Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 4P22
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 ARG 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY 3.5 3.2 + - - -
80A LEU* 1.3 80.0 - - - +
82A GLY* 1.3 70.4 + - - +
83A LEU* 3.3 4.0 + - + +
84A GLY 3.4 1.2 + - - +
85A VAL* 3.2 15.1 + - - +
110A ALA* 3.8 12.1 + - - +
111A ASP* 3.0 34.0 + - + +
115A GLN* 3.7 8.3 - - - -
127A ARG* 3.7 25.6 - - - +
165A THR* 4.8 2.2 - - + +
166A ASN* 3.1 39.1 + - + +
191A THR 5.6 4.2 + - - -
393A ASP* 3.5 37.1 + - - +
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Residues in contact with GLY 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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81A ARG* 1.3 79.3 - - - +
83A LEU* 1.3 62.6 + - - +
85A VAL* 3.2 6.3 - - - +
86A GLU* 3.0 28.8 + - - +
111A ASP 5.2 1.4 + - - -
114A SER* 3.7 37.0 - - - -
115A GLN* 3.9 4.8 - - - +
393A ASP* 4.9 3.8 + - - -
398A ASN* 4.1 4.5 - - - -
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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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81A ARG* 3.3 3.3 - - + +
82A GLY* 1.3 74.6 - - - +
84A GLY* 1.3 57.4 + - - +
86A GLU* 3.4 2.4 + - - +
87A ILE* 3.1 37.1 + - + +
165A THR* 3.8 15.9 - - + +
166A ASN 6.1 0.4 - - - +
189A ALA* 3.6 11.2 - - + +
190A ASP* 3.4 45.5 - - - +
191A THR* 3.8 8.5 - - - +
393A ASP* 5.6 0.4 + - - -
398A ASN* 3.6 40.4 - - - +
401A ILE* 3.9 9.2 - - + -
402A GLY* 3.8 15.9 - - - +
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Residues in contact with GLY 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 VAL* 3.7 11.2 - - - +
79A GLY 3.3 19.7 - - - -
80A LEU* 4.0 5.8 - - - -
81A ARG 3.4 3.6 + - - -
82A GLY 3.3 0.4 - - - -
83A LEU* 1.3 76.9 - - - +
85A VAL* 1.3 55.1 + - - +
87A ILE* 3.6 4.1 - - - +
88A ALA* 2.7 35.9 + - - +
165A THR* 3.8 15.0 - - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.7 9.0 - - + +
81A ARG 3.2 11.2 + - - +
82A GLY* 3.2 17.0 - - - +
84A GLY* 1.3 73.5 - - - +
86A GLU* 1.3 60.6 + - - +
88A ALA* 4.4 1.3 - - - +
89A LYS* 2.9 29.1 + - - +
114A SER 4.8 0.4 - - - +
115A GLN* 3.4 39.7 - - + +
116A PHE* 3.8 22.1 - - + -
117A TYR* 3.7 28.7 - - + -
131A SER* 4.7 0.2 - - - +
135A LEU* 4.1 14.4 - - + -
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Residues in contact with GLU 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 GLY* 3.0 20.5 + - - +
83A LEU 3.5 8.1 - - - +
85A VAL* 1.3 77.8 - - + +
87A ILE* 1.3 60.8 + - - +
89A LYS* 3.1 29.9 + - - +
90A ASN* 2.9 33.7 + - - +
114A SER* 4.7 5.5 + - - +
116A PHE* 3.4 21.6 - - + -
395A ALA* 5.1 3.1 - - - +
398A ASN* 4.0 26.8 - - + +
399A ALA* 4.1 15.2 - - - +
402A GLY* 4.4 5.6 - - - -
89B LYS* 3.2 23.2 + - - +
90B ASN* 4.3 2.4 - - - +
93B LEU* 4.8 2.6 - - - +
399B ALA* 5.6 0.9 - - - +
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Residues in contact with ILE 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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77A VAL* 4.8 4.5 - - + -
83A LEU* 3.1 21.4 + - + +
84A GLY* 3.2 7.6 + - - +
86A GLU* 1.3 77.1 - - - +
88A ALA* 1.3 62.9 + - - +
90A ASN* 3.3 8.9 + - - +
91A ILE* 3.0 30.1 + - + +
163A VAL* 4.0 27.8 - - + -
165A THR* 3.8 20.0 - - - +
189A ALA* 4.1 9.4 - - + -
402A GLY* 3.9 11.0 - - - +
405A ALA* 3.7 27.1 - - + -
406A ALA* 4.5 10.4 - - - +
409A VAL* 4.5 17.3 - - + -
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Residues in contact with ALA 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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77A VAL* 4.3 12.3 - - + -
