Contacts of the helix formed by residues 79 - 90 (chain D) in PDB entry 4H7Y
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 ALA 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D LYS* 3.9 6.3 - - + -
72D ALA* 3.6 42.0 - - + +
75D GLU 3.9 5.8 - - - +
76D PRO 3.4 8.6 + - - +
77D ASP 3.7 0.2 - - - -
78D ASP* 1.3 77.6 - - - +
80D ARG* 1.3 65.9 + - - +
81D ASP 3.3 2.7 - - - -
82D TYR* 3.1 23.7 + - - +
83D PHE* 3.3 16.2 - - + -
103D PHE* 4.1 4.5 - - + -
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO 5.8 0.6 + - - -
77D ASP* 5.5 7.2 + - - +
78D ASP 3.5 2.8 - - - -
79D ALA* 1.3 78.1 - - - +
81D ASP* 1.3 66.1 + - - +
82D TYR 3.2 0.3 + - - -
83D PHE* 3.2 5.6 + - - +
84D GLN* 3.1 44.3 + - + +
100D PHE* 4.3 7.0 - - + -
103D PHE* 3.9 26.5 - - + -
104D GLU* 2.8 41.4 + - - +
107D GLN* 4.6 6.5 - - - +
109D ASN* 3.4 15.2 - - - +
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Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.1 13.3 - - + +
49A LEU 4.8 0.9 - - - +
51A PRO* 3.6 24.1 - - + +
60A PHE* 4.2 1.7 - - - -
64A GLN* 3.2 13.8 + - - -
85A MET* 3.6 16.4 - - - +
89A ASN* 3.0 34.3 + - - +
78D ASP 4.7 0.8 + - - +
79D ALA 3.3 0.8 - - - -
80D ARG* 1.3 79.9 - - - +
82D TYR* 1.3 70.2 + - + +
84D GLN* 3.3 10.4 + - - +
85D MET* 3.0 33.0 + - - +
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 3.8 12.8 - - - -
47A GLU* 3.4 43.4 + - - +
49A LEU 4.4 1.7 - - - -
50A PRO* 3.5 34.5 - - - +
51A PRO* 4.0 4.4 - - + +
52A ASP* 5.4 0.2 + - - -
64D GLN 4.6 1.0 - - - +
67D PHE* 3.7 11.9 - + + -
68D ALA* 3.7 23.8 - - + +
71D LYS* 3.5 46.3 + - + -
78D ASP* 3.4 21.5 + - + +
79D ALA* 3.1 17.6 + - - +
81D ASP* 1.3 83.4 - - + +
83D PHE* 1.3 58.9 + - - +
85D MET* 3.5 2.4 + - - +
86D ALA* 3.1 25.6 + - - +
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 4.9 1.3 - - + -
68D ALA* 3.6 41.1 - - + -
69D GLU* 3.9 9.2 - - + -
72D ALA* 4.0 6.5 - - + -
79D ALA 3.3 23.3 - - - -
80D ARG 3.2 4.8 + - - +
82D TYR* 1.3 76.2 - - - +
84D GLN* 1.3 59.7 + - - +
86D ALA* 3.3 6.2 + - + +
87D ARG* 2.9 31.0 + - - +
96D VAL* 5.3 1.0 - - - +
99D SER* 3.3 31.9 - - - -
100D PHE* 3.5 46.5 - + + +
103D PHE* 3.5 40.4 - + + -
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Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASP* 4.0 26.7 + - - +
82A TYR* 4.0 14.0 - - + -
85A MET* 4.0 22.0 - - + +
80D ARG* 3.1 33.5 + - + +
81D ASP* 3.3 11.4 - - - +
83D PHE* 1.3 75.7 - - - +
85D MET* 1.3 71.2 + - + +
87D ARG* 3.5 17.9 + - - +
88D ALA* 2.9 28.2 + - - +
100D PHE* 3.6 27.0 - - + -
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Residues in contact with MET 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A SER* 3.7 33.0 - - - +
46A ILE* 3.8 22.0 - - + -
47A GLU* 3.5 34.1 - - + +
67A PHE* 3.6 30.3 - - + -
82A TYR* 4.5 1.6 - - + -
85A MET* 3.9 23.1 - - + -
64D GLN* 3.8 2.0 - - - -
81D ASP 3.0 17.8 + - - +
82D TYR 3.9 0.4 - - - +
83D PHE 3.2 0.2 - - - -
84D GLN* 1.3 86.9 - - + +
86D ALA* 1.3 60.8 + - - +
88D ALA* 3.2 1.9 + - - +
89D ASN* 2.9 39.6 + - - +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLN* 3.5 40.5 + - + +
65D VAL* 4.2 7.0 - - + +
68D ALA* 5.3 0.7 - - + -
82D TYR 3.1 17.6 + - - +
83D PHE* 3.3 8.3 + - + +
85D MET* 1.3 76.0 - - - +
87D ARG* 1.3 58.6 + - - +
90D CYS* 2.9 35.4 + - - +
96D VAL* 3.5 14.6 - - + +
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Residues in contact with ARG 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP 5.5 2.0 + - - -
81A ASP* 2.5 40.0 + - - +
82A TYR* 4.5 11.4 + - - +
83D PHE 2.9 16.9 + - - +
84D GLN* 3.8 14.6 + - - +
86D ALA* 1.3 77.0 - - - +
88D ALA* 1.3 61.8 + - - +
89D ASN 3.4 0.2 + - - -
91D LYS* 3.4 24.7 + - + +
96D VAL* 3.7 12.7 - - + +
97D HIS* 3.6 39.2 + - + +
100D PHE* 3.9 20.7 - - + -
116D LEU* 3.4 27.1 - - - +
119D LYS* 4.5 20.8 - - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.0 19.7 - - + -
71A LYS* 3.8 19.9 + - - +
82A TYR* 3.2 31.3 + - + +
84D GLN 2.9 15.8 + - - +
85D MET* 3.2 6.7 + - - +
87D ARG* 1.3 79.1 - - - +
89D ASN* 1.3 64.2 + - - +
91D LYS* 4.7 7.6 + - - +
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 5.3 3.8 - - - +
40A GLY* 4.9 2.6 - - - -
43A SER* 3.1 33.3 + - - -
47A GLU* 5.6 0.6 - - - +
67A PHE* 5.6 0.9 - - - -
71A LYS* 5.8 0.5 + - - -
51D PRO* 3.7 22.6 - - + +
55D GLY* 3.4 24.4 - - - -
60D PHE* 4.1 8.9 - - + -
64D GLN* 3.1 32.3 + - - +
85D MET* 2.9 17.7 + - - +
88D ALA* 1.3 83.6 - - - +
90D CYS* 1.3 64.6 - - - +
91D LYS* 3.8 1.3 - - - -
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Residues in contact with CYS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D TYR 5.3 0.2 - - - -
55D GLY 4.1 10.3 - - - +
57D ASN 5.7 0.2 - - - -
60D PHE* 3.7 22.7 - - - -
61D ALA* 3.7 39.0 - - + -
64D GLN* 3.9 10.3 - - - -
86D ALA* 2.9 19.6 + - - +
87D ARG 4.7 0.2 - - - -
89D ASN* 1.3 87.3 - - - +
91D LYS* 1.3 64.8 + - - +
92D LYS 3.1 4.3 + - - -
93D PHE* 3.3 13.0 + - + -
96D VAL* 3.7 17.8 - - + +
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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