Contacts of the helix formed by residues 72 - 88 (chain B) in PDB entry 1INL
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 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B THR* 3.0 23.4 + - - +
71B LYS* 1.3 81.8 - - - +
73B GLU* 1.3 68.1 + - - +
74B PHE* 3.0 10.1 + - - -
75B MET* 3.0 24.0 + - + +
236B MET* 3.1 17.7 - - + +
237B THR* 2.7 29.7 + - - +
238B THR* 2.6 37.5 + - - +
209C PHE* 3.7 6.9 - - + -
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.2 15.3 - - + -
69B THR 2.9 24.6 + - - +
70B GLU* 4.3 1.8 + - - +
71B LYS 4.0 0.2 - - - -
72B ASP* 1.3 77.3 + - - +
74B PHE* 1.3 67.1 + - - +
75B MET 3.1 0.5 + - - -
76B TYR* 3.2 5.6 + - - +
77B HIS* 2.8 61.6 + - + +
106B ARG* 2.8 38.6 + - - -
136B GLN* 2.9 27.1 - - - +
137B THR* 3.6 13.5 - - + -
236B MET* 4.4 5.4 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU 5.4 2.0 - - - -
71B LYS 3.4 26.2 - - - -
72B ASP* 3.0 7.9 + - - -
73B GLU* 1.3 91.3 + - - +
75B MET* 1.3 81.7 + - + +
77B HIS 4.6 0.7 - - - +
78B GLU* 3.0 46.9 + - - +
106B ARG* 4.4 10.1 - - - +
107B GLU* 5.6 0.2 - - - +
272B LYS* 3.5 55.9 - - + +
273B TYR* 3.8 9.4 - - + -
288C PHE* 3.8 27.1 - + + -
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Residues in contact with MET 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 3.0 22.3 + - + +
74B PHE* 1.3 105.2 - - + +
76B TYR* 1.3 60.7 + - - +
79B MET* 3.5 28.2 + - - +
235B PHE* 3.5 28.8 - - - +
236B MET* 4.1 3.1 - - + -
237B THR* 3.2 46.2 - - + +
246B TYR* 4.1 1.6 + - - -
273B TYR* 3.8 21.5 - - + -
209C PHE* 4.0 10.5 - - + -
243C MET* 5.2 0.2 - - - +
288C PHE* 3.8 24.2 - - + -
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Residues in contact with TYR 76 (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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67B MET 5.5 0.2 - - - -
72B ASP 4.1 0.4 + - - -
73B GLU* 3.2 7.8 + - - +
75B MET* 1.3 78.4 - - - +
77B HIS* 1.3 92.7 + + - +
79B MET 3.3 1.4 + - - -
80B LEU* 3.0 34.0 + - + +
170B ASP* 2.7 32.3 + - - -
171B SER* 3.4 7.8 + - - -
204B GLU* 3.3 26.4 - - + +
236B MET* 3.9 20.2 - - + +
239B TYR* 3.7 28.9 - + + -
244B TRP* 3.7 22.2 - + - -
246B TYR* 3.5 33.4 + + - -
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Residues in contact with HIS 77 (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 THR* 3.9 15.3 - - + +
73B GLU* 2.8 47.1 + - + +
74B PHE 4.5 0.2 - - - +
76B TYR* 1.3 100.0 - + - +
78B GLU* 1.3 62.0 + - - +
80B LEU* 4.1 1.3 - - - +
81B ALA* 3.1 27.9 + - - +
101B ASP* 3.2 32.2 + - - -
103B GLY* 3.6 27.8 - - - +
104B THR* 3.3 23.1 + - - +
106B ARG* 4.2 2.2 - - - +
107B GLU* 3.8 9.1 - - + +
137B THR* 4.4 0.8 - - - +
170B ASP* 4.2 2.2 - - - -
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Residues in contact with GLU 78 (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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74B PHE* 3.0 31.8 + - - +
77B HIS* 1.3 75.9 - - - +
79B MET* 1.3 60.1 + - - +
82B HIS* 2.9 45.0 + - + +
83B VAL 4.3 0.3 + - - -
107B GLU* 3.6 24.6 - - - +
110B LYS* 4.6 2.8 + - - -
270B GLU 4.5 1.7 - - - +
271B LEU* 3.7 12.9 - - - -
272B LYS* 2.8 31.5 + - - +
273B TYR* 2.8 27.8 + - + -
274B TYR* 2.9 21.9 + - + +
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Residues in contact with MET 79 (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 MET 3.5 18.5 + - - +
76B TYR 3.3 2.0 + - - -
78B GLU* 1.3 75.9 - - - +
80B LEU* 1.3 63.6 + - - +
81B ALA 3.5 0.2 + - - -
83B VAL* 3.6 16.5 + - + +
232B TYR* 2.8 37.9 + - + -
233B LEU 4.2 6.3 - - - +
234B GLY* 4.8 3.1 - - - -
246B TYR* 3.9 21.5 - - + +
273B TYR* 3.5 34.8 - - + +
274B TYR* 3.9 20.9 - - + -
278B VAL* 4.0 11.9 - - + +
279B HIS* 5.3 0.2 - - - -
282B SER* 3.6 34.3 - - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.0 41.9 + - + +
77B HIS* 4.1 3.4 - - - +
79B MET* 1.3 76.3 - - - +
81B ALA* 1.3 56.5 + - - +
84B PRO* 3.3 11.6 - - - +
104B THR* 3.6 20.6 - - - +
168B ILE* 3.6 19.0 - - + +
169B ILE 4.0 3.4 - - - +
