Contacts of the helix formed by residues 88 - 100 (chain A) in PDB entry 1P9B
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 HIS 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA* 4.8 9.8 - - + +
67A LEU* 3.4 11.0 - - + +
86A VAL 3.9 2.0 + - - -
87A ILE* 1.3 70.5 - - - +
89A VAL* 1.3 66.5 + - - +
90A LYS* 3.1 31.0 - - + +
91A SER* 2.7 41.3 + - - +
92A LEU 3.0 8.7 + - - -
116A LEU* 3.2 43.4 - - + +
117A PHE 4.4 1.3 - - - -
118A ASP* 2.9 27.3 + - - -
121A GLN* 3.9 24.8 + - - +
143A ARG 5.5 0.9 - - - +
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Residues in contact with VAL 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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87A ILE* 2.9 19.5 + - + +
88A HIS* 1.3 70.5 - - - +
90A LYS* 1.3 62.8 + - - +
92A LEU* 3.1 10.4 + - + +
93A MET* 2.9 23.7 + - - +
115A ILE* 4.0 9.6 - - + -
116A LEU 4.1 3.6 + - - -
160A LEU* 4.4 20.0 - - + -
163A LEU* 4.9 2.9 - - + -
198A PHE* 3.8 26.9 - - + -
201A TYR* 3.4 35.0 - - + -
205A LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 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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88A HIS* 3.1 28.7 - - + +
89A VAL* 1.3 79.0 - - - +
91A SER* 1.3 63.8 + - - +
93A MET* 3.4 3.1 + - - +
94A GLU* 3.1 45.4 + - + +
118A ASP* 4.6 14.4 + - - +
193A LYS* 5.9 2.4 - - - +
197A LEU* 5.3 9.5 - - + +
198A PHE* 5.2 2.8 - - + -
201A TYR* 3.3 31.5 + - + +
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Residues in contact with SER 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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50A ALA* 4.7 9.4 - - - +
66A HIS* 6.0 1.3 - - - -
67A LEU* 3.9 13.0 - - - -
88A HIS* 2.7 34.5 + - - +
90A LYS* 1.3 75.1 - - - +
92A LEU* 1.3 67.4 + - - +
94A GLU* 3.2 18.9 + - - +
95A GLU* 3.1 30.5 + - - +
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Residues in contact with LEU 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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67A LEU* 3.6 17.6 - - + +
68A LEU* 3.8 30.3 - - + -
81A LEU* 4.2 15.7 - - + -
87A ILE* 3.9 19.1 - - + -
88A HIS 3.0 11.4 + - - +
89A VAL* 3.1 13.7 + - + +
91A SER* 1.3 76.1 - - - +
93A MET* 1.3 63.5 + - - +
95A GLU* 3.1 4.1 + - - -
96A ILE* 2.9 36.6 + - + +
109A LEU* 4.1 33.4 - - + -
160A LEU* 5.7 2.5 - - + -
205A LEU* 4.3 11.7 - - + -
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Residues in contact with MET 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 VAL 2.9 13.8 + - - +
90A LYS 3.7 5.6 - - - +
92A LEU* 1.3 76.3 - - - +
94A GLU* 1.3 63.0 + - + +
96A ILE* 3.3 10.1 + - + +
97A GLU* 3.0 60.7 + - + +
104A LEU* 6.4 0.9 - - + -
201A TYR* 3.2 39.3 - - + -
204A LYS* 3.8 29.6 - - + +
205A LEU* 3.7 38.1 - - + -
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Residues in contact with GLU 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 LYS* 3.1 39.7 - - + +
91A SER* 3.2 19.1 + - - +
93A MET* 1.3 77.6 - - + +
95A GLU* 1.3 57.8 + - + +
97A GLU* 3.5 10.3 + - - +
98A SER* 2.9 29.0 + - - -
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Residues in contact with GLU 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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64A ALA 4.4 1.7 - - - +
65A LEU* 3.7 12.4 - - + +
66A HIS* 2.8 43.3 + - - +
67A LEU* 3.0 12.6 + - - +
68A LEU* 3.0 43.3 + - + +
91A SER* 3.1 17.6 + - - +
92A LEU 3.7 4.9 - - - +
94A GLU* 1.3 74.6 - - + +
96A ILE* 1.3 65.2 + - - +
98A SER* 3.5 7.4 - - - -
99A VAL* 3.0 29.8 + - - +
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Residues in contact with ILE 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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68A LEU* 4.1 15.9 - - + -
92A LEU* 2.9 40.8 + - + +
93A MET* 3.5 15.0 - - + +
95A GLU* 1.3 77.5 - - - +
97A GLU* 1.3 61.1 + - + +
99A VAL* 3.3 5.0 + - - +
100A GLY* 3.0 25.6 + - - +
103A LEU* 4.1 13.6 - - + +
104A LEU* 4.0 24.9 - - + -
107A LEU* 3.6 18.2 - - + -
205A LEU* 3.5 30.5 - - + -
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Residues in contact with GLU 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 MET* 3.0 37.9 + - + +
94A GLU* 3.9 7.5 - - - +
96A ILE* 1.3 75.7 - - + +
98A SER* 1.3 65.7 + - - +
100A GLY* 3.4 12.5 + - - +
204A LYS* 3.3 26.0 + - + +
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Residues in contact with SER 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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94A GLU 2.9 18.2 + - - -
95A GLU* 3.5 9.6 - - - -
96A ILE 3.2 0.2 - - - -
97A GLU* 1.3 77.4 - - - +
99A VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 99 (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* 4.9 5.8 - - + -
68A LEU* 3.7 19.1 - - + -
72A VAL* 4.2 35.9 - - + +
73A LEU* 6.4 0.9 - - + -
95A GLU 3.0 20.0 + - - +
96A ILE 3.6 6.1 - - - +
98A SER* 1.3 79.4 - - - +
100A GLY* 1.3 69.5 + - - +
101A GLY 3.8 0.9 + - - -
103A LEU* 4.2 18.4 - - + -
106A ARG* 5.6 2.9 - - - +
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Residues in contact with GLY 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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96A ILE 3.0 13.1 + - - -
97A GLU* 3.4 11.6 + - - -
98A SER 3.3 2.0 - - - -
99A VAL* 1.3 83.7 - - - +
101A GLY* 1.3 68.4 + - - +
103A LEU* 3.4 20.4 + - - +
106A ARG* 4.9 1.0 + - - -
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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