Contacts of the helix formed by residues 78 - 92 (chain Y) in PDB entry 1O1F
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 ASN 78 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68Y LYS* 5.4 0.8 - - - +
70Y PRO* 3.2 17.1 + - + +
76Y ILE* 4.0 2.4 - - - +
77Y THR* 1.3 79.7 - - + +
79Y TRP* 1.3 62.8 + - - +
80Y ASP* 3.3 17.6 + - - +
81Y ASP* 3.0 44.8 + - + +
82Y MET* 3.1 25.8 + - - +
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Residues in contact with TRP 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Y ILE* 3.8 49.2 + - + -
77Y THR 4.6 7.3 + - - -
78Y ASN* 1.3 72.9 + - - +
80Y ASP* 1.3 63.1 + - - +
82Y MET* 3.8 4.1 - - + +
83Y GLU* 3.3 25.6 + - - +
86Y TRP* 4.6 5.6 - + - -
115Y ASN* 3.6 53.1 + - + -
118Y LYS* 3.8 31.3 - - + +
119Y MET* 3.8 22.7 - - + -
122Y ILE* 3.6 23.0 - - + +
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Residues in contact with ASP 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ARG* 3.3 13.8 + - - -
78Y ASN* 3.3 16.1 + - - +
79Y TRP* 1.3 76.3 - - - +
81Y ASP* 1.3 86.2 + - - +
82Y MET 3.5 0.2 + - - -
83Y GLU* 3.6 8.0 + - - +
84Y LYS* 3.3 37.0 + - - +
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Residues in contact with ASP 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y VAL* 3.4 19.5 - - + +
37Y ARG* 2.9 27.0 + - - -
68Y LYS* 3.1 32.1 - - - +
70Y PRO* 3.4 19.2 - - + +
78Y ASN* 3.0 27.9 + - - +
80Y ASP* 1.3 89.5 + - - +
82Y MET* 1.3 61.1 + - - +
84Y LYS* 3.5 10.7 - - - +
85Y ILE* 3.3 17.0 + - - +
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Residues in contact with MET 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y ASN* 3.5 26.0 - - + +
17Y VAL* 5.8 0.9 - - + -
33Y SER* 5.3 1.6 - - - +
70Y PRO* 3.9 10.3 - - - -
71Y ILE* 3.7 36.3 - - + -
76Y ILE* 3.8 19.5 - - + -
78Y ASN 3.1 16.8 + - - +
79Y TRP* 4.0 6.3 - - + +
80Y ASP 3.3 0.6 - - - -
81Y ASP* 1.3 71.5 - - - +
83Y GLU* 1.3 59.0 + - - +
84Y LYS 3.0 1.6 - - - -
85Y ILE* 2.7 44.8 + - + +
86Y TRP* 2.9 45.5 + - + +
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Residues in contact with GLU 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y TRP 3.3 16.4 + - - +
80Y ASP* 3.8 7.5 - - - +
81Y ASP 3.5 0.2 - - - -
82Y MET* 1.3 76.0 - - - +
84Y LYS* 1.3 57.3 + - - +
86Y TRP* 3.9 13.4 - - + -
87Y HIS* 2.9 32.0 + - + +
122Y ILE* 4.1 19.3 - - + +
126Y THR* 4.2 27.9 + - - +
127Y PHE* 3.7 17.1 - - + -
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Residues in contact with LYS 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y VAL* 4.0 10.3 - - + -
37Y ARG* 3.4 34.9 - - - +
51Y ASP* 5.2 5.5 + - - +
52Y SER* 3.5 26.0 - - - +
54Y VAL* 4.4 10.7 - - + +
80Y ASP* 3.3 25.7 + - - +
81Y ASP* 3.5 25.8 - - - +
82Y MET 3.0 0.2 - - - -
83Y GLU* 1.3 78.9 - - - +
85Y ILE* 1.4 62.7 + - - +
87Y HIS* 3.2 7.8 + - + +
88Y HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y VAL* 3.7 29.4 - - + -
31Y PHE* 4.2 11.1 - - + -
33Y SER* 3.9 26.0 - - - +
34Y ILE 4.1 1.1 - - - +
35Y VAL* 3.8 13.0 - - + -
54Y VAL* 4.0 12.6 - - + -
70Y PRO* 3.6 36.1 - - + -
81Y ASP 3.3 8.0 + - - +
82Y MET* 2.7 28.9 + - + +
