Contacts of the helix formed by residues 78 - 92 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68V LYS* 5.5 0.8 - - - +
70V PRO* 3.2 15.8 + - + +
76V ILE* 4.1 2.2 - - - -
77V THR* 1.3 79.7 - - + +
79V TRP* 1.3 62.6 + - - +
80V ASP* 3.3 16.9 + - - +
81V ASP* 3.0 46.2 + - + +
82V MET* 3.1 26.3 + - - +
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Residues in contact with TRP 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V ILE* 3.8 48.7 + - + -
77V THR 4.6 7.1 + - - -
78V ASN* 1.3 72.5 + - - +
80V ASP* 1.3 63.2 + - - +
82V MET* 3.8 3.7 - - + +
83V GLU* 3.3 25.6 + - - +
86V TRP* 4.6 6.1 - + - -
115V ASN* 3.6 53.5 + - + -
118V LYS* 3.8 32.0 - - + +
119V MET* 3.8 23.6 - - + -
122V ILE* 3.6 22.8 - - + +
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Residues in contact with ASP 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ARG* 3.3 13.6 + - - -
78V ASN* 3.3 14.2 + - - +
79V TRP* 1.3 75.3 - - - +
81V ASP* 1.3 87.5 + - - +
82V MET 3.5 0.2 + - - -
83V GLU* 3.6 7.1 + - - +
84V LYS* 3.3 36.6 + - - +
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Residues in contact with ASP 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35V VAL* 3.4 19.8 - - + +
37V ARG* 2.9 26.2 + - - -
68V LYS* 3.1 32.0 - - - +
70V PRO* 3.4 20.0 - - + +
78V ASN* 3.0 28.4 + - + +
80V ASP* 1.3 89.5 + - - +
82V MET* 1.3 61.2 + - - +
84V LYS* 3.5 10.0 - - - +
85V ILE* 3.3 16.5 + - - +
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Residues in contact with MET 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V ASN* 3.5 26.2 - - + +
17V VAL* 5.8 0.7 - - + -
33V SER* 5.3 1.3 - - - +
70V PRO* 3.9 10.7 - - - +
71V ILE* 3.7 37.2 - - + -
76V ILE* 3.8 20.0 - - + -
78V ASN 3.1 16.3 + - - +
79V TRP* 4.0 6.7 - - + +
80V ASP 3.3 0.6 - - - -
81V ASP* 1.3 71.5 - - - +
83V GLU* 1.3 59.1 + - - +
84V LYS 3.0 2.0 - - - -
85V ILE* 2.7 44.7 + - + +
86V TRP* 2.9 45.4 + - + +
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Residues in contact with GLU 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V TRP 3.3 17.0 + - - +
80V ASP* 3.8 7.7 - - - +
82V MET* 1.3 76.6 - - - +
84V LYS* 1.3 55.3 + - - +
86V TRP* 3.9 14.2 - - + -
87V HIS* 2.9 31.6 + - + +
122V ILE* 4.1 19.9 - - + +
126V THR* 4.2 27.6 + - - +
127V PHE* 3.7 16.0 - - + -
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Residues in contact with LYS 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V VAL* 4.0 9.6 - - + -
37V ARG* 3.4 33.8 - - - +
51V ASP* 5.2 5.5 + - - +
52V SER* 3.5 26.7 - - - +
54V VAL* 4.4 10.4 - - + +
80V ASP* 3.3 26.7 + - - +
81V ASP* 3.5 25.6 - - - +
82V MET 3.0 0.2 - - - -
83V GLU* 1.3 79.5 - - - +
85V ILE* 1.4 62.3 + - - +
87V HIS* 3.2 7.9 + - + +
88V HIS* 3.1 22.7 + - - +
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Residues in contact with ILE 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V VAL* 3.7 28.7 - - + -
31V PHE* 4.2 10.9 - - + -
33V SER* 3.9 26.9 - - - +
34V ILE 4.1 0.7 - - - +
35V VAL* 3.8 12.6 - - + -
54V VAL* 4.0 13.2 - - + -
70V PRO* 3.6 36.8 - - + -
81V ASP 3.3 8.0 + - - +
82V MET* 2.7 27.5 + - + +