170B ASP* 3.9 13.0 - - - -
202B SER* 2.9 41.1 + - - +
203B ALA 3.9 3.4 - - - +
204B GLU* 3.7 25.8 - - - +
232B TYR* 3.6 3.5 + - - +
246B TYR* 3.9 20.3 - - + -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS 3.1 17.8 + - - +
80B LEU* 1.3 78.1 - - - +
82B HIS* 1.3 65.2 + - - +
83B VAL 3.4 0.7 - - - -
84B PRO* 3.3 4.7 - - - +
85B MET* 3.0 28.6 + - + +
104B THR* 4.2 10.3 - - + -
107B GLU* 3.8 21.5 - - + -
108B VAL* 4.1 21.8 - - + +
168B ILE* 4.1 6.7 - - - -
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Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 2.9 41.1 + - + +
81B ALA* 1.3 71.4 - - - +
83B VAL* 1.3 65.9 + - - +
85B MET* 4.3 1.8 - - - -
86B PHE* 3.0 45.8 + + + +
107B GLU* 2.8 54.4 + - + +
110B LYS* 4.4 5.6 - - + -
111B HIS* 2.9 27.2 + + - -
267B PHE* 4.6 2.2 - + - -
271B LEU* 3.4 26.5 - - + +
274B TYR* 3.9 15.5 - - + -
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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
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79B MET* 3.6 14.2 + - + +
81B ALA 3.4 0.2 - - - -
82B HIS* 1.3 79.4 - - - +
84B PRO* 1.3 71.6 - - + +
86B PHE 4.2 0.2 - - - -
87B LEU* 3.3 32.7 + - + +
232B TYR* 3.5 48.0 - - + +
248B PHE* 4.2 5.4 - - + -
274B TYR* 3.8 18.2 - - + -
279B HIS* 3.9 24.3 + - + +
282B SER* 4.8 2.9 - - - +
283B PHE* 4.0 14.4 - - + -
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Residues in contact with PRO 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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80B LEU 3.3 22.2 - - - +
81B ALA 3.3 11.4 - - - +
83B VAL* 1.3 97.7 - - + +
85B MET* 1.3 60.6 + - - +
87B LEU* 3.2 0.7 + - - -
88B HIS* 3.1 19.8 + - - +
166B VAL* 4.2 5.8 - - + -
168B ILE* 4.4 10.3 - - + -
200B VAL* 3.4 26.2 - - + +
201B PHE 4.4 3.4 - - - +
202B SER* 3.5 24.5 - - - +
232B TYR* 3.9 0.2 - - - +
248B PHE* 4.0 18.2 - - + -
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Residues in contact with MET 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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81B ALA* 3.0 28.7 + - - +
82B HIS 4.1 0.7 - - - +
84B PRO* 1.3 78.0 - - - +
86B PHE* 1.3 61.2 + - - +
87B LEU 3.5 0.2 + - - -
88B HIS* 3.5 13.0 + - - +
91B PRO* 3.7 29.9 - - + +
94B VAL* 3.9 19.1 - - + -
108B VAL* 4.0 23.6 - - + +
111B HIS* 3.5 43.9 - - + +
114B VAL* 3.5 32.3 - - + -
166B VAL* 4.0 18.8 - - - -
168B ILE* 4.8 2.0 - - + -
263B LYS* 4.8 0.7 + - - -
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Residues in contact with PHE 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 HIS* 3.0 38.3 + + + +
83B VAL 4.4 0.9 - - - +
85B MET* 1.3 76.4 - - - +
87B LEU* 1.3 60.5 + - - +
111B HIS* 3.5 23.6 - + - -
259B PHE* 4.6 9.8 - - + -
260B ASP 5.5 1.4 + - - -
263B LYS* 2.9 62.4 + - + +
264B VAL* 3.9 15.9 - - + -
267B PHE* 3.5 43.5 - + + -
271B LEU* 4.5 4.3 - - + -
274B TYR* 3.4 38.6 - + - +
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Residues in contact with LEU 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* 3.3 24.3 + - + +
84B PRO 3.2 5.4 + - - +
86B PHE* 1.3 76.5 - - - +
88B HIS* 1.3 63.2 + - - +
89B PRO* 3.6 5.9 - - - +
200B VAL* 4.9 0.7 - - + -
248B PHE* 3.6 28.0 - - + -
253B ILE* 3.8 22.9 - - + +
254B ASP 3.9 6.5 - - - +
255B PRO* 3.6 44.9 - - + +
258B ASP 4.0 10.2 - - - +
259B PHE* 3.9 26.5 - - + -
263B LYS* 4.9 0.3 + - - -
279B HIS* 3.6 14.4 - - - +
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO 3.1 14.6 + - - +
85B MET 3.6 11.3 - - - +
86B PHE 3.3 0.6 - - - -
87B LEU* 1.3 77.8 - - - +
89B PRO* 1.3 74.0 - - + +
90B ASN* 3.0 38.8 + - - +
91B PRO* 3.1 29.2 - - + +
165B ASP* 3.3 44.1 + - + +
166B VAL* 4.2 0.2 - - + -
198B ASP* 3.4 37.2 + - - -
200B VAL* 4.0 11.6 - - + +
253B ILE* 4.5 2.9 - - - -
263B LYS* 3.0 18.8 + - - -
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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
------------------------------------------------------------
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