84Y LYS* 1.4 69.6 - - - +
86Y TRP* 1.3 56.2 + - + +
88Y HIS* 3.3 3.6 + - - +
89Y THR* 2.7 32.0 + - - +
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Residues in contact with TRP 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y CYS* 4.0 16.5 - - - -
12Y ASN* 2.9 37.6 + - - +
76Y ILE* 4.2 10.1 - - + -
79Y TRP* 4.6 2.0 - + - -
82Y MET* 2.9 37.1 + - + +
83Y GLU* 3.8 18.4 - - - +
85Y ILE* 1.3 75.7 - - + +
87Y HIS* 1.3 59.6 + - - +
89Y THR* 2.8 24.2 + - - -
90Y PHE* 3.0 27.8 + + + -
105Y LEU* 4.4 5.1 - - + +
119Y MET* 3.9 29.6 - - + -
122Y ILE* 4.1 24.5 - - + -
123Y MET* 3.3 30.0 - - + +
127Y PHE* 3.6 20.0 - + + -
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Residues in contact with HIS 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y GLU* 2.9 19.5 + - + +
84Y LYS* 3.2 8.9 + - + +
86Y TRP* 1.3 75.9 - - - +
88Y HIS* 1.3 59.8 + - - +
90Y PHE* 4.5 0.2 - - - -
91Y TYR* 2.9 65.8 + + + +
92Y ASN* 4.6 6.1 + - - -
127Y PHE* 3.9 18.1 - - + -
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Residues in contact with HIS 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Y PHE* 3.6 20.5 - + - -
54Y VAL* 3.9 38.3 + - + +
55Y GLY* 5.2 0.6 - - - -
84Y LYS 3.1 9.6 + - - +
85Y ILE 3.4 8.3 - - - +
87Y HIS* 1.3 80.2 - - - +
89Y THR* 1.3 62.5 + - - +
92Y ASN* 2.8 54.9 + - + +
93Y GLU* 2.9 41.3 + - + +
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Residues in contact with THR 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y CYS* 4.7 9.4 - - + -
17Y VAL* 4.5 7.5 - - + +
19Y ALA* 3.6 31.6 - - + -
31Y PHE* 3.7 19.7 - - + -
85Y ILE* 2.7 27.0 + - - +
86Y TRP* 2.8 14.7 + - - -
88Y HIS* 1.3 76.4 - - - +
90Y PHE* 1.3 62.2 - - + -
93Y GLU* 3.4 8.4 - - + +
94Y LEU* 2.9 36.9 + - + +
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Residues in contact with PHE 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y LEU* 4.0 28.5 - - + -
10Y CYS* 5.8 5.6 - - + -
86Y TRP* 3.0 29.0 + + + +
87Y HIS* 4.1 1.8 - - - +
89Y THR* 1.3 82.0 - - + +
91Y TYR* 1.3 63.9 + + + +
94Y LEU* 3.5 4.9 - - + -
95Y ARG 2.8 26.3 + - - -
96Y VAL* 3.1 23.1 + - + +
98Y PRO* 3.9 26.7 - - + -
103Y THR* 4.4 16.8 - - + -
105Y LEU* 6.1 0.4 - - + -
123Y MET* 4.1 24.5 - - + -
127Y PHE* 3.6 44.9 - + - -
129Y VAL* 4.8 0.7 - - + -
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Residues in contact with TYR 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y HIS* 2.9 61.5 + + - +
90Y PHE* 1.3 83.0 - - + +
92Y ASN* 1.3 72.5 + - - +
95Y ARG* 3.4 17.0 - - - +
96Y VAL 3.8 12.3 - - - -
97Y ALA* 4.6 4.7 - - + -
98Y PRO* 3.7 35.5 - - + +
99Y GLU* 4.1 10.8 + - - -
127Y PHE* 4.9 9.6 + + - -
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Residues in contact with ASN 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y HIS* 4.2 7.5 + - - +
88Y HIS* 2.8 49.3 + - + +
91Y TYR* 1.3 92.1 + - - +
93Y GLU* 1.3 69.4 + - - +
95Y ARG* 3.3 17.1 - - - +
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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
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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