Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 2IDZ
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 PRO 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A THR* 3.7 10.1 - - + +
110A ASP 3.1 11.4 - - - +
111A ALA* 1.3 84.3 - - - +
113A TYR* 1.3 66.0 + - - +
114A ALA* 4.2 10.3 - - + +
115A ASP* 2.9 42.4 + - - +
116A VAL* 3.2 9.7 + - - +
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Residues in contact with TYR 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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111A ALA 3.6 2.2 + - - -
112A PRO* 1.3 71.4 - - - +
114A ALA* 1.3 55.3 + - - +
116A VAL* 3.2 25.9 + - + -
117A SER* 2.7 60.2 + - - -
120A ILE* 5.1 9.0 - - + +
160A TRP* 6.2 2.0 - + - -
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Residues in contact with ALA 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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112A PRO* 3.1 7.2 + - + +
113A TYR* 1.3 78.3 - - - +
115A ASP* 1.3 63.1 + - - +
117A SER* 3.8 5.5 - - - -
118A LYS* 3.1 27.0 + - - +
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Residues in contact with ASP 115 (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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98A MET* 4.5 0.9 - - - -
99A PRO* 3.3 32.6 - - + +
101A THR* 2.9 40.4 + - + +
112A PRO* 2.9 25.5 + - - +
114A ALA* 1.3 78.7 - - - +
116A VAL* 1.3 67.2 + - - +
118A LYS* 3.2 3.7 + - - +
119A GLY 2.9 17.8 + - - -
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Residues in contact with VAL 116 (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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98A MET* 4.0 9.8 - - + +
111A ALA* 3.8 15.3 - - + +
112A PRO 3.2 12.4 + - - +
113A TYR* 3.7 19.7 - - + +
115A ASP* 1.3 76.7 - - - +
117A SER* 1.3 50.2 + - - +
119A GLY* 2.9 4.5 + - - -
120A ILE* 2.8 53.2 + - + +
160A TRP* 3.3 61.5 - - + -
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Residues in contact with SER 117 (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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113A TYR* 2.7 53.1 + - - -
114A ALA* 3.8 6.3 - - - -
116A VAL* 1.3 69.3 - - - +
118A LYS* 1.3 60.7 + - - +
120A ILE* 3.7 6.5 - - - +
121A HIS* 2.8 31.8 + - - +
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Residues in contact with LYS 118 (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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66A GLN* 3.6 28.0 - - - +
97A PHE* 3.8 31.2 - - + -
99A PRO* 4.4 7.4 - - + +
114A ALA 3.1 15.7 + - - +
115A ASP* 3.2 11.9 + - - +
117A SER* 1.3 76.6 - - - +
119A GLY* 1.3 63.1 + - - +
121A HIS* 3.2 7.1 + - - +
122A ILE* 3.0 35.1 + - + +
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Residues in contact with GLY 119 (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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97A PHE* 3.2 20.1 - - - +
98A MET* 3.4 21.1 - - - -
99A PRO* 4.0 3.3 - - - +
115A ASP 2.9 7.1 + - - -
116A VAL 2.9 7.7 + - - -
118A LYS* 1.3 78.5 - - - +
120A ILE* 1.3 57.0 + - - +
123A SER* 2.8 34.7 + - - -
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Residues in contact with ILE 120 (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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98A MET* 4.7 1.8 - - + -
113A TYR* 5.1 9.9 - - + +
116A VAL* 2.8 40.2 + - + +
117A SER* 4.0 7.4 - - - +
119A GLY* 1.3 70.0 - - - +
121A HIS* 1.3 66.9 + - - +
124A ALA* 2.9 31.8 + - + +
125A TYR* 2.9 13.5 + - + +
160A TRP* 5.6 0.7 - - + -
163A VAL* 4.6 16.2 - - + -
164A ALA* 4.1 24.9 - - + +
167A ALA* 4.6 10.5 - - + -
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Residues in contact with HIS 121 (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 VAL 3.9 21.2 + - - -
66A GLN* 3.3 41.2 + - + +
68A GLU* 5.4 5.3 + - - -
71A LEU* 5.9 0.7 - - + -
117A SER* 2.8 19.3 + - - +
118A LYS* 3.4 6.3 - - - +
120A ILE* 1.3 79.6 - - - +
122A ILE* 1.3 59.0 + - - +
125A TYR* 3.6 36.3 - + + -
126A SER* 2.9 29.7 + - - -
129A SER* 5.0 0.2 - - - -
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Residues in contact with ILE 122 (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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41A PHE* 6.2 0.7 - - + -
65A VAL* 3.9 6.3 - - + -
66A GLN* 3.5 42.0 - - + +
93A HIS* 4.0 0.3 + - - -
95A ILE* 3.3 28.8 - - + +
97A PHE* 3.7 45.1 - - + +
118A LYS* 3.0 17.6 + - - +
119A GLY 4.2 0.2 - - - +
121A HIS* 1.3 80.0 - - - +
123A SER* 1.3 57.7 + - - +
126A SER* 2.4 24.0 + - - -
300A ZID 3.5 31.2 - - + +
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Residues in contact with SER 123 (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 HIS* 4.1 8.5 - - - -
95A ILE 4.0 9.6 - - - +
96A GLY* 4.3 1.1 - - - -
97A PHE 2.7 39.7 + - - -
119A GLY 2.8 12.2 + - - -
122A ILE* 1.3 79.0 - - - +
124A ALA* 1.3 55.9 + - - +
126A SER* 4.4 1.8 - - - -
161A MET* 3.4 22.6 - - - +
164A ALA* 3.9 14.1 - - - -
165A LYS* 4.9 2.4 + - - +
168A LEU* 3.4 23.1 - - - +
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Residues in contact with ALA 124 (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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120A ILE* 2.9 20.7 + - + +
122A ILE 3.6 0.2 - - - -
123A SER* 1.3 77.9 - - - +
125A TYR* 1.3 64.9 + - - +
126A SER 3.3 1.1 - - - -
127A TYR* 3.1 21.2 + - - +
164A ALA 3.5 22.7 - - - +
167A ALA* 3.8 14.8 - - + +
168A LEU* 3.6 17.9 - - - +
171A VAL* 3.8 14.4 - - + +
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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