Contacts of the helix formed by residues 87 - 98 (chain A) in PDB entry 2YZ5
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 THR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A MET* 3.8 15.9 - - + +
42A PRO* 4.1 17.9 - - + -
44A TRP* 3.6 35.9 - - + -
82A ASP 4.6 2.1 + - - -
84A HIS* 2.5 39.5 + - + +
85A PRO 4.6 0.2 - - - +
86A GLY* 1.3 81.6 - - - +
88A GLU* 1.3 65.3 + - - +
89A GLY 3.3 2.7 - - - -
90A PHE* 3.2 10.3 + - - +
91A LEU* 3.1 23.3 + - - +
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Residues in contact with GLU 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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83A PHE* 3.7 29.2 - - + -
84A HIS 4.3 1.1 - - - +
85A PRO* 3.8 6.9 - - - +
86A GLY* 2.8 29.5 + - - -
87A THR* 1.3 79.4 + - - +
89A GLY* 1.3 58.0 + - - +
91A LEU* 3.3 2.6 + - - +
92A ALA* 2.8 32.3 + - - +
146A SER* 4.9 5.3 - - - +
148A LEU* 3.9 28.6 - - + +
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Residues in contact with GLY 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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86A GLY 5.1 1.2 + - - -
87A THR* 3.3 0.8 - - - +
88A GLU* 1.3 78.8 + - - +
90A PHE* 1.3 63.5 + - - +
92A ALA* 3.3 6.0 + - - +
93A GLN* 3.1 24.3 + - - +
96A ARG* 5.4 0.2 + - - -
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Residues in contact with PHE 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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40A PRO* 3.5 12.1 - - + -
41A MET* 3.4 35.2 - - - -
42A PRO* 3.6 35.7 - - + -
43A PRO* 5.6 2.2 - - + -
53A LEU* 4.1 31.2 - - + -
87A THR* 3.2 12.4 + - - +
89A GLY* 1.3 74.9 - - - +
91A LEU* 1.3 71.8 + - + +
93A GLN* 3.5 9.1 + - - +
94A LEU* 3.1 34.8 + - + +
97A ARG* 4.9 3.5 + - - -
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Residues in contact with LEU 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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39A SER* 3.9 15.3 - - - +
40A PRO 4.1 5.4 - - - +
41A MET* 3.9 23.6 - - - -
81A ALA* 4.0 18.2 - - + -
82A ASP 3.2 26.7 - - - +
83A PHE* 5.0 1.1 - - + -
87A THR* 3.1 18.8 + - - +
88A GLU 3.8 5.4 - - - +
89A GLY 3.3 0.2 - - - -
90A PHE* 1.3 81.5 - - + +
92A ALA* 1.3 61.1 + - - +
94A LEU* 3.1 8.1 + - + +
95A LEU* 2.8 42.0 + - + +
148A LEU* 4.4 13.7 - - + -
149A PHE* 4.1 15.5 - - + -
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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 GLU 2.8 21.2 + - - +
89A GLY* 3.7 6.5 - - - +
91A LEU* 1.3 72.6 - - - +
93A GLN* 1.3 63.0 + - - +
95A LEU* 3.9 4.5 - - - +
96A ARG* 3.0 44.4 + - + +
148A LEU* 3.9 18.3 - - + +
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Residues in contact with GLN 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 GLY 3.1 16.6 + - - +
90A PHE* 3.7 9.0 - - - +
92A ALA* 1.3 76.8 - - - +
94A LEU* 1.3 63.4 + - - +
96A ARG* 3.2 39.5 + - - +
97A ARG* 3.2 40.9 + - + +
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Residues in contact with LEU 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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39A SER* 5.0 1.1 - - - -
40A PRO* 3.6 47.3 - - + +
53A LEU* 3.9 10.5 - - + -
56A LEU* 4.6 7.4 - - + -
79A LEU* 3.9 25.6 - - + -
90A PHE* 3.1 19.5 + - + +
91A LEU* 3.1 14.7 + - + +
93A GLN* 1.3 80.1 - - - +
95A LEU* 1.3 64.1 + - + +
97A ARG* 2.9 50.3 + - - +
98A TYR 4.0 1.6 + - - -
100A PHE* 4.0 12.8 - - + -
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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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79A LEU* 4.4 7.4 - - + -
81A ALA* 5.4 5.6 - - + -
91A LEU* 2.8 33.6 + - + +
92A ALA* 4.0 4.3 - - - +
94A LEU* 1.3 81.4 - - + +
96A ARG* 1.3 57.5 + - + +
97A ARG 3.2 0.2 - - - -
98A TYR 3.0 23.0 - - - +
100A PHE* 3.9 25.3 - - + -
103A VAL* 4.0 28.5 - - + -
148A LEU* 3.4 38.1 - - + +
149A PHE* 5.2 2.2 - - + -
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Residues in contact with ARG 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* 3.0 36.8 + - + +
93A GLN* 3.5 40.3 + - - +
94A LEU 3.1 1.0 - - - -
95A LEU* 1.3 76.0 - - + +
97A ARG* 1.3 64.2 + - - +
98A TYR* 3.2 3.1 + - - +
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Residues in contact with ARG 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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53A LEU* 3.8 34.8 - - - +
56A LEU* 4.3 16.2 - - + +
90A PHE* 4.9 3.0 + - - -
93A GLN* 3.2 49.6 - - + +
94A LEU* 2.9 38.3 + - - +
96A ARG* 1.3 79.8 - - - +
98A TYR* 1.3 64.2 + - + +
99A PRO* 4.8 0.9 - - - +
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Residues in contact with TYR 98 (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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60A LEU* 3.7 47.6 - - + -
64A GLU* 2.8 30.0 + - - +
67A ARG* 4.2 7.9 + - - -
77A ILE* 3.4 32.9 - - + +
94A LEU 4.0 1.4 + - - -
95A LEU 3.0 19.6 + - - +
96A ARG 3.2 2.8 - - - -
97A ARG* 1.3 84.3 - - + +
99A PRO* 1.3 95.5 - - + +
100A PHE* 2.9 39.1 + + + -
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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