80A LEU* 4.8 1.1 - - + -
84A GLY 2.7 22.1 + - - +
85A VAL* 4.1 2.9 - - - +
87A ILE* 1.3 74.6 - - - +
89A LYS* 1.3 63.3 + - - +
91A ILE* 3.2 12.0 - - + +
92A ILE* 3.0 28.3 + - + +
99A VAL* 4.9 0.4 - - + -
101A LEU* 4.0 27.1 - - + -
135A LEU* 4.0 14.6 - - + -
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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 VAL 2.9 17.8 + - - +
86A GLU* 3.1 28.5 + - - -
88A ALA* 1.3 76.8 - - - +
90A ASN* 1.3 81.5 + - - +
92A ILE 3.3 0.2 + - - -
93A LEU* 3.1 40.5 + - + +
116A PHE* 3.7 24.9 - - + -
135A LEU* 3.6 15.8 - - + +
138A LEU* 3.8 12.7 - - + +
86B GLU* 2.7 37.9 + - - +
89B LYS* 3.5 4.6 - - - +
116B PHE* 4.1 21.8 - - + -
399B ALA* 4.5 1.2 - - - +
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Residues in contact with ASN 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 GLU* 2.9 22.1 + - - +
87A ILE 3.7 0.4 - - - +
88A ALA 3.3 0.2 - - - -
89A LYS* 1.3 97.9 + - - +
91A ILE* 1.3 57.3 + - - +
93A LEU* 4.8 0.8 - - - +
94A GLY* 3.0 23.2 + - - -
399A ALA 5.1 0.2 + - - -
402A GLY 3.1 31.7 + - - -
403A GLY* 3.9 0.6 - - - +
406A ALA* 3.5 18.7 - - + +
410A MET* 3.7 5.2 - - - +
86B GLU* 4.3 1.2 - - - +
395B ALA* 3.8 17.8 - - - +
396B PRO* 4.5 7.4 - - + +
399B ALA* 3.3 26.7 - - - +
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Residues in contact with ILE 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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75A VAL* 3.7 26.0 - - + -
77A VAL* 4.2 9.2 - - + -
87A ILE* 3.0 17.2 + - + +
88A ALA* 3.2 16.2 - - - +
90A ASN* 1.3 75.5 - - - +
92A ILE* 1.3 67.1 + - - +
94A GLY* 3.4 1.9 + - - -
95A GLY 3.2 14.0 + - - -
96A VAL* 3.5 16.4 + - + +
99A VAL* 3.5 24.2 - - + -
406A ALA* 5.0 2.9 - - + +
409A VAL* 3.3 44.4 - - + -
410A MET* 3.5 15.2 - - + +
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Residues in contact with ILE 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 ALA* 3.0 24.5 + - + +
89A LYS 3.9 2.7 - - - +
91A ILE* 1.3 82.4 - - + +
93A LEU* 1.3 56.0 + - - +
94A GLY 3.1 1.6 - - - -
95A GLY* 3.0 12.5 + - - +
99A VAL* 4.1 14.6 - - + -
135A LEU* 3.7 31.6 - - + +
138A LEU* 3.8 19.7 - - + -
139A ASN* 2.5 48.1 + - - +
142A VAL* 3.8 12.9 - - + +
144A VAL* 3.5 32.3 - - + -
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Residues in contact with LEU 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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64A HIS* 3.2 16.0 + - - +
67A MET* 5.4 1.2 - - - +
89A LYS* 3.1 32.1 + - + +
90A ASN* 3.9 1.3 - - - +
92A ILE* 1.3 76.2 - - - +
94A GLY* 1.3 60.0 + - - +
95A GLY 3.4 0.5 + - - -
138A LEU* 4.1 31.9 - - + +
139A ASN* 4.3 4.0 - - + +
141A TYR* 3.7 11.6 + - - -
86B GLU* 5.1 3.8 - - - +
112B LEU 4.9 2.5 - - - +
113B SER* 3.3 30.1 - - - +
114B SER* 4.5 5.6 - - - +
115B GLN 5.1 0.2 - - - +
116B PHE* 4.0 37.5 - - + -
395B ALA* 3.6 20.4 - - + -
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Residues in contact with GLY 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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64A HIS* 3.0 44.5 - - - +
67A MET* 4.9 3.7 - - - +
71A GLN* 5.3 0.7 - - - +
90A ASN 3.0 11.7 + - - -
91A ILE 3.4 1.1 + - - -
92A ILE 3.1 0.6 - - - -
93A LEU* 1.3 79.6 - - - +
95A GLY* 1.3 60.9 + - - +
96A VAL* 3.7 1.5 - - - +
141A TYR* 5.1 0.2 - - - -
410A MET* 3.6 21.2 - - - +
395B ALA* 4.9 0.4 - - - -
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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