84V LYS* 1.4 70.2 - - - +
86V TRP* 1.3 54.3 + - + +
88V HIS* 3.3 3.8 + - - +
89V THR* 2.7 32.5 + - - +
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Residues in contact with TRP 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V CYS* 4.0 16.0 - - - -
12V ASN* 2.9 37.2 + - - +
17V VAL* 6.1 0.2 - - + -
76V ILE* 4.2 11.0 - - + -
79V TRP* 4.6 1.3 - + - -
82V MET* 2.9 39.1 + - + +
83V GLU* 3.8 18.2 - - - +
85V ILE* 1.3 74.7 - - + +
87V HIS* 1.3 60.5 + - - +
89V THR* 2.8 23.7 + - - -
90V PHE* 3.0 27.5 + + + -
105V LEU* 4.4 4.7 - - + +
119V MET* 3.9 30.3 - - + -
122V ILE* 4.1 24.0 - - + -
123V MET* 3.3 29.3 - - + +
127V PHE* 3.6 19.5 - + + -
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Residues in contact with HIS 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567J LYS* 3.5 28.1 + - - -
83V GLU* 2.9 20.1 + - + +
84V LYS* 3.2 8.3 + - - +
86V TRP* 1.3 76.8 - - - +
88V HIS* 1.3 58.9 + - - +
90V PHE* 4.5 0.4 - - - -
91V TYR* 2.9 64.7 + + + +
92V ASN* 4.6 6.8 + - - -
127V PHE* 3.9 17.9 - - + -
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Residues in contact with HIS 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V PHE* 3.6 21.4 - + - -
54V VAL* 3.9 38.9 + - + +
55V GLY* 5.2 0.6 - - - -
56V ASP 5.9 0.2 + - - -
84V LYS 3.1 9.2 + - - +
85V ILE 3.4 8.3 - - - +
87V HIS* 1.3 79.3 - - - +
89V THR* 1.3 63.6 + - - +
92V ASN* 2.8 54.9 + - + -
93V GLU* 2.9 41.6 + - + -
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Residues in contact with THR 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V CYS* 4.7 9.4 - - + -
17V VAL* 4.5 8.2 - - + +
19V ALA* 3.6 30.7 - - + -
31V PHE* 3.7 19.8 - - + -
85V ILE* 2.7 26.2 + - - +
86V TRP* 2.8 15.4 + - - -
88V HIS* 1.3 76.1 - - - +
90V PHE* 1.3 63.5 + - + -
93V GLU* 3.4 8.7 - - + +
94V LEU* 2.9 36.5 + - + +
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Residues in contact with PHE 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V LEU* 4.0 28.3 - - + -
10V CYS* 5.8 6.1 - - + -
86V TRP* 3.0 27.7 + + + +
87V HIS* 4.1 2.2 - - - +
89V THR* 1.3 84.5 - - + +
91V TYR* 1.3 62.1 + + + +
94V LEU* 3.5 4.2 - - + -
95V ARG 2.8 25.8 + - - -
96V VAL* 3.1 24.5 + - + +
98V PRO* 3.9 26.5 - - + -
103V THR* 4.4 17.3 - - + -
105V LEU* 6.1 0.4 - - + -
123V MET* 4.1 23.8 - - + -
127V PHE* 3.6 45.1 - + - -
129V VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V HIS* 2.9 61.9 + + - +
90V PHE* 1.3 83.5 - - + +
92V ASN* 1.3 70.4 + - - +
95V ARG* 3.4 16.3 - - - +
96V VAL 3.8 12.1 - - - -
97V ALA* 4.6 4.9 - - + -
98V PRO* 3.7 35.2 - - + +
99V GLU* 4.2 10.5 + - - -
127V PHE* 4.9 9.9 - + - -
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Residues in contact with ASN 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567J LYS* 6.0 2.6 - - - +
87V HIS* 4.2 7.6 + - - +
88V HIS* 2.8 50.0 + - + +
91V TYR* 1.3 93.7 + - - +
93V GLU* 1.3 69.2 + - - +
95V ARG* 3.3 17.5 - - - +
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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
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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