Contacts of the helix formed by residues 81 - 98 (chain B) in PDB entry 1Y7Q
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 THR 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 3.3 7.1 + - - -
80B HIS* 1.3 84.2 - - - +
82B LYS* 1.3 83.1 + - + +
83B GLU* 2.8 49.1 + - + +
84B GLN 3.3 6.4 + - - -
85B ILE* 3.5 11.6 + - - +
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Residues in contact with LYS 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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72A ARG* 5.3 13.2 - - + +
77A PRO* 3.5 46.0 - - + +
81B THR* 1.3 95.0 + - - +
83B GLU* 1.3 64.1 + - - +
84B GLN 3.4 0.2 - - - -
85B ILE* 4.0 11.0 - - - -
86B LEU* 2.7 61.7 + - + +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 5.8 3.1 - - + -
81B THR* 2.8 26.5 + - + +
82B LYS* 1.3 88.4 - - - +
84B GLN* 1.3 61.0 + - - +
86B LEU* 3.7 4.9 - - + +
87B GLU* 3.0 29.8 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 5.3 4.9 - - - +
76B GLN 6.1 0.2 - - - +
80B HIS* 2.8 59.8 + - + +
81B THR 3.3 2.0 + - - +
83B GLU* 1.3 79.0 - - - +
85B ILE* 1.3 58.3 + - + +
87B GLU* 3.3 11.8 + - - +
88B LEU* 2.7 56.3 + - + +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.0 31.2 - - + -
77A PRO* 4.4 3.1 - - + -
82A LYS* 4.5 15.3 - - + +
85A ILE* 3.0 56.3 - - + -
75B LEU* 4.3 10.3 - - + +
80B HIS 3.8 9.4 - - - +
81B THR 3.5 22.1 + - - +
82B LYS* 3.6 5.6 + - - +
83B GLU 3.3 0.2 - - - -
84B GLN* 1.3 80.2 - - + +
86B LEU* 1.3 58.7 + - + +
88B LEU* 2.8 23.1 - - - +
89B LEU* 2.8 23.9 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 5.7 4.3 - - + +
71A CYS* 3.4 18.2 - - - -
72A ARG* 3.7 35.0 - - + +
75A LEU* 3.9 10.8 - - + -
77A PRO* 4.2 6.5 - - + -
82B LYS* 2.7 57.9 + - + +
83B GLU* 3.7 5.4 - - - +
85B ILE* 1.3 81.5 - - + +
87B GLU* 1.3 56.7 + - - +
88B LEU 2.7 13.6 + - - -
89B LEU* 2.9 10.6 + - - +
90B VAL* 2.9 27.0 + - + +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU 3.0 15.2 + - - +
84B GLN* 3.5 14.2 + - - +
86B LEU* 1.3 78.4 - - - +
88B LEU* 1.3 55.9 - - - +
90B VAL* 3.7 16.8 - - + +
91B MET* 3.0 38.7 + - + +
114B SER* 5.6 4.7 + - - +
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Residues in contact with LEU 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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43B GLU* 3.5 21.8 - - - +
46B ARG* 4.3 1.0 + - - -
74B TRP* 3.2 33.3 - - + +
75B LEU* 3.2 48.2 - - + +
84B GLN* 2.7 42.8 + - + +
85B ILE 2.8 15.3 - - - +
86B LEU 2.7 1.6 + - - -
87B GLU* 1.3 77.1 - - - +
89B LEU* 1.3 62.7 + - - +
91B MET* 3.2 5.1 + - + +
92B GLU* 3.1 23.4 + - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.1 19.0 - - + -
71A CYS* 3.2 13.9 - - + +
74A TRP* 3.1 32.1 - - + -
75A LEU* 3.0 47.1 - - + -
85A ILE* 5.6 2.0 - - + -
89A LEU* 5.9 4.5 - - + -
74B TRP* 5.1 4.0 - - + -
75B LEU* 5.7 2.2 - - + -
85B ILE* 2.8 24.9 - - + +
86B LEU* 2.9 20.2 + - - +
88B LEU* 1.3 73.0 - - + +
90B VAL* 1.3 65.4 + - - +
92B GLU* 4.5 3.1 - - - -
93B GLN* 2.5 34.2 + - - +
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Residues in contact with VAL 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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49A PHE* 4.3 5.8 - - - -
64A LEU* 3.0 47.1 - - + +
67A LEU* 4.4 3.3 - - - +
68A ARG* 3.3 19.1 - - + +
71A CYS* 3.1 24.0 - - + -
86B LEU* 2.9 29.5 + - + +
87B GLU* 3.7 16.6 - - + +
89B LEU* 1.3 78.9 - - - +
91B MET* 1.3 54.3 + - + +
93B GLN* 3.6 2.3 - - - +
94B PHE* 2.7 34.8 + - - +
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 4.2 21.1 - - - +
46B ARG* 5.6 0.2 - - - -
