Contacts of the helix formed by residues 80 - 95 (chain A) in PDB entry 3OM0
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 SER 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ASP* 3.2 29.0 + - - -
54A ASP* 5.6 1.7 + - - -
77A PRO* 4.0 17.0 + - - +
78A SER 3.7 1.4 - - - -
79A SER* 1.3 78.3 - - - +
81A PRO* 1.3 70.4 - - - +
82A ALA* 3.3 2.1 + - - +
83A SER* 3.2 19.2 + - - -
84A ALA* 2.9 22.7 + - - +
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Residues in contact with PRO 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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79A SER 3.9 5.2 - - - +
80A SER* 1.3 87.5 - - - +
82A ALA* 1.3 63.1 + - - +
84A ALA* 3.3 0.4 + - + -
85A SER* 3.0 9.7 + - - -
103A PRO* 5.5 10.8 - - + +
104A GLU 6.0 0.2 - - - +
105A GLU* 2.5 47.5 - - + +
150A GLU* 6.1 0.7 - - - +
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Residues in contact with ALA 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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54A ASP* 5.9 2.0 - - - +
56A GLN* 3.7 21.4 - - + +
80A SER* 3.3 0.6 - - - +
81A PRO* 1.3 79.2 - - - +
83A SER* 1.3 62.4 + - - +
85A SER* 3.2 8.8 + - - -
86A THR* 3.1 24.3 + - - -
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Residues in contact with SER 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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12A ASP* 4.9 0.5 + - - -
51A LEU* 3.7 17.8 - - - +
53A ARG 5.7 0.3 + - - -
55A SER 4.8 1.6 + - - -
56A GLN* 3.1 19.8 + - - +
59A THR* 2.9 24.5 + - - +
77A PRO* 4.0 4.3 - - - -
80A SER* 3.2 25.3 + - - -
82A ALA* 1.3 75.5 - - - +
84A ALA* 1.3 66.1 + - - +
86A THR* 3.1 2.9 + - - -
87A VAL* 2.9 28.2 + - - +
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Residues in contact with ALA 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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77A PRO* 3.9 29.5 - - + +
80A SER 2.9 13.3 + - - +
81A PRO* 4.4 0.7 - - + -
82A ALA 3.3 0.2 - - - -
83A SER* 1.3 77.9 - - - +
85A SER* 1.3 56.3 + - - +
87A VAL* 3.4 2.6 + - - -
88A SER* 2.9 31.5 + - - -
98A HIS* 3.3 11.9 - - + -
100A LYS* 4.5 3.1 - - + +
105A GLU* 3.3 23.6 - - - +
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Residues in contact with SER 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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81A PRO 3.0 6.0 + - - -
82A ALA* 3.5 10.3 - - - -
83A SER 3.2 0.2 - - - -
84A ALA* 1.3 78.1 - - - +
86A THR* 1.3 55.8 + - - +
88A SER* 3.3 6.9 + - - -
89A HIS* 3.0 28.1 + - - +
105A GLU* 2.9 35.8 + - - +
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Residues in contact with THR 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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56A GLN* 2.9 38.6 + - + +
59A THR* 4.0 11.7 - - + -
60A THR* 3.6 24.9 - - - +
82A ALA 3.1 7.4 + - - -
83A SER 3.1 3.8 + - - -
85A SER* 1.3 72.3 - - - +
87A VAL* 1.3 66.8 + - - +
89A HIS* 3.2 6.2 + - - +
90A ILE* 3.1 36.4 + - + +
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Residues in contact with VAL 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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10A ILE* 3.7 21.8 - - + -
59A THR* 3.8 15.5 - - + -
63A MET* 3.9 16.3 - - + +
74A VAL* 3.9 21.3 - - + -
76A GLY 3.9 1.8 - - - +
77A PRO* 4.2 8.5 - - + -
83A SER 2.9 17.5 + - - +
84A ALA 3.6 6.7 - - - +
86A THR* 1.3 75.3 - - - +
88A SER* 1.3 56.9 + - - +
89A HIS 3.3 0.2 + - - -
90A ILE* 3.3 1.0 + - - +
