Contacts of the helix formed by residues 106 - 123 (chain A) in PDB entry 1Z0X
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 TYR 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 4.4 13.7 - - + -
58A ALA* 3.3 36.4 + - + +
59A GLU* 3.7 38.4 - - + +
62A GLU* 3.7 22.9 - - + -
99A GLU* 4.0 24.4 + - - +
102A THR* 4.2 2.2 + - - -
103A VAL 3.5 18.6 - - - -
104A PRO* 3.9 5.2 - - + -
105A ALA* 1.3 82.4 - - - +
107A PRO* 1.3 75.6 - - + +
108A GLN* 4.9 2.2 - - + +
109A ARG* 3.3 50.0 + - + +
110A LEU* 3.3 12.4 + - - +
168B GLN* 6.4 0.2 - - - -
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Residues in contact with PRO 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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59A GLU* 5.4 5.8 - - - +
105A ALA 3.8 4.4 - - - +
106A TYR* 1.3 84.0 - - + +
108A GLN* 1.3 76.1 + - + +
109A ARG 3.2 0.2 + - - -
110A LEU* 3.2 2.6 + - - +
111A ARG* 2.9 31.2 + - - +
175B TYR* 3.8 45.5 - - + +
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Residues in contact with GLN 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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59A GLU* 5.9 2.2 - - + -
62A GLU* 3.3 26.4 - - + +
63A GLU* 3.9 39.8 + - + +
67A GLU* 4.8 2.3 - - - +
106A TYR* 3.5 4.3 + - + +
107A PRO* 1.3 86.0 - - + +
109A ARG* 1.3 63.3 + - - +
111A ARG* 3.4 29.6 + - - +
112A HIS* 3.1 45.4 + - + -
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Residues in contact with ARG 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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62A GLU* 3.1 19.6 + - - +
85A TYR* 3.2 37.8 + - - -
89A TYR* 3.8 6.5 + - - -
99A GLU* 3.5 38.4 + - - +
104A PRO* 3.5 26.7 - - + -
106A TYR* 3.3 34.6 + - + +
107A PRO 3.2 0.2 - - - -
108A GLN* 1.3 75.7 - - - +
110A LEU* 1.3 67.5 + - - +
112A HIS* 3.0 3.6 + - - +
113A LEU* 2.8 48.9 + - + +
138A GLN* 3.5 26.5 + - - +
142A PHE* 4.4 0.8 - - - -
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Residues in contact with LEU 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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104A PRO* 3.2 26.2 - - + +
105A ALA 3.7 23.3 - - - +
106A TYR 3.3 6.7 + - - +
107A PRO 3.2 5.8 + - - +
109A ARG* 1.3 76.1 - - - +
111A ARG* 1.3 62.3 + - - +
113A LEU* 4.1 4.2 - - + +
114A ASN* 3.0 28.8 + - - +
172B MSE 4.0 20.0 - - + +
175B TYR* 3.8 28.7 - - + -
176B VAL* 4.1 4.9 - - + -
181B LEU* 3.9 16.8 - - + +
184B MSE 3.9 31.8 - - + +
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Residues in contact with ARG 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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67A GLU* 5.9 3.2 + - - -
107A PRO* 2.9 24.6 + - - +
108A GLN* 3.6 30.4 + - - +
110A LEU* 1.3 75.2 - - - +
112A HIS* 1.3 65.2 + - + +
114A ASN* 4.0 2.5 - - - +
115A GLN* 3.0 40.3 + - - +
175B TYR* 3.9 26.9 - - + +
181B LEU* 4.7 11.2 - - + -
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Residues in contact with HIS 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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62A GLU* 2.9 23.5 + - + +
65A PHE* 3.3 31.6 - + + -
67A GLU* 2.5 32.9 + - - -
81A PHE* 4.4 8.5 - + + -
85A TYR* 3.3 21.6 + - + +
108A GLN* 3.1 26.8 + - - -
109A ARG 3.0 6.5 + - - +
111A ARG* 1.3 81.0 + - + +
113A LEU* 1.3 60.9 + - - +
115A GLN* 3.3 18.7 + - - +
116A MSE 2.9 36.9 + - - +
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Residues in contact with LEU 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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104A PRO* 4.3 13.0 - - + -
109A ARG* 2.8 62.7 + - + +
110A LEU* 4.1 2.0 - - - +
112A HIS* 1.3 72.5 - - - +
114A ASN* 1.3 61.7 + - - +
116A MSE 3.3 24.2 + - + +
117A MSE 2.9 35.6 + - - +
134A VAL* 4.4 12.6 - - + -
138A GLN* 4.8 4.7 - - + +
184B MSE 3.8 28.5 - - + -
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Residues in contact with ASN 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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110A LEU 3.0 19.9 + - - +
111A ARG 4.2 2.3 - - - +
113A LEU* 1.3 76.8 - - - +
115A GLN* 1.3 61.3 + - - +
117A MSE 4.5 0.4 - - - -
118A GLY 3.0 18.4 + - - -
181B LEU* 3.2 33.1 - - + +
182B THR 3.6 0.6 + - - +
183B TYR* 2.8 37.4 - - - +
184B MSE 2.8 43.4 - - + +
