Contacts of the helix formed by residues 74 - 85 (chain A) in PDB entry 1OFU
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ALA* 4.0 1.0 - - - +
72A GLY* 2.8 12.4 - - - +
73A ALA* 1.3 77.4 - - - +
75A PRO* 1.3 68.5 - - - +
76A GLU* 2.9 25.6 + - - +
77A VAL* 3.1 36.6 + - + +
78A GLY 3.4 5.4 + - - -
108A GLY* 3.3 8.2 - - - -
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Residues in contact with PRO 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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73A ALA 3.1 12.1 - - - +
74A ASN* 1.3 84.6 - - - +
76A GLU* 1.3 59.4 + - + +
78A GLY 3.4 0.8 + - - -
79A ARG* 3.0 24.8 + - - +
107A GLY 3.9 3.8 - - - +
108A GLY* 3.3 13.0 - - - +
111A THR* 2.9 26.7 - - - +
112A GLY* 3.3 10.6 - - - +
146A ILE* 3.9 25.1 - - + -
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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
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74A ASN* 2.9 15.6 + - - +
75A PRO* 1.3 77.2 - - + +
77A VAL* 1.3 62.3 + - + +
79A ARG* 3.1 30.1 + - - +
80A GLN* 2.9 58.6 + - + +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.6 9.7 - - + +
66A THR* 3.6 28.3 - - + -
70A GLY 4.5 1.1 - - - +
71A ALA* 3.8 20.6 - - + -
72A GLY 5.0 1.1 - - - +
74A ASN* 3.1 34.5 + - + +
76A GLU* 1.3 79.6 - - + +
78A GLY* 1.3 58.4 + - - +
80A GLN* 3.3 5.8 + - - +
81A ALA* 2.9 29.3 + - - +
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Residues in contact with GLY 78 (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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45A THR* 4.9 3.1 - - - +
71A ALA* 4.4 2.0 - - - +
74A ASN 3.4 6.9 + - - -
75A PRO 3.4 0.2 + - - -
76A GLU 3.2 0.8 - - - -
77A VAL* 1.3 80.4 - - - +
79A ARG* 1.3 61.1 + - - +
81A ALA* 3.4 5.3 + - - +
82A ALA* 3.1 23.6 + - - +
108A GLY 3.5 18.8 - - - -
109A THR* 4.0 13.9 - - - -
113A ALA* 3.6 12.6 - - - +
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Residues in contact with ARG 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 PRO 3.0 17.4 + - - +
76A GLU* 3.1 26.3 + - - +
78A GLY* 1.3 76.2 - - - +
80A GLN* 1.3 79.2 + - - +
82A ALA 3.2 0.7 + - - -
83A LEU* 2.9 42.3 + - - +
112A GLY* 3.5 18.3 - - - +
116A ILE* 2.9 41.0 - - + +
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Residues in contact with GLN 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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65A VAL* 4.0 22.8 - - + +
76A GLU* 2.9 45.5 + - + +
77A VAL* 3.8 4.5 - - - +
79A ARG* 1.3 92.7 + - - +
81A ALA* 1.3 66.0 + - - +
83A LEU* 3.3 17.7 + - - +
84A GLU* 3.1 22.3 + - - +
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Residues in contact with ALA 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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45A THR* 3.6 29.6 - - + -
61A LEU* 3.9 2.6 - - + -
62A GLY* 3.4 32.3 + - - +
65A VAL* 4.3 6.6 - - - +
66A THR* 4.1 7.6 - - + -
77A VAL 2.9 16.6 + - - +
78A GLY 3.8 2.9 - - - +
80A GLN* 1.3 76.6 - - - +
82A ALA* 1.3 62.4 + - - +
84A GLU* 3.3 11.8 + - - +
85A ASP* 3.3 10.2 + - - +
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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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61A LEU* 4.5 6.9 - - + +
78A GLY 3.1 15.2 + - - +
80A GLN 3.2 0.2 - - - -
81A ALA* 1.3 74.6 - - - +
83A LEU* 1.3 65.3 + - - +
85A ASP 3.0 12.6 + - - -
86A ARG* 3.2 12.1 + - - +
89A ILE* 3.7 16.0 - - + +
113A ALA* 3.6 21.1 - - + +
116A ILE* 3.5 32.3 - - + -
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Residues in contact with LEU 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 ARG* 2.9 48.8 + - - +
80A GLN* 3.3 26.9 + - - +
82A ALA* 1.3 77.6 - - - +
84A GLU* 1.3 61.1 - - - +
85A ASP 3.4 0.2 + - - -
86A ARG* 3.7 38.1 + - - +
116A ILE* 3.3 18.6 - - + +
119A GLU* 5.2 3.8 - - - +
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Residues in contact with GLU 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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62A GLY* 3.4 9.9 - - - -
63A PRO* 3.2 14.0 - - - +
64A GLY* 3.1 22.2 + - - -
65A VAL* 2.8 42.4 + - + +
80A GLN 3.1 12.5 + - - +
81A ALA 3.4 8.7 - - - +
82A ALA 3.1 0.2 - - - -
83A LEU* 1.3 79.4 - - - +
85A ASP* 1.3 62.4 + - - +
86A ARG 3.8 0.9 + - - -
87A GLU* 5.2 1.2 + - - +
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Residues in contact with ASP 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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59A LEU* 5.1 1.1 - - + -
60A GLN 4.4 0.4 - - - -
61A LEU* 3.5 16.7 - - + -
62A GLY* 2.7 30.9 + - - -
63A PRO* 3.4 4.8 - - - +
81A ALA 3.3 5.9 + - - +
82A ALA 3.0 8.3 + - - +
84A GLU* 1.3 85.2 - - - +
86A ARG* 1.3 63.2 + - - +
87A GLU* 3.1 3.6 - - - +
88A ARG* 2.7 55.3 + - + +
89A ILE* 2.8 22.6 + - + +
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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