 3.4 42.9 - - + +
110B ALA* 3.6 13.7 - - + -
111B LYS* 3.7 30.3 - - - -
114B LEU* 3.8 20.6 - - + -
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Residues in contact with THR 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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60B ILE* 4.2 15.0 - - + +
61B ILE* 3.9 19.3 - - + -
94B ASP* 2.9 20.9 + - - +
95B ASN* 3.6 4.2 - - - -
97B MET* 1.3 79.6 - - - +
99B TYR* 1.3 65.3 + - - +
100B ASN 3.7 1.7 + - - +
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Residues in contact with TYR 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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54B ALA* 3.0 31.4 - - + -
55B PRO* 2.8 31.6 + - - +
57B TYR* 3.5 37.0 - + + -
60B ILE* 3.7 32.8 - - + -
61B ILE* 4.3 5.4 - - + -
95B ASN 2.9 15.4 + - - +
98B THR* 1.3 81.6 - - - +
100B ASN* 1.3 75.7 + - - +
101B ARG* 4.1 3.1 + - - +
7Y GLY* 3.3 37.0 + - - -
8Y KCR 4.0 11.0 - - + -
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Residues in contact with ASN 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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96B ALA* 3.0 28.1 + - - +
97B MET 3.4 7.8 - - - +
98B THR 4.3 1.3 - - - +
99B TYR* 1.3 96.2 - - - +
101B ARG* 1.3 63.6 + - - +
102B PRO* 4.4 0.5 - - - +
104B THR* 3.5 17.1 + - - +
106B TYR* 3.6 30.8 - - - +
107B TYR* 3.4 21.7 - - - +
7Y GLY* 5.3 2.0 - - - -
8Y KCR 2.9 36.7 + - - +
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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