Contacts of the helix formed by residues 74 - 89 (chain A) in PDB entry 1O0C
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.3 5.6 + - - +
73A GLU* 1.3 79.1 - - - +
75A ILE* 1.3 72.0 + - - +
76A GLU* 3.2 31.8 + - + +
77A TYR* 3.1 38.9 + - + +
78A VAL* 3.7 6.9 + - - +
199A HIS* 4.6 9.0 - - - -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 1.3 77.9 + - - +
76A GLU* 1.3 67.8 + - + +
77A TYR 3.1 0.7 + - - -
78A VAL* 3.3 25.8 + - + +
79A GLU* 3.3 31.0 + - + +
199A HIS* 4.2 22.7 - - + +
200A GLN* 3.5 27.8 - - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 2.6 35.9 + - + +
74A ASP* 3.1 17.1 + - + +
75A ILE* 1.3 84.5 - - + +
77A TYR* 1.3 66.8 + - + +
79A GLU* 3.8 12.1 + - - +
80A SER* 3.3 21.0 + - - -
285A TRP* 5.2 2.4 - - - -
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.1 32.5 - - + +
36A ASN* 3.7 13.7 + - - -
37A GLY* 3.5 35.9 - - - +
38A TYR* 3.7 26.0 - + - -
72A LYS 4.6 4.5 - - - -
74A ASP* 3.1 33.0 + - + +
76A GLU* 1.3 85.9 - - + +
78A VAL* 1.3 66.3 + - - +
80A SER* 3.0 6.3 + - - -
81A ILE* 3.0 28.0 + - - +
274A ASN* 4.4 7.6 + - - -
285A TRP* 4.3 17.6 + - - -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.9 15.4 - - + +
65A PHE* 3.5 31.8 - - + -
74A ASP 3.8 12.8 - - - +
75A ILE* 3.3 30.2 + - + +
77A TYR* 1.3 74.5 - - - +
79A GLU* 1.3 69.7 + - + +
81A ILE 3.2 0.2 + - - -
82A LYS* 3.1 42.1 + - - +
98A TYR* 4.1 11.9 - - + +
199A HIS* 4.3 16.8 - - + +
200A GLN* 4.5 2.5 - - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.3 34.5 + - + +
76A GLU* 3.9 9.8 - - - +
77A TYR 3.2 0.4 - - - -
78A VAL* 1.3 89.2 - - + +
80A SER* 1.3 60.5 + - - +
82A LYS* 3.5 11.9 + - - +
83A ASN* 3.1 21.9 + - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.8 41.1 - - - -
39A LEU 6.3 0.2 - - - -
76A GLU 3.3 12.9 + - - -
77A TYR* 3.0 18.2 + - - -
79A GLU* 1.3 75.8 - - - +
81A ILE* 1.3 63.5 + - - +
83A ASN* 3.2 12.5 + - - +
84A ASP* 2.9 37.7 + - - +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.9 0.2 - - + -
33A PRO* 3.9 17.3 - - + -
34A GLU 4.3 6.1 - - - +
35A PRO* 4.2 17.0 - - + -
37A GLY 3.9 18.4 - - - +
39A LEU* 3.4 44.9 - - + +
63A LEU* 4.7 3.1 - - + -
65A PHE* 3.6 31.6 - - + -
77A TYR 3.0 21.5 + - - +
80A SER* 1.3 79.2 - - - +
82A LYS* 1.3 62.2 + - - +
84A ASP* 3.2 2.5 + - - -
85A VAL* 3.0 34.9 + - + +
270A LYS* 6.0 0.4 - - - -
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.7 25.6 - - + -
65A PHE* 3.8 7.4 - - + -
78A VAL* 3.1 39.2 + - - +
79A GLU* 3.8 10.1 - - - +
81A ILE* 1.3 75.2 - - - +
83A ASN* 1.3 61.2 + - - +
85A VAL* 3.9 1.9 - - - +
86A GLU* 3.2 35.7 + - - +
92A TRP* 4.0 14.3 - - + -
96A VAL* 3.7 21.2 - - + +
98A TYR* 3.7 17.4 + - - -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU 3.1 15.0 + - - +
80A SER* 3.3 15.7 + - - +
82A LYS* 1.3 78.2 - - - +
84A ASP* 1.3 58.2 + - - +
86A GLU* 3.4 7.9 + - - +
87A TRP* 2.9 27.8 + - - +
297A ARG* 3.4 26.6 + - - +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.9 2.6 - - - -
39A LEU* 4.1 24.3 + - + +
80A SER* 2.9 29.1 + - - +
81A ILE 4.0 2.5 - - - +
83A ASN* 1.3 70.9 + - - +
85A VAL* 1.3 67.2 + - - +
87A TRP* 3.3 5.2 + - - +
88A LEU* 2.9 29.1 + - - +
293A ILE* 3.6 29.0 - - + +
294A SER* 3.9 11.4 + - - -
297A ARG* 2.7 39.4 + - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.3 13.9 - - + -
39A LEU* 4.2 7.2 - - + +
47A ILE* 3.9 27.4 - - + -
51A PHE* 4.0 21.8 - - + -
63A LEU* 4.4 10.8 - - + -
81A ILE* 3.0 23.4 + - + +
82A LYS* 3.9 4.7 - - - +
84A ASP* 1.3 76.4 - - - +
86A GLU* 1.3 63.7 + - - +
88A LEU* 3.3 10.8 + - - +
89A GLY 3.5 6.8 + - - -
90A PHE* 3.5 17.0 + - + +
92A TRP* 3.9 26.0 - - + -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 3.2 24.6 + - - +
83A ASN* 3.6 6.2 - - - +
85A VAL* 1.3 74.7 - - - +
87A TRP* 1.3 60.0 + - - +
89A GLY* 2.8 23.0 + - - -
90A PHE 4.0 10.2 + - - +
91A HIS* 5.5 10.5 + - + +
92A TRP* 3.6 27.7 - - + -
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 2.9 16.9 + - - +
84A ASP 3.6 2.2 - - - +
86A GLU* 1.3 76.6 - - - +
88A LEU* 1.3 75.0 + - + +
89A GLY* 3.2 1.7 + - - -
293A ILE* 3.5 34.8 - - + -
297A ARG* 3.3 54.7 - - + +
301A TYR 3.5 22.7 - - - -
302A THR* 4.5 0.4 - - - -
303A ALA* 3.3 36.1 - - + +
306A ILE* 3.7 20.9 - - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.8 21.3 - - + +
47A ILE* 3.8 36.3 - - + -
48A CYS* 5.5 1.8 - - - -
84A ASP 2.9 13.6 + - - +
85A VAL 3.5 9.9 - - - +
86A GLU 3.2 0.2 - - - -
87A TRP* 1.3 100.1 - - + +
89A GLY* 1.3 58.7 + - - +
90A PHE* 3.9 11.8 - - + -
293A ILE* 4.5 10.5 - - + -
303A ALA* 3.9 11.4 - - + +
306A ILE* 4.0 26.7 - - + -
307A ARG* 2.9 35.0 + - + +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN* 5.6 0.5 - - - +
85A VAL 3.5 0.2 + - - -
86A GLU 2.8 13.9 + - - -
87A TRP 3.1 1.7 - - - -
88A LEU* 1.3 78.9 - - - +
90A PHE* 1.3 70.1 + - - +
91A HIS* 4.4 11.2 + - - -
307A ARG* 4.8 6.2 + - - -
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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