Contacts of the helix formed by residues 80 - 98 (chain B) in PDB entry 1O01
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
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Residue Dist Surf HB Arom Phob DC
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78B ARG 3.4 1.8 + - - +
79B MET* 1.3 77.1 - - - +
81B ALA* 1.3 61.1 + - - +
82B SER* 4.0 6.5 - - - +
83B HIS* 2.9 26.1 + - + +
84B ARG* 3.2 9.4 + - - +
147C ASP* 3.5 33.5 - - - +
148C GLY* 2.9 29.4 + - - -
498C LYS* 2.9 16.6 + - - +
127D LYS* 5.4 2.4 + - - -
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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
----------------------------------------------------------
79B MET 3.5 3.0 + - - -
80B ASP* 1.3 71.1 - - - +
82B SER* 1.3 62.0 + - - +
84B ARG* 3.1 34.9 + - - +
85B GLY 3.2 7.6 + - - -
136B ALA* 3.2 33.6 - - - +
137B ASP* 3.7 14.8 - - + -
145C PRO* 4.0 23.8 + - + +
146C ILE 5.5 0.4 + - - -
147C ASP* 4.9 0.2 + - - -
498C LYS* 5.0 2.4 - - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 4.0 2.6 - - - +
81B ALA* 1.3 79.7 - - - +
83B HIS* 1.3 60.5 + - - +
85B GLY* 3.1 5.2 + - - +
86B ARG* 3.0 30.0 + - - +
136B ALA* 5.2 0.2 - - - -
137B ASP* 3.4 28.5 - - - +
145C PRO 5.2 0.2 + - - -
147C ASP* 2.9 32.9 + - - -
127D LYS* 5.2 6.5 - - - +
462D GLN* 3.7 5.4 - - - -
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Residues in contact with HIS 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 33.8 - - + +
80B ASP* 2.9 18.7 + - + +
82B SER* 1.3 79.7 + - - +
84B ARG* 1.3 59.6 + - - +
85B GLY 3.0 1.6 - - - -
86B ARG* 3.0 21.2 + - + +
87B LEU* 2.9 40.9 + - + +
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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
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76B TRP* 3.7 29.9 + - + -
79B MET* 3.9 23.6 + - + -
80B ASP 3.2 9.9 + - - +
81B ALA* 3.1 27.0 + - - +
83B HIS* 1.3 75.7 - - - +
85B GLY* 1.3 62.4 + - - +
87B LEU* 3.3 7.1 + - - +
88B LEU* 3.0 28.3 + - + +
136B ALA* 3.1 22.5 + - + -
183B LEU 3.5 17.9 + - - +
184B ALA 2.9 25.6 + - - -
185B THR* 3.8 9.1 + - - +
186B GLY* 3.3 16.9 - - - +
213B PHE* 4.9 0.9 - - - -
145C PRO* 5.8 0.8 - - - +
500C SER* 3.9 25.3 - - - -
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Residues in contact with GLY 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 3.2 4.4 + - - -
82B SER* 3.1 8.8 + - - -
83B HIS 3.0 0.8 - - - -
84B ARG* 1.3 80.3 - - - +
86B ARG* 1.3 62.1 + - - +
88B LEU 3.3 0.7 + - - -
89B ASN* 3.0 25.6 + - - +
133B ALA* 3.3 37.2 - - - +
136B ALA* 3.7 5.5 - - - +
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Residues in contact with ARG 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 SER* 3.0 17.0 + - - +
83B HIS* 3.0 30.7 + - + +
85B GLY* 1.3 78.0 - - - +
87B LEU* 1.3 57.2 + - + +
89B ASN* 3.4 20.5 + - - +
90B ARG* 2.9 28.9 + - - +
89D ASN* 5.4 1.6 + - - -
93D ASP* 5.1 2.4 + - - -
96D GLU* 4.4 3.4 + - - -
130D ARG* 3.4 60.8 - - - +
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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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76B TRP* 4.1 3.6 - - + -
79B MET* 3.6 38.4 - - + -
83B HIS* 2.9 27.7 + - + +
84B ARG 3.7 5.2 - - - +
85B GLY 3.3 0.2 - - - -
86B ARG* 1.3 75.0 - - + +
88B LEU* 1.3 60.1 + - - +
90B ARG* 3.2 5.7 + - + +
91B LEU 2.9 24.4 + - - -
211B ALA* 3.3 26.8 - - - +
212B GLY* 4.0 19.1 - - - +
213B PHE* 3.5 40.8 - - + -
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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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84B ARG 3.0 20.3 + - - +
87B LEU* 1.3 75.6 - - - +
89B ASN* 1.3 57.9 + - - +
91B LEU* 3.3 8.1 + - + +
92B ALA* 3.0 26.7 + - - +
129B LEU* 4.1 31.6 - - + +
132B TYR* 4.1 0.7 - - + -
133B ALA* 3.7 36.1 - - + +
136B ALA* 5.3 0.2 - - + -
180B GLY* 3.9 12.6 - - - +
183B LEU* 4.1 20.9 - - + -
184B ALA* 3.8 31.0 - - - +
213B PHE* 4.1 17.0 - - + -
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Residues in contact with ASN 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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85B GLY 3.0 20.6 + - - +
86B ARG* 3.6 21.3 - - - +
88B LEU* 1.3 72.5 - - - +
