Contacts of the helix formed by residues 99 - 114 (chain A) in PDB entry 2PZ9
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 3.1 28.3 + - + +
98A ALA* 1.3 79.3 - - - +
100A LEU* 1.3 58.0 + - - +
101A PRO* 3.4 1.9 - - - +
102A GLY* 2.7 35.4 + - - -
103A TYR* 3.0 21.1 + - - +
215A ARG* 3.2 38.4 + - - +
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Residues in contact with LEU 100 (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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95A LEU* 3.9 27.8 - - + -
96A ASP 3.9 3.1 - - - +
97A PRO* 3.6 15.9 - - + +
98A ALA 4.0 0.6 - - - -
99A ASP* 1.3 72.7 - - - +
101A PRO* 1.4 66.0 - - + +
103A TYR* 3.0 11.4 + - + +
104A ALA* 2.9 25.5 + - - +
150A LEU* 4.0 16.8 - - + -
158A LEU 6.1 0.2 - - - +
159A LEU* 3.7 29.6 - - + -
168A VAL* 4.5 2.0 - - + -
172A ILE* 4.0 23.9 - - + +
209A VAL* 3.9 7.5 - - + +
213A PHE* 3.8 24.0 - - + +
215A ARG* 4.8 0.4 - - - +
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Residues in contact with PRO 101 (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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99A ASP* 3.4 11.4 - - - +
100A LEU* 1.4 91.2 - - + +
102A GLY* 1.3 57.0 + - - -
104A ALA* 3.2 2.5 + - - +
105A GLY 3.0 22.3 + - - -
206A VAL* 3.3 47.3 - - + +
209A VAL* 3.6 15.2 - - + -
210A GLU* 3.8 19.5 - - + +
213A PHE 4.5 6.7 - - - +
215A ARG* 3.8 24.7 - - + -
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Residues in contact with GLY 102 (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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99A ASP* 2.7 33.9 + - - -
101A PRO* 1.3 69.6 - - - +
103A TYR* 1.3 65.8 + - - +
105A GLY* 3.2 3.0 + - - -
106A ILE* 3.0 33.7 + - - +
202A ARG* 4.9 2.2 + - - -
206A VAL* 4.8 2.6 - - - +
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Residues in contact with TYR 103 (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 THR* 3.7 29.9 - - + +
94A GLN 4.2 6.1 - - - -
95A LEU* 3.8 39.5 - - + -
96A ASP* 4.5 4.0 - - - +
99A ASP 3.0 15.6 + - - +
100A LEU* 3.0 17.7 - - + +
102A GLY* 1.3 76.6 - - - +
104A ALA* 1.3 59.2 + - - +
106A ILE* 3.1 21.4 + - + +
107A LEU* 3.1 38.7 + - + +
146A LYS* 3.1 25.0 + - + +
169A LEU* 4.6 6.4 - - + +
172A ILE* 3.8 26.5 - - + -
173A ASN* 3.9 18.4 + - - -
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Residues in contact with ALA 104 (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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100A LEU 2.9 11.9 + - - +
101A PRO 3.2 8.5 + - - +
103A TYR* 1.3 73.7 - - - +
105A GLY* 1.3 60.8 + - - +
107A LEU* 3.3 9.1 + - - +
108A PHE* 2.8 28.7 + - - +
172A ILE* 4.1 14.8 - - + +
176A ALA* 4.0 7.2 - - + +
205A LEU* 4.1 15.6 - - + +
206A VAL* 5.0 0.9 - - + -
209A VAL* 3.8 26.7 - - + -
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Residues in contact with GLY 105 (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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101A PRO 3.0 11.1 + - - -
102A GLY* 3.2 3.3 + - - -
104A ALA* 1.3 75.6 - - - +
106A ILE* 1.3 56.8 + - - +
108A PHE* 3.1 6.9 + - - +
109A ASP* 2.8 35.7 + - - +
202A ARG* 3.3 29.4 - - - -
206A VAL* 3.9 12.7 - - - +
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Residues in contact with ILE 106 (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 3.6 24.9 - - - +
93A THR* 3.8 17.7 - - - +
94A GLN 5.2 2.5 - - - +
102A GLY* 3.0 26.0 + - - +
103A TYR* 3.1 21.5 + - + +
105A GLY* 1.3 77.3 - - - +
107A LEU* 1.3 62.6 + - - +
109A ASP* 3.2 10.1 + - - +
110A HIS* 3.1 21.9 + - + +
202A ARG* 5.1 5.6 - - - +
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Residues in contact with LEU 107 (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 LEU* 4.3 16.2 - - + -
93A THR* 3.2 31.0 - - + +
103A TYR* 3.1 47.1 + - + +
104A ALA* 3.3 3.8 + - - +
106A ILE* 1.3 71.7 - - - +
108A PHE* 1.3 67.9 + - - +
110A HIS* 3.3 4.5 + - - +
111A PHE* 3.2 36.7 + - + -
172A ILE 4.7 1.8 - - - +
173A ASN* 4.2 22.7 - - - +
176A ALA* 3.7 26.2 - - + -
177A MSE 4.9 3.1 - - + -
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Residues in contact with PHE 108 (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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104A ALA 2.8 14.5 + - - +
105A GLY* 3.1 10.5 + - - +
107A LEU* 1.3 77.3 - - - +
109A ASP* 1.3 60.4 + - - +
111A PHE* 3.3 2.0 + - - +
112A ALA* 2.8 45.4 + - + +
176A ALA* 4.0 15.9 - - - +
178A THR* 5.2 0.2 - - + -
179A TRP* 3.8 30.5 - + + -
198A VAL* 4.0 35.2 - - + -
199A THR* 5.5 0.2 - - - -
201A ARG* 4.1 6.1 - - + -
202A ARG* 3.6 35.2 - - + -
205A LEU* 3.6 27.4 - - + -
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Residues in contact with ASP 109 (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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105A GLY 2.8 16.8 + - - +
106A ILE* 3.3 13.9 - - - +
108A PHE* 1.3 78.9 - - - +
110A HIS* 1.3 56.1 + - - +
112A ALA* 3.2 7.8 + - - +
113A ALA* 2.8 31.4 + - - +
202A ARG* 2.8 44.1 + - - -
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Residues in contact with HIS 110 (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* 4.5 6.3 - - + -
89A LEU* 3.8 44.4 - - + +
92A ALA* 3.9 22.0 - - + +
93A THR* 5.5 2.0 + - - +
106A ILE 3.1 9.6 + - - +
107A LEU* 3.6 11.7 - - - +
109A ASP* 1.3 79.9 - - - +
111A PHE* 1.3 73.8 + + + +
113A ALA* 3.3 4.9 + - - +
114A ARG* 2.9 47.7 + - + +
117A HIS* 3.4 22.1 + - - -
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Residues in contact with PHE 111 (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 LEU* 4.1 26.9 - - + -
107A LEU* 3.2 28.7 + - + +
108A PHE* 4.2 1.8 - - - +
110A HIS* 1.3 80.9 - + - +
112A ALA* 1.3 66.2 + - - +
113A ALA 3.2 0.4 - - - -
114A ARG 3.5 10.0 - - - -
115A PRO* 3.4 21.7 - - - +
117A HIS* 3.7 32.5 - + + -
118A TYR* 3.9 26.7 - + + -
121A ILE* 4.6 8.5 - - + -
176A ALA 5.7 1.8 - - - +
177A MSE 3.5 51.8 - - + -
180A ALA* 5.2 8.2 - - + +
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Residues in contact with ALA 112 (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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108A PHE* 2.8 37.3 + - + +
109A ASP* 3.2 10.1 + - - +
111A PHE* 1.3 79.2 - - - +
113A ALA* 1.3 63.0 + - - +
115A PRO* 3.8 9.9 - - - +
198A VAL* 5.1 7.6 - - + -
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Residues in contact with ALA 113 (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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109A ASP 2.8 17.0 + - - +
110A HIS* 3.4 6.5 - - - +
112A ALA* 1.3 77.8 - - - +
114A ARG* 1.3 87.4 + - + +
115A PRO* 2.9 11.8 - - - +
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Residues in contact with ARG 114 (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 LYS* 6.4 2.2 - - - +
85A GLU* 5.4 5.8 - - - +
110A HIS* 2.9 39.6 + - + +
111A PHE* 3.5 11.7 - - - +
113A ALA* 1.3 89.9 + - - +
115A PRO* 1.4 66.8 - - - +
116A ASP* 3.1 11.0 - - - +
117A HIS* 3.1 28.0 + - + +
118A TYR 3.8 2.4 + - - -
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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