91A CYS* 2.8 31.6 + - - +
98A HIS* 3.4 29.6 - - + +
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Residues in contact with SER 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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84A ALA 2.9 8.5 + - - -
85A SER* 3.3 10.3 + - - -
87A VAL* 1.3 75.4 - - - +
89A HIS* 1.3 58.4 + - - +
91A CYS* 3.7 2.2 - - - +
92A GLY* 2.8 27.2 + - - -
98A HIS* 2.7 28.8 + - - +
100A LYS* 2.7 28.5 + - - -
116A SER* 5.8 2.0 - - - -
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Residues in contact with HIS 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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85A SER 3.0 14.0 + - - +
86A THR* 3.7 9.2 - - - +
87A VAL 3.2 0.4 - - - -
88A SER* 1.3 77.5 - - - +
90A ILE* 1.3 66.8 + - + +
92A GLY* 3.2 2.5 + - - -
93A GLU* 3.0 49.4 + - + +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A THR* 4.2 21.1 - - + +
63A MET* 3.7 44.2 - - + -
67A LEU* 4.3 19.7 - - + -
86A THR* 3.1 30.2 + - + +
87A VAL 4.1 2.0 - - - +
89A HIS* 1.3 76.3 - - - +
91A CYS* 1.3 66.9 + - - +
93A GLU* 3.1 25.5 + - + +
94A LYS* 3.1 26.2 + - + +
315A CYS* 5.2 6.1 - - - -
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Residues in contact with CYS 91 (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 MET* 3.8 11.0 - - - -
67A LEU* 6.2 0.2 - - - -
74A VAL* 3.8 35.7 - - - -
87A VAL* 2.8 23.2 + - - +
88A SER 3.7 3.6 - - - +
90A ILE* 1.3 76.5 - - - +
92A GLY* 1.3 57.4 + - - +
94A LYS* 3.3 2.0 + - - +
95A GLU* 2.8 25.5 + - - -
96A ILE* 3.0 37.3 + - - +
97A PRO 4.3 0.2 - - - -
98A HIS* 3.9 20.4 - - + +
114A PHE* 4.8 0.7 - - + -
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Residues in contact with GLY 92 (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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88A SER 2.8 18.2 + - - -
89A HIS 3.6 2.0 - - - -
90A ILE 3.2 0.2 - - - -
91A CYS* 1.3 78.1 - - - +
93A GLU* 1.3 62.1 + - - +
95A GLU* 3.3 17.8 + - - +
114A PHE* 3.8 32.0 - - - +
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Residues in contact with GLU 93 (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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89A HIS* 3.0 40.8 + - + +
90A ILE* 3.1 30.2 + - - +
92A GLY* 1.3 77.1 - - - +
94A LYS* 1.3 73.3 + - - +
95A GLU* 4.4 1.2 - - - +
320A ILE* 3.4 8.0 - - - +
404A ACT 3.2 43.3 - - + +
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Residues in contact with LYS 94 (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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67A LEU* 3.8 30.1 - - + -
90A ILE* 3.1 19.3 + - + +
91A CYS* 4.1 2.7 - - - +
93A GLU* 1.3 88.2 + - - +
95A GLU* 1.3 64.2 + - - +
96A ILE* 4.0 18.0 - - + +
313A LEU* 4.2 9.6 - - + +
314A ALA 3.1 16.6 + - - +
315A CYS* 4.2 10.9 + - - +
317A SER 2.7 28.9 + - - -
319A ASN 3.9 6.1 - - - +
320A ILE* 4.1 3.8 - - - +
321A TRP* 2.9 30.3 + - - +
404A ACT 2.9 34.7 + - - +
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Residues in contact with GLU 95 (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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91A CYS 2.8 8.5 + - - -
92A GLY 3.3 12.9 + - - +
93A GLU 4.4 0.6 - - - +
94A LYS* 1.3 81.6 - - - +
96A ILE* 1.3 57.9 + - - +
114A PHE* 3.7 28.9 - - + -
320A ILE* 3.4 35.6 - - + +
321A TRP* 3.6 17.5 - - - +
324A GLY* 3.1 23.5 - - - -
325A THR* 3.5 19.5 + - - -
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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