Contacts of the helix formed by residues 79 - 95 (chain A) in PDB entry 2H1C
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.4 22.0 + - + +
78A PHE* 1.3 75.8 - - - +
80A GLU* 1.3 65.8 + - - +
81A PRO* 3.2 21.2 - - + +
82A VAL* 2.9 24.0 + - - +
83A ALA* 2.9 22.4 + - - +
113A GLN* 5.3 2.1 - - - +
114A HIS* 5.9 1.2 + - - -
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Residues in contact with GLU 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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79A ASP* 1.3 76.9 - - - +
81A PRO* 1.3 82.4 - - + +
83A ALA* 3.2 17.1 + - + +
84A ALA* 3.2 18.0 + - - +
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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 ASP* 3.2 20.6 - - + +
80A GLU* 1.3 108.3 - - + +
82A VAL* 1.3 60.6 + - - +
84A ALA* 3.3 15.2 + - + +
85A ILE* 3.4 16.5 + - - +
113A GLN* 4.4 22.2 - - + +
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Residues in contact with VAL 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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77A PRO 3.9 15.0 - - - +
78A PHE* 3.5 26.2 - - + -
79A ASP* 2.9 27.7 + - - +
81A PRO* 1.3 73.2 - - - +
83A ALA* 1.3 61.5 + - - +
85A ILE* 3.2 3.9 + - - +
86A TYR* 2.8 26.3 + - - +
109A ALA* 3.6 17.2 - - + +
110A THR* 3.6 20.9 - - - +
113A GLN* 4.0 26.7 - - + +
114A HIS* 5.1 3.6 - - - +
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Residues in contact with ALA 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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78A PHE* 3.7 24.2 - - + -
79A ASP 2.9 13.0 + - - +
80A GLU* 3.2 14.5 + - + +
82A VAL* 1.3 77.8 - - - +
84A ALA* 1.3 61.5 + - - +
86A TYR* 3.3 5.0 + - + +
87A ALA* 3.1 23.0 + - - +
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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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80A GLU* 3.2 16.9 + - - +
81A PRO* 3.5 10.8 - - + +
82A VAL 3.2 0.4 - - - -
83A ALA* 1.3 80.9 - - - +
85A ILE* 1.3 63.5 + - + +
87A ALA* 3.4 5.6 + - - +
88A GLN* 3.1 32.8 + - - +
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Residues in contact with ILE 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 3.4 8.3 + - - +
82A VAL 3.2 7.2 + - - +
84A ALA* 1.3 75.2 - - + +
86A TYR* 1.3 66.3 + - - +
88A GLN* 3.2 17.0 + - + +
89A ILE* 2.9 44.9 + - + +
109A ALA* 3.8 13.2 - - + +
112A LYS* 3.7 20.4 - - + -
113A GLN* 3.4 48.5 - - + +
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Residues in contact with TYR 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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78A PHE* 3.9 12.8 - + + -
82A VAL 2.8 13.8 + - - +
83A ALA* 3.4 11.4 - - + +
84A ALA 3.2 0.2 - - - -
85A ILE* 1.3 76.6 - - - +
87A ALA* 1.3 70.3 + - + +
89A ILE* 3.8 2.9 - - - +
90A ARG* 2.8 75.3 + - + +
102A ALA* 3.7 18.1 - - - +
105A GLY* 3.7 15.3 - - - -
106A TYR* 3.4 39.1 + + - -
109A ALA* 3.6 12.3 - - + +
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Residues in contact with ALA 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 ALA 3.1 10.5 + - - +
84A ALA* 3.9 9.0 - - - +
86A TYR* 1.3 87.7 - - + +
88A GLN* 1.3 61.6 + - + +
90A ARG* 4.4 2.0 - - - +
91A SER* 2.9 32.5 + - - -
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Residues in contact with GLN 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* 3.1 21.2 + - - +
85A ILE* 3.5 20.7 + - - +
87A ALA* 1.3 77.6 - - + +
89A ILE* 1.3 60.3 + - + +
91A SER* 3.1 6.5 + - - -
92A TYR* 3.0 32.0 + - - +
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Residues in contact with ILE 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 ILE* 2.9 39.1 + - + +
86A TYR* 3.8 3.4 - - - +
88A GLN* 1.3 79.3 - - + +
90A ARG* 1.3 67.1 + - + +
92A TYR* 3.5 4.8 + - - +
93A ALA* 3.1 22.9 + - - +
100A ILE* 3.7 10.5 - - + -
105A GLY* 5.4 3.1 - - - +
108A ALA* 4.2 2.2 - - + -
109A ALA* 4.1 19.5 - - + +
112A LYS* 4.0 18.8 - - + +
128A ALA 4.9 1.4 - - - +
129A ALA* 3.3 51.1 - - + +
131A VAL* 4.2 3.6 - - + -
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Residues in contact with ARG 90 (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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86A TYR* 2.8 67.5 + - + +
87A ALA* 4.4 1.8 - - - +
89A ILE* 1.3 75.2 - - + +
91A SER* 1.3 66.8 + - - +
93A ALA* 3.5 5.8 + - - +
94A LYS* 3.0 47.1 + - - +
100A ILE* 3.0 41.1 + - + +
101A ALA* 4.4 3.2 - - - +
102A ALA* 3.6 24.6 - - - +
105A GLY* 4.6 2.9 - - - -
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Residues in contact with SER 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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87A ALA 2.9 24.1 + - - -
88A GLN* 3.1 8.0 + - - -
90A ARG* 1.3 74.0 - - - +
92A TYR* 1.3 64.3 + - - +
94A LYS* 3.1 6.5 + - - +
95A THR* 2.8 39.5 + - - +
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Residues in contact with TYR 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 GLN 3.0 15.3 + - - +
89A ILE* 3.8 5.4 - - - +
91A SER* 1.3 83.0 + - - +
93A ALA* 1.3 65.4 + - - +
95A THR* 3.1 7.5 + - - -
96A HIS* 2.8 68.0 + + + +
98A LYS* 4.5 12.8 - - - -
128A ALA 5.0 3.4 - - - -
130A ASP* 4.3 19.5 - - - -
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Residues in contact with ALA 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 ILE 3.1 10.4 + - - +
90A ARG 3.8 4.3 - - - +
92A TYR* 1.3 77.1 - - - +
94A LYS* 1.3 62.1 + - + +
96A HIS 3.1 6.9 + - - -
98A LYS* 2.7 56.6 + - + +
100A ILE* 3.4 38.1 - - + +
128A ALA 4.4 3.6 - - - +
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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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90A ARG* 3.0 38.8 + - - +
91A SER* 3.5 7.0 - - - +
93A ALA* 1.3 77.4 - - + +
95A THR* 1.3 59.4 + - + +
96A HIS 3.1 4.5 + - - -
97A GLY* 3.4 10.4 + - - -
98A LYS 4.1 11.7 - - - +
99A GLU* 6.3 1.1 - - - +
100A ILE 5.7 4.5 - - - +
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Residues in contact with THR 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 SER* 2.8 25.8 + - - +
92A TYR* 3.1 8.1 + - - -
94A LYS* 1.3 74.7 - - + +
96A HIS* 1.3 82.1 + - - +
97A GLY 3.6 0.7 - - - -
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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