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Residues in contact with GLN 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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67A GLU* 4.3 9.5 + - - +
68A PRO* 5.7 0.2 - - - +
70A LEU* 4.6 15.0 - - - +
81A PHE* 3.4 34.2 - - + -
111A ARG* 3.0 29.6 + - - +
112A HIS* 3.5 18.4 - - - +
113A LEU 3.2 0.2 - - - -
114A ASN* 1.3 80.4 - - - +
116A MSE 1.3 65.2 + - - +
117A MSE 3.2 0.2 - - - -
118A GLY* 3.1 3.2 + - - +
119A ILE* 3.0 28.4 + - + +
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Residues in contact with MSE 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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78A LEU* 3.7 18.8 - - + +
81A PHE* 3.4 30.1 - - + -
82A MSE 3.2 34.5 - - - +
85A TYR* 3.7 20.0 - - + +
112A HIS 2.9 21.6 + - - +
113A LEU* 3.3 35.2 + - + +
115A GLN* 1.3 76.6 - - - +
117A MSE 1.3 61.4 + - - +
119A ILE* 3.2 25.8 + - - +
120A LEU* 3.5 6.1 + - - +
134A VAL* 4.3 17.9 - - + -
137A LEU* 6.4 0.2 - - - -
138A GLN* 3.8 7.0 - - - +
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Residues in contact with MSE 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 LEU* 2.9 26.7 + - - +
116A MSE 1.3 73.8 - - - +
118A GLY* 1.3 60.5 + - - +
120A LEU 3.4 0.3 + - - -
121A ARG* 3.0 28.8 + - + +
127A PRO 5.6 0.2 - - - +
130A THR* 3.3 24.1 - - + +
131A HIS* 3.6 34.8 - - + +
134A VAL* 3.8 22.7 - - + -
135A THR* 5.5 2.5 - - + -
183B TYR* 3.7 23.8 - - + +
184B MSE 4.1 12.1 - - - +
187B SER* 3.0 41.5 - - - +
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Residues in contact with GLY 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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114A ASN 3.0 10.2 + - - -
115A GLN* 3.1 6.2 + - - -
116A MSE 3.1 0.8 - - - -
117A MSE 1.3 75.8 - - - +
119A ILE* 1.3 65.4 + - - +
122A GLU* 3.1 36.7 + - - +
183B TYR* 3.3 31.9 - - - -
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Residues in contact with ILE 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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70A LEU* 5.0 8.1 - - + -
72A GLY* 6.2 0.4 - - - -
73A GLU 4.6 0.7 - - - +
74A TRP* 3.3 39.8 - - + +
77A ASP* 4.2 28.0 - - + +
78A LEU* 4.5 10.8 - - + +
81A PHE* 4.8 8.5 - - + -
115A GLN* 3.0 18.5 + - + +
116A MSE 3.3 15.5 - - - +
118A GLY* 1.3 79.1 - - - +
120A LEU* 1.3 60.1 + - + +
122A GLU* 4.3 2.9 - - - +
123A ALA* 3.3 20.3 + - - +
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Residues in contact with LEU 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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74A TRP* 4.0 23.8 - - + -
78A LEU* 4.1 20.6 - - + -
116A MSE 3.9 8.5 - - - +
117A MSE 3.4 0.8 + - - -
118A GLY 3.2 0.2 - - - -
119A ILE* 1.3 80.1 - - + +
121A ARG* 1.3 64.7 + - - +
123A ALA* 2.9 11.0 + - - -
124A GLY 3.1 0.3 + - - -
125A PHE* 3.0 44.4 + - + -
129A MSE 5.0 0.2 - - - -
130A THR* 3.5 50.3 - - + +
133A ALA* 3.8 15.3 - - + -
134A VAL* 3.8 10.1 - - + -
211A LEU* 4.6 4.9 - - + -
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Residues in contact with ARG 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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117A MSE 3.0 20.1 + - - +
118A GLY 4.3 0.4 - - - +
120A LEU* 1.3 76.6 - - - +
122A GLU* 1.3 62.9 + - - +
124A GLY* 3.1 17.6 + - - -
125A PHE 3.0 23.6 + - - -
126A SER* 4.1 3.0 - - - +
127A PRO* 3.0 40.1 - - - +
130A THR* 3.6 15.3 - - + +
183B TYR* 3.5 31.4 - - + -
186B GLU* 2.9 27.2 + - - +
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Residues in contact with GLU 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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118A GLY* 3.1 25.0 + - - +
119A ILE* 4.4 2.9 - - - +
121A ARG* 1.3 76.8 - - - +
123A ALA* 1.3 58.6 + - - +
124A GLY* 3.1 1.6 + - - -
183B TYR* 3.5 28.8 + - - +
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Residues in contact with ALA 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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74A TRP* 3.8 33.6 - - + -
119A ILE 3.3 18.3 + - - +
120A LEU 2.9 8.1 + - - +
122A GLU* 1.3 77.6 - - - +
124A GLY* 1.3 58.2 + - - +
125A PHE* 3.7 9.1 - - + -
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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