Contacts of the helix formed by residues 78 - 92 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68X LYS* 5.4 0.8 - - - +
70X PRO* 3.2 16.9 + - + +
76X ILE* 4.0 2.6 - - - +
77X THR* 1.3 80.9 - - + +
79X TRP* 1.3 63.3 + - - +
80X ASP* 3.3 17.2 + - - +
81X ASP* 3.0 45.8 + - + +
82X MET* 3.1 26.3 + - - +
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Residues in contact with TRP 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X ILE* 3.8 49.1 + - + -
77X THR 4.6 6.8 + - - -
78X ASN* 1.3 73.3 + - - +
80X ASP* 1.3 62.4 + - - +
82X MET* 3.8 4.3 - - + +
83X GLU* 3.3 25.6 + - - +
86X TRP* 4.6 5.6 - + - -
115X ASN* 3.6 53.1 + - + -
118X LYS* 3.8 31.3 - - + +
119X MET* 3.8 23.1 - - + -
122X ILE* 3.6 23.9 - - + +
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Residues in contact with ASP 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ARG* 3.3 14.1 + - - -
78X ASN* 3.3 16.5 + - - +
79X TRP* 1.3 75.6 - - - +
81X ASP* 1.3 85.9 + - - +
83X GLU* 3.6 7.7 + - - +
84X LYS* 3.3 37.4 + - - +
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Residues in contact with ASP 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X VAL* 3.4 20.1 - - + +
37X ARG* 2.9 26.9 + - - -
68X LYS* 3.1 32.5 - - - +
70X PRO* 3.4 19.3 - - + +
78X ASN* 3.0 27.1 + - + +
80X ASP* 1.3 88.9 + - - +
82X MET* 1.3 61.5 + - - +
84X LYS* 3.5 9.9 - - - +
85X ILE* 3.3 16.6 + - - +
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Residues in contact with MET 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ASN* 3.5 26.7 - - + +
17X VAL* 5.8 0.7 - - + -
33X SER* 5.3 1.6 - - - +
70X PRO* 3.9 10.5 - - - -
71X ILE* 3.7 36.8 - - + -
76X ILE* 3.8 19.5 - - + -
78X ASN 3.1 18.1 + - - +
79X TRP* 4.0 6.5 - - + +
80X ASP 3.3 0.4 - - - -
81X ASP* 1.3 70.3 - - - +
83X GLU* 1.3 58.3 + - - +
84X LYS 3.0 1.3 - - - -
85X ILE* 2.7 44.5 + - + +
86X TRP* 2.9 45.7 + - + +
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Residues in contact with GLU 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X TRP 3.3 15.6 + - - +
80X ASP* 3.8 7.5 - - - +
81X ASP 3.5 0.2 - - - -
82X MET* 1.3 75.8 - - - +
84X LYS* 1.3 57.0 + - - +
86X TRP* 3.9 12.9 - - + -
87X HIS* 2.9 31.2 + - + +
122X ILE* 4.1 20.3 - - + +
126X THR* 4.2 26.6 + - - +
127X PHE* 3.7 16.4 - - + -
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Residues in contact with LYS 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X VAL* 4.0 9.9 - - + -
37X ARG* 3.4 35.1 - - - +
51X ASP* 5.2 5.7 + - - +
52X SER* 3.5 26.2 - - - +
54X VAL* 4.4 10.5 - - + +
80X ASP* 3.3 26.3 + - - +
81X ASP* 3.5 26.0 - - - +
83X GLU* 1.3 77.2 - - - +
85X ILE* 1.4 61.4 + - - +
87X HIS* 3.2 8.8 + - + +
88X HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X VAL* 3.7 29.8 - - + -
31X PHE* 4.2 10.2 - - + -
33X SER* 3.9 27.4 - - - +
34X ILE 4.1 1.1 - - - +
35X VAL* 3.8 11.9 - - + -
54X VAL* 4.0 13.2 - - + -
70X PRO* 3.6 36.6 - - + -
81X ASP 3.3 8.0 + - - +
82X MET* 2.7 27.5 + - + +
84X LYS* 1.4 68.9 - - - +
86X TRP* 1.3 54.9 + - + +
