Contacts of the helix formed by residues 80 - 97 (chain A) in PDB entry 4WFH
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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73A LEU* 3.8 1.3 - - - -
79A VAL* 1.3 79.5 - - - +
81A ASP* 1.3 66.0 + - - +
82A GLN* 3.7 10.7 + - - -
83A GLU* 2.7 46.9 + - - +
84A LEU* 3.0 18.0 + - - +
90D TRP* 6.5 0.2 - - - -
33E ILE* 3.8 17.6 - - - +
50E LEU* 4.1 19.3 - - - -
57E TYR* 3.8 5.9 - - - -
100E ASN* 4.6 3.4 - - - -
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Residues in contact with ASP 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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69A ARG* 2.3 33.2 + - - -
73A LEU* 3.7 25.3 - - + +
80A SER* 1.3 72.4 - - - +
82A GLN* 1.3 66.3 + - - +
84A LEU* 3.2 3.4 + - - +
85A GLY* 2.9 24.9 + - - -
104B GLN* 2.9 21.0 + - - -
90D TRP* 4.0 20.8 + - + +
92D ASN 4.6 0.3 - - - -
93D SER* 2.7 25.3 + - - +
100E ASN 4.8 4.5 + - - +
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Residues in contact with GLN 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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80A SER* 3.1 1.4 - - - -
81A ASP* 1.3 84.4 + - - +
83A GLU* 1.3 65.6 + - - +
85A GLY* 3.2 10.0 + - - -
86A LEU* 3.3 18.7 + - - +
90D TRP* 4.2 5.2 - - - -
93D SER* 3.1 33.2 + - - +
95D PRO* 5.1 0.2 - - - +
47E TRP* 3.9 18.2 - - - -
50E LEU* 3.7 25.2 - - - +
57E TYR* 3.2 23.6 + - + +
59E THR* 3.5 27.2 + - + +
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Residues in contact with GLU 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 VAL* 4.5 5.6 - - + -
80A SER* 2.7 40.8 + - - +
82A GLN* 1.3 74.7 - - - +
84A LEU* 1.3 64.5 + - - +
86A LEU* 3.2 20.7 + - + +
87A LEU* 3.2 11.8 + - - +
72B PHE* 4.3 5.9 - - + -
76B HIS* 3.5 20.2 + - + +
52E ASN* 2.8 26.0 + - - +
55E THR* 2.9 25.3 + - - +
57E TYR* 3.4 32.7 - - + +
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Residues in contact with LEU 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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69A ARG* 3.7 43.1 - - + +
72A PHE* 4.0 18.6 - - + -
73A LEU* 4.0 18.2 - - + -
79A VAL* 4.1 7.1 - - + +
80A SER 3.0 13.2 + - - +
81A ASP* 3.5 8.7 - - - +
83A GLU* 1.3 77.1 - - - +
85A GLY* 1.3 62.8 + - - +
87A LEU* 3.3 14.1 + - + +
88A ILE* 3.1 36.3 + - + +
72B PHE* 4.7 3.6 - - + -
87B LEU* 3.9 29.2 - - + -
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Residues in contact with GLY 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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69A ARG* 5.4 5.3 - - - +
81A ASP 2.9 14.3 + - - -
82A GLN* 3.2 6.7 + - - -
83A GLU 3.1 0.8 - - - -
84A LEU* 1.3 78.2 - - - +
86A LEU* 1.3 60.9 + - - +
88A ILE* 3.1 11.3 + - - +
89A LYS* 3.0 28.2 + - - +
101B PRO 5.1 4.5 - - - +
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Residues in contact with LEU 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 GLN 3.3 11.6 + - - +
83A GLU* 3.2 10.6 + - + +
85A GLY* 1.3 72.8 - - - +
87A LEU* 1.3 68.8 + - - +
89A LYS* 3.2 28.1 + - + +
90A GLU* 2.9 35.8 + - - +
57E TYR* 4.1 29.6 - - + +
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Residues in contact with LEU 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 GLU 3.2 10.0 + - - +
84A LEU* 3.5 17.9 - - + +
85A GLY 3.2 0.2 - - - -
86A LEU* 1.3 79.6 - - - +
88A ILE* 1.3 59.9 + - + +
90A GLU* 3.2 8.8 + - - +
91A VAL* 2.8 40.3 + - + +
68B VAL* 3.4 29.8 - - + +
69B ARG* 5.6 0.7 - - - -
72B PHE* 4.0 35.0 - - + -
84B LEU* 3.9 16.4 - - + -
87B LEU* 3.6 31.6 - - + -
88B ILE* 5.4 3.8 - - + -
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Residues in contact with ILE 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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65A LEU* 4.6 13.2 - - + -