90B ARG* 1.3 61.0 + - - +
92B ALA* 3.2 5.8 + - - +
93B ASP* 3.0 36.5 + - - +
130B ARG* 3.7 23.8 + - - +
133B ALA* 3.6 19.6 - - - +
86D ARG* 5.3 3.4 + - - -
89D ASN* 4.2 26.0 + - - +
130D ARG* 6.3 0.4 - - - +
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Residues in contact with ARG 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 ARG 2.9 14.8 + - - +
87B LEU* 3.2 13.2 + - + +
89B ASN* 1.3 77.2 - - - +
91B LEU* 1.3 61.9 + - - +
93B ASP* 3.2 21.4 + - - +
94B LEU* 3.0 56.7 + - + +
97B ARG* 5.4 1.2 - - - +
210B GLU* 4.8 11.3 + - - +
211B ALA* 3.7 28.2 + - - +
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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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87B LEU 2.9 15.5 + - - +
88B LEU* 3.6 9.9 - - + +
89B ASN 3.3 0.2 - - - -
90B ARG* 1.3 75.5 - - - +
92B ALA* 1.3 58.8 + - - +
94B LEU* 3.3 3.1 + - - +
95B ILE* 3.0 41.4 + - + +
129B LEU* 4.3 19.7 - - + -
179B LEU* 5.1 6.1 - - + -
183B LEU* 5.3 2.9 - - + -
204B VAL* 4.4 4.7 - - + +
207B LEU* 3.8 38.8 - - + +
208B ILE* 3.9 25.8 - - + +
211B ALA* 4.0 6.7 - - + +
213B PHE* 4.1 17.7 - - + -
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Residues in contact with ALA 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 LEU 3.0 13.7 + - - +
89B ASN 3.4 9.0 - - - +
91B LEU* 1.3 78.4 - - - +
93B ASP* 1.3 57.0 + - - +
95B ILE* 3.2 1.3 + - - -
96B GLU* 2.9 24.6 + - - +
126B LEU* 3.1 20.1 - - + +
129B LEU* 4.3 17.5 - - + -
130B ARG* 3.7 36.3 - - + +
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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
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89B ASN* 3.0 20.9 + - - +
90B ARG* 3.2 25.1 + - - +
92B ALA* 1.3 75.2 - - - +
94B LEU* 1.3 59.1 + - - +
96B GLU* 3.3 3.9 + - - +
97B ARG* 2.9 27.9 + - - +
130B ARG* 3.0 26.0 + - - +
86D ARG* 4.5 6.1 + - - -
93D ASP* 5.5 2.9 - - - +
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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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90B ARG* 3.0 42.6 + - - +
91B LEU 3.6 6.5 - - - +
92B ALA 3.2 0.2 - - - -
93B ASP* 1.3 73.8 - - - +
95B ILE* 1.3 65.6 + - - +
97B ARG* 3.4 35.2 + - + +
98B ASP* 3.2 26.9 + - - +
207B LEU* 3.4 41.8 - - + +
210B GLU* 3.7 20.2 - - + +
211B ALA* 3.6 22.7 - - + +
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Residues in contact with ILE 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* 3.0 27.3 + - + +
92B ALA 3.7 4.0 - - - +
94B LEU* 1.3 76.5 - - - +
96B GLU* 1.3 58.9 + - - +
98B ASP 3.3 3.8 - - - -
99B ARG* 3.0 25.5 + - - +
102B LEU* 3.9 9.3 - - + +
122B LEU* 3.9 24.0 - - + -
125B VAL* 4.1 12.8 - - + -
126B LEU* 3.8 14.8 - - + -
129B LEU* 3.6 29.2 - - + -
172B LEU* 6.1 1.1 - - + -
204B VAL* 4.2 18.8 - - + -
207B LEU* 3.7 22.2 - - + -
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Residues in contact with GLU 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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92B ALA 2.9 16.3 + - - +
93B ASP* 3.6 5.2 - - - +
94B LEU 3.2 0.2 - - - -
95B ILE* 1.3 76.2 - - - +
97B ARG* 1.3 65.2 + - - +
99B ARG* 3.2 33.6 + - - +
126B LEU* 3.7 23.2 - - + +
130B ARG* 2.7 37.4 + - - +
86D ARG* 4.4 2.9 + - - -
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Residues in contact with ARG 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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90B ARG* 5.4 1.2 - - - +
93B ASP 2.9 14.2 + - - +
94B LEU* 3.5 24.3 + - + +
96B GLU* 1.3 77.1 - - - +
98B ASP* 1.3 91.6 + - - +
99B ARG 3.3 2.0 + - - -
100B THR 5.2 0.3 + - - -
203B TYR* 4.5 1.8 + - - -
207B LEU* 3.6 7.1 - - - +
210B GLU* 2.8 42.0 + - - -
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Residues in contact with ASP 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 9.3 + - - +
95B ILE 3.3 5.2 - - - +
96B GLU 3.2 0.2 - - - -
97B ARG* 1.3 117.4 + - - +
99B ARG* 1.3 57.9 + - - +
100B THR 3.5 2.2 - - - -
101B TYR* 3.4 13.3 + - + +
102B LEU* 3.0 32.2 + - + +
203B TYR* 2.7 43.0 + - + +
207B LEU* 3.5 5.1 - - + +
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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