Contacts of the helix formed by residues 109 - 120 (chain B) in PDB entry 1ZX1
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASP* 3.8 0.2 - - - +
10B ALA* 4.1 23.1 - - + +
42B TYR* 3.8 18.2 - - - +
101B PHE* 3.7 12.6 - - + -
102B PRO* 3.4 29.8 - - + +
104B TYR* 3.6 29.4 - - + -
108B VAL* 1.3 87.5 - - + +
110B ALA* 1.3 66.4 + - - +
111B ILE* 3.2 6.5 - - + +
112B LEU* 3.0 9.2 + - + +
113B LYS 3.0 17.0 + - - -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.5 15.5 - - + +
110A ALA* 3.5 14.3 - - - +
113A LYS* 3.9 10.1 - - - +
114A GLY* 3.4 39.0 - - - +
117A ASP* 2.9 14.6 + - - +
48B PRO* 3.8 3.5 - - - +
108B VAL 3.5 1.0 + - - -
109B PRO* 1.3 69.9 - - - +
111B ILE* 1.3 57.2 + - - +
113B LYS* 3.2 5.7 + - - +
114B GLY 2.9 24.3 + - - -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO 5.1 1.4 + - - -
49A ARG* 4.1 20.5 - - + +
10B ALA* 4.2 12.6 - - + -
41B LEU* 3.3 43.4 - - + +
42B TYR* 3.6 51.0 + - + +
45B ASN 4.8 0.2 - - - -
46B PHE* 3.6 32.9 - - + +
48B PRO* 4.2 8.4 - - + +
109B PRO* 3.1 3.0 + - + -
110B ALA* 1.3 77.0 - - - +
112B LEU* 1.3 60.6 + - - +
114B GLY* 3.4 2.4 + - - -
115B TRP* 3.2 22.9 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.7 31.6 - - + +
10B ALA* 4.1 16.2 - - + -
41B LEU* 3.8 7.6 - - + -
99B PHE* 3.9 23.6 - - + -
101B PHE* 3.6 41.3 - - + -
108B VAL* 3.6 21.8 - - + -
109B PRO* 3.0 9.2 + - + +
111B ILE* 1.3 78.0 - - - +
113B LYS* 1.3 66.0 + - - +
114B GLY 3.2 0.2 - - - -
115B TRP* 3.2 7.2 + - + -
116B MET* 3.1 24.7 + - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 2.8 32.3 + - - +
105A TRP* 4.2 7.6 - - - -
107A SER* 3.7 17.5 - - - +
108A VAL 2.8 28.5 + - - +
110A ALA* 3.8 14.4 - - + -
113A LYS* 4.5 10.3 - - + -
107B SER* 5.6 1.8 - - - +
108B VAL* 3.6 19.8 - - + +
109B PRO 3.0 9.3 + - - +
110B ALA* 3.2 13.4 + - - +
112B LEU* 1.3 75.0 - - - +
114B GLY* 1.3 56.6 + - - +
116B MET* 3.3 19.8 + - + +
117B ASP* 2.6 55.6 + - - +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.4 8.0 - - - +
46B PHE* 3.9 6.2 - - - -
48B PRO* 3.4 30.7 - - - -
110B ALA 2.9 10.7 + - - -
111B ILE 3.8 0.2 - - - -
112B LEU 3.2 0.2 - - - -
113B LYS* 1.3 73.6 - - - +
115B TRP* 1.3 66.0 + - - +
117B ASP* 4.2 2.9 - - - -
118B ARG* 2.9 29.3 + - - +
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Residues in contact with TRP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.3 2.2 - - + -
8B VAL* 3.8 31.1 - - + +
41B LEU* 3.5 31.6 - - + -
46B PHE* 3.3 27.7 - + + -
87B GLU* 2.9 29.4 + - + +
91B VAL* 3.7 31.6 - - + -
97B VAL* 5.2 1.3 - - + -
99B PHE* 3.9 28.3 - + - -
111B ILE 3.2 10.9 + - - +
112B LEU* 3.4 9.9 - - + +
114B GLY* 1.3 75.4 - - - +
116B MET* 1.3 64.8 + - + +
119B VAL* 2.8 50.4 + - + +
120B LEU* 4.4 24.5 - - + -
181B PHE* 6.4 1.8 - + - -
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.1 30.1 + - + +
99B PHE* 5.2 6.7 - - + -
108B VAL* 4.1 20.0 - - - -
112B LEU* 3.1 24.7 + - + +
113B LYS* 3.3 22.9 + - + +
115B TRP* 1.3 93.4 - - + +
117B ASP* 1.3 62.7 + - - +
120B LEU* 3.3 27.6 + - + +
171B LEU* 3.8 24.0 - - + -
175B THR* 3.5 36.3 - - + +
176B LEU* 6.4 0.4 - - + -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 3.5 25.3 - - + +
105A TRP* 3.4 16.8 + - - +
110A ALA* 3.0 35.0 + - - +
232A FAD 3.5 17.4 - - + +
48B PRO 4.8 1.0 - - - +
50B ALA* 4.9 6.1 - - + +
67B TYR* 4.1 8.2 - - - -
113B LYS* 2.6 44.8 + - - +
114B GLY* 3.3 6.2 + - - +
116B MET* 1.3 77.2 - - - +
118B ARG* 1.3 63.3 + - + +
120B LEU 4.8 4.9 + - - +
121B CYS* 5.5 2.4 - - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.5 19.2 - - + -
47B GLU* 2.8 40.8 + - - +
48B PRO 4.4 5.8 - - - +
49B ARG 3.1 18.4 - - - +
50B ALA* 4.4 4.9 - - - -
54B ASP* 2.8 50.4 + - - -
67B TYR* 3.5 14.3 + - - +
71B THR* 6.0 0.9 - - - +
80B LEU* 5.5 0.5 - - - +
81B ALA* 4.8 1.8 - - - +
83B ASP* 2.5 40.2 + - - -
84B ILE* 3.5 32.0 - - + +
114B GLY 2.9 17.1 + - - +
117B ASP* 1.3 80.1 - - + +
119B VAL* 1.3 63.7 + - - +
121B CYS* 4.5 10.0 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.0 11.2 - - + -
84B ILE* 4.3 11.2 - - - +
87B GLU* 3.6 35.9 - - + +
88B GLN* 2.8 48.7 + - + +
91B VAL* 4.5 4.5 - - + -
115B TRP* 2.8 59.0 + - + +
118B ARG* 1.3 75.9 - - + +
120B LEