Contacts of the helix formed by residues 77 - 90 (chain A) in PDB entry 4TZ1
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR 3.7 1.2 + - - -
76A PRO* 1.3 75.5 - - + +
78A ILE* 1.3 65.9 + - - +
79A GLN* 3.0 2.7 - - - +
80A GLY* 2.8 26.3 + - - -
81A LYS* 2.8 31.6 + - - +
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Residues in contact with ILE 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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71A PHE* 3.3 34.1 - - + -
72A ASP 3.2 27.4 - - - +
73A PRO* 5.2 1.3 - - + -
75A THR* 4.0 17.6 + - - +
76A PRO 3.1 3.0 + - - -
77A ASP* 1.3 75.9 - - - +
79A GLN* 1.3 60.7 + - + +
81A LYS 3.5 0.3 - - - -
82A VAL* 2.7 40.4 + - + +
103A PHE* 4.2 4.0 - - + -
108A TYR* 3.8 20.0 - - + -
111A ILE* 3.6 30.1 - - + -
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Residues in contact with GLN 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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77A ASP* 3.0 2.1 - - - +
78A ILE* 1.3 84.1 - - + +
80A GLY* 1.3 58.5 + - - +
82A VAL* 3.4 4.2 + - - +
83A ASP* 2.9 59.8 + - - +
110A ASP 3.3 9.6 - - - +
111A ILE* 3.2 15.6 - - - +
112A ASN* 3.1 44.9 + - - +
113A ALA* 5.3 0.6 - - - +
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Residues in contact with GLY 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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77A ASP* 2.8 28.2 + - - -
79A GLN* 1.3 75.4 - - - +
81A LYS* 1.3 59.5 + - - +
83A ASP* 3.2 11.4 - - - +
84A GLU* 3.1 29.6 + - - +
87A ARG* 5.0 1.3 + - - -
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Residues in contact with LYS 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 LEU* 4.3 5.2 - - + +
71A PHE* 3.7 29.0 - - + -
75A THR* 4.1 5.7 - - - +
76A PRO* 2.7 52.6 + - - +
77A ASP* 2.8 25.0 + - + +
80A GLY* 1.3 80.0 - - - +
82A VAL* 1.3 60.3 + - - +
84A GLU* 4.3 6.8 - - - +
85A VAL* 3.8 18.5 + - - +
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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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71A PHE* 3.9 23.6 - - + -
78A ILE* 2.7 35.8 + - + +
79A GLN* 4.1 6.1 - - - +
81A LYS* 1.3 72.3 - - - +
83A ASP* 1.3 60.0 + - - +
84A GLU 3.3 0.2 - - - -
85A VAL* 3.1 23.7 + - - +
86A PHE* 3.2 11.4 + - - +
101A LEU* 4.1 19.3 - - + +
103A PHE* 4.1 13.0 - - + -
111A ILE* 5.2 4.0 - - + -
112A ASN 5.3 1.1 - - - +
113A ALA* 3.8 32.3 - - + -
114A GLN 4.9 5.8 - - - +
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Residues in contact with ASP 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 GLN* 2.9 51.0 + - - +
80A GLY* 3.2 12.5 - - - +
82A VAL* 1.3 69.5 - - - +
84A GLU* 1.3 68.0 + - - +
86A PHE* 3.3 9.8 + - - +
87A ARG* 3.0 44.5 + - - +
112A ASN 4.9 1.2 - - - +
114A GLN* 4.8 11.6 + - - -
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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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80A GLY 3.1 15.3 + - - +
81A LYS* 4.5 7.2 - - - +
82A VAL 3.3 0.6 - - - -
83A ASP* 1.3 79.5 - - - +
85A VAL* 1.3 64.3 + - + +
87A ARG* 3.4 23.1 + - - +
88A LYS* 3.2 41.2 + - + +
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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
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69A LEU* 3.7 29.6 - - + -
81A LYS 3.8 10.1 - - - +
82A VAL 3.1 8.9 + - - +
84A GLU* 1.3 79.0 - - + +
86A PHE* 1.3 59.0 + - - +
88A LYS* 3.1 14.2 + - - +
89A GLN* 2.8 33.6 + - + +
99A TYR* 3.9 38.1 - - + -
101A LEU* 4.4 10.1 - - + -
119A THR* 4.1 18.2 - - + +
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Residues in contact with PHE 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 VAL 3.2 8.4 + - - +
83A ASP* 3.3 13.2 + - - +
85A VAL* 1.3 81.5 - - - +
87A ARG* 1.3 66.3 + - + +
89A GLN* 4.3 3.1 - - - +
90A GLU* 2.8 79.0 + - + +
114A GLN* 3.2 76.9 - - + +
115A ILE 4.4 3.8 - - - -
116A GLY* 3.8 15.9 - - - +
1C BGC 5.8 0.7 - - - -
2C BGC 5.6 0.2 - - - -
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Residues in contact with ARG 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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80A GLY* 5.0 1.2 + - - -
83A ASP* 3.0 47.5 + - - +
84A GLU* 4.0 20.2 + - - +
86A PHE* 1.3 85.9 - - + +
88A LYS* 1.3 59.4 + - - +
90A GLU* 4.3 14.1 + - - +
91A SER 5.4 1.0 + - - -
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Residues in contact with LYS 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 GLU* 3.2 32.9 + - + +
85A VAL* 3.1 15.5 + - - +
87A ARG* 1.3 79.2 - - - +
89A GLN* 1.3 69.2 + - + +
91A SER 5.2 0.4 + - - -
92A ASN* 3.5 16.8 + - - +
97A ASP* 4.5 8.3 - - - +
99A TYR* 3.2 35.8 + - - +
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Residues in contact with GLN 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* 2.8 22.8 + - + +
86A PHE* 4.3 0.9 - - - +
88A LYS* 1.3 77.9 - - - +
90A GLU* 1.3 65.4 + - - +
91A SER 3.3 2.5 - - - -
92A ASN* 2.9 40.4 + - - +
97A ASP* 3.4 30.3 + - - +
99A TYR* 3.5 35.2 - - + -
116A GLY* 4.2 3.8 - - - -
117A PHE* 3.0 48.9 + - - +
118A TYR* 3.8 8.5 - - - +
119A THR* 3.8 9.4 - - - +
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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 PHE* 2.8 49.7 + - + +
87A ARG* 4.3 12.4 + - - +
88A LYS 3.7 1.2 - - - -
89A GLN* 1.3 77.7 - - - +
91A SER* 1.3 70.2 + - - +
116A GLY* 4.2 10.7 - - - -
117A PHE* 3.3 19.2 + - - -
142A GLY* 5.0 0.7 + - - -
143A TRP* 3.7 30.9 + - + +
154A ARG* 5.1 1.9 + - - -
1C BGC 3.6 20.8 + - - -
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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