88X HIS* 3.3 4.0 + - - +
89X THR* 2.7 31.9 + - - +
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Residues in contact with TRP 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X CYS* 4.0 16.7 - - - -
12X ASN* 2.9 38.0 + - - +
17X VAL* 6.1 0.2 - - + -
76X ILE* 4.2 10.8 - - + -
79X TRP* 4.6 1.8 - + - -
82X MET* 2.9 38.4 + - + +
83X GLU* 3.8 17.9 - - - +
85X ILE* 1.3 75.3 - - + +
87X HIS* 1.3 58.1 + - - +
89X THR* 2.8 23.9 + - - -
90X PHE* 3.0 26.9 + + + -
105X LEU* 4.4 4.5 - - + +
119X MET* 3.9 30.1 - - + -
122X ILE* 4.1 24.5 - - + -
123X MET* 3.3 28.0 - - + +
127X PHE* 3.6 20.9 - + + -
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Residues in contact with HIS 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X GLU* 2.9 19.5 + - + +
84X LYS* 3.4 8.3 - - + +
86X TRP* 1.3 77.3 - - - +
88X HIS* 1.3 60.2 + - - +
90X PHE* 4.5 0.7 - - - -
91X TYR* 2.9 65.4 + + + +
92X ASN* 4.6 6.1 + - - -
127X PHE* 3.9 17.4 - - + -
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Residues in contact with HIS 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X PHE* 3.6 20.5 - + - -
54X VAL* 3.9 38.5 + - + +
55X GLY* 5.2 0.6 - - - -
56X ASP 5.9 0.2 + - - -
84X LYS 3.1 9.4 + - - +
85X ILE 3.4 8.7 - - - +
87X HIS* 1.3 78.8 - - - +
89X THR* 1.3 61.8 + - - +
92X ASN* 2.8 54.4 + - + -
93X GLU* 2.9 41.2 + - + +
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Residues in contact with THR 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X CYS* 4.7 9.4 - - + -
17X VAL* 4.5 7.9 - - + +
19X ALA* 3.6 30.5 - - + -
31X PHE* 3.7 20.7 - - + -
85X ILE* 2.7 26.4 + - - +
86X TRP* 2.8 13.9 + - - -
88X HIS* 1.3 77.0 - - - +
90X PHE* 1.3 63.7 + - + -
93X GLU* 3.4 8.6 - - + +
94X LEU* 2.9 37.0 + - + +
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Residues in contact with PHE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X LEU* 4.0 28.7 - - + -
10X CYS* 5.8 5.4 - - + -
86X TRP* 3.0 29.3 + + + +
87X HIS* 4.1 2.2 - - - +
89X THR* 1.3 82.3 - - + +
91X TYR* 1.3 63.0 + + + +
94X LEU* 3.5 4.1 - - + -
95X ARG 2.8 26.9 + - - -
96X VAL* 3.1 24.1 + - + +
98X PRO* 3.9 27.4 - - + -
103X THR* 4.4 17.0 - - + -
105X LEU* 6.1 0.7 - - + -
123X MET* 4.1 23.6 - - + -
127X PHE* 3.6 44.2 - + - -
129X VAL* 4.8 1.3 - - + -
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Residues in contact with TYR 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X HIS* 2.9 61.4 + + - +
90X PHE* 1.3 82.2 - - + +
92X ASN* 1.3 72.6 + - - +
95X ARG* 3.4 16.9 - - - +
96X VAL 3.8 12.8 - - - -
97X ALA* 4.6 4.5 - - + -
98X PRO* 3.7 35.7 - - + +
99X GLU* 4.1 10.6 + - - -
127X PHE* 4.9 9.7 + + - -
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Residues in contact with ASN 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X HIS* 4.2 7.7 + - - +
88X HIS* 2.8 49.7 + - + +
91X TYR* 1.3 92.7 + - - +
93X GLU* 1.3 69.7 + - - +
94X LEU 3.6 0.2 - - - -
95X ARG* 3.3 17.4 + - - +
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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