69A ARG* 3.5 40.8 - - + -
84A LEU* 3.1 29.0 + - + +
85A GLY* 3.1 7.8 + - - +
87A LEU* 1.3 82.7 - - + +
89A LYS* 1.3 56.9 + - - +
91A VAL* 3.8 7.3 - - - +
92A ALA* 3.0 26.9 + - - +
87B LEU* 5.7 1.1 - - + -
91B VAL* 3.9 37.0 - - + -
95B LEU* 4.8 1.4 - - + +
101B PRO* 4.2 25.1 - - + +
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Residues in contact with LYS 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 GLY* 3.0 18.0 + - - +
86A LEU* 3.5 28.8 - - + +
88A ILE* 1.3 74.9 - - - +
90A GLU* 1.3 67.3 + - + +
92A ALA* 3.2 4.2 + - - +
93A ASP* 3.0 30.5 + - - +
101B PRO* 4.3 19.3 - - + +
102B GLU* 3.1 46.0 + - - +
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Residues in contact with GLU 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 LEU* 2.9 30.7 + - + +
87A LEU* 3.6 7.3 - - - +
89A LYS* 1.3 77.9 - - + +
91A VAL* 1.3 65.6 + - - +
93A ASP* 3.4 11.3 + - - +
94A ALA* 3.2 20.8 + - - +
68B VAL* 3.8 36.8 - - + +
71B LYS* 5.4 8.8 - - - +
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Residues in contact with VAL 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 LEU* 2.8 35.5 + - + +
88A ILE* 3.8 6.7 - - - +
90A GLU* 1.3 76.6 - - - +
92A ALA* 1.3 65.2 + - - +
94A ALA* 3.2 4.0 + - - +
95A LEU* 2.9 44.2 + - + +
65B LEU* 3.9 22.4 - - + -
68B VAL* 4.5 3.8 - - + -
88B ILE* 3.9 33.0 - - + -
91B VAL* 4.2 17.5 - - + -
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Residues in contact with ALA 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 ILE 3.0 19.4 + - - +
89A LYS* 3.2 5.6 + - - +
91A VAL* 1.3 76.7 - - - +
93A ASP* 1.3 59.8 + - - +
95A LEU* 3.2 4.3 + - - +
96A GLY* 2.8 27.4 + - - -
95B LEU* 3.9 18.6 - - + -
101B PRO* 3.5 26.9 - - + -
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Residues in contact with ASP 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 LYS* 3.0 22.8 + - - +
90A GLU* 3.7 11.7 - - - +
91A VAL 3.2 0.2 - - - -
92A ALA* 1.3 76.4 - - - +
94A ALA* 1.3 63.7 + - - +
96A GLY* 3.2 3.3 + - - -
97A GLY* 3.0 18.7 + - - -
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Residues in contact with ALA 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 GLU 3.2 9.2 + - - +
91A VAL 3.2 7.7 + - - +
93A ASP* 1.3 75.1 - - - +
95A LEU* 1.3 66.8 + - - +
97A GLY* 3.0 11.8 + - - +
98A GLY 3.2 0.9 + - - -
99A ALA* 3.0 18.2 + - + +
61B ALA* 3.6 26.6 - - - +
64B GLU* 4.7 9.2 - - + -
65B LEU* 3.9 26.9 - - + +
68B VAL* 6.1 0.7 - - + -
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Residues in contact with LEU 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 VAL* 2.9 41.4 + - + +
92A ALA 3.7 3.6 - - - +
94A ALA* 1.3 76.9 - - + +
96A GLY* 1.3 58.2 + - - +
98A GLY* 2.8 21.7 + - - -
99A ALA* 3.4 26.9 + - + +
101A PRO* 3.8 26.5 - - + -
65B LEU* 4.7 6.7 - - + -
88B ILE* 5.4 0.4 - - + -
92B ALA* 3.7 22.9 - - + -
95B LEU* 3.8 20.2 - - + -
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Residues in contact with GLY 96 (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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92A ALA 2.8 15.2 + - - -
93A ASP* 3.6 5.8 - - - -
95A LEU* 1.3 79.2 - - - +
97A GLY* 1.3 55.4 + - - +
98A GLY 3.2 0.6 + - - -
136A ALA* 6.0 0.2 - - - +
138A ARG* 3.1 31.4 + - - -
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Residues in contact with GLY 97 (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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93A ASP 3.0 12.8 + - - -
94A ALA 3.0 7.5 + - - -
96A GLY* 1.3 77.4 - - - +
98A GLY* 1.3 56.2 + - - +
99A ALA 3.6 0.2 - - - -
138A ARG* 3.9 19.0 - - - +
57B HIS* 3.7 23.0 + - - -
58B GLU* 3.9 9.9 - - - +
61B ALA* 3.6 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