87B GLU* 3.0 29.1 + - + +
88B LEU* 3.5 4.5 - - + +
90B VAL* 1.3 73.3 - - + +
92B GLU* 1.3 55.9 - - - +
93B GLN 2.5 6.5 + - - -
94B PHE* 2.5 28.2 + - + -
95B LEU* 2.8 57.3 + - + +
111B LEU* 5.5 5.4 - - + -
112B MET 5.7 3.6 - - - +
113B SER 4.9 0.7 - - - -
114B SER* 3.3 45.5 - - - +
117B ILE* 5.3 3.8 - - + -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 6.3 0.4 - - + -
93A GLN* 5.3 0.7 + - - -
46B ARG* 2.5 48.1 + - - +
47B GLN* 4.8 4.8 - - - +
49B PHE* 5.2 0.9 - - - -
50B ARG* 3.8 28.6 - - - +
74B TRP* 3.6 32.3 - - + -
88B LEU 3.1 6.2 + - - +
89B LEU* 4.1 0.4 - - - +
91B MET* 1.3 78.1 - - - +
93B GLN* 1.3 74.1 + - - +
95B LEU* 3.4 9.3 + - - +
96B THR* 3.1 26.9 + - - -
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 2.8 55.4 - - + +
50A ARG* 2.9 35.6 - - - +
67A LEU* 3.6 16.4 - - + -
74A TRP* 4.0 5.8 - - - -
74B TRP* 5.9 0.2 - - - -
89B LEU* 2.5 34.9 + - - +
90B VAL 3.6 1.3 - - - +
91B MET 2.5 4.6 + - - -
92B GLU* 1.3 87.6 - - - +
94B PHE* 1.3 53.9 + - - +
95B LEU 2.7 8.0 + - - -
96B THR* 2.8 7.4 + - + +
97B ILE* 2.6 36.0 + - - +
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Residues in contact with PHE 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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63A ALA* 3.4 15.5 - - + -
64A LEU* 2.7 35.4 - - + -
67A LEU* 3.6 3.3 - - + +
90B VAL 2.7 20.1 + - - +
91B MET* 2.5 20.4 + - + +
93B GLN* 1.3 70.5 - - - +
95B LEU* 1.3 73.0 + - + -
97B ILE* 3.4 8.1 - - - -
98B LEU* 2.7 65.1 - - + +
114B SER* 3.3 17.5 - - - -
117B ILE* 2.8 25.1 - - + -
118B VAL* 2.9 37.5 - - + -
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Residues in contact with LEU 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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46B ARG* 3.3 28.3 - - - +
47B GLN* 6.4 0.4 - - + -
91B MET* 2.8 45.7 + - + +
92B GLU* 3.4 7.0 - - - +
93B GLN 2.7 1.0 + - - -
94B PHE* 1.3 108.1 - - + +
96B THR* 1.3 57.7 + - - +
97B ILE 3.1 1.8 - - - -
98B LEU* 2.5 31.5 - - - +
100B GLU* 5.8 0.7 - - - -
102B ILE* 4.9 7.5 - - + +
111B LEU* 3.4 27.4 - - + -
117B ILE* 4.8 6.7 - - + -
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Residues in contact with THR 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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50A ARG* 2.9 36.3 + - + +
51A ARG* 5.1 0.9 - - - -
53A CYS* 5.3 2.9 - - - +
50B ARG* 5.8 3.8 - - - -
92B GLU* 3.1 15.4 + - - -
93B GLN* 2.8 29.5 + - - +
95B LEU* 1.3 76.9 - - - +
97B ILE* 1.3 65.3 + - + +
98B LEU 4.1 1.8 - - - +
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Residues in contact with ILE 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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49A PHE 4.5 0.7 - - - +
51A ARG* 5.2 0.2 - - - -
52A PHE* 3.1 50.7 - - + +
53A CYS* 3.2 37.2 - - - +
54A TYR* 3.6 23.5 + - + +
63A ALA* 3.7 15.0 - - + -
67A LEU* 3.7 7.6 - - + -
93B GLN 2.6 28.4 + - - +
94B PHE* 3.3 9.9 - - - +
96B THR* 1.3 86.0 - - + +
98B LEU* 1.3 87.9 + - + +
99B PRO* 4.0 1.9 - - - +
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Residues in contact with LEU 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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54A TYR* 2.8 52.7 - - + +
94B PHE* 2.7 60.8 - - + +
95B LEU 2.5 23.2 + - - +
96B THR 4.1 2.4 - - - +
97B ILE* 1.3 86.9 - - + +
99B PRO* 1.4 73.1 - - + +
100B GLU 3.6 1.6 + - - -
102B ILE* 3.6 12.7 - - + +
117B ILE* 3.3 14.4 - - + -
121B VAL* 4.2 10.5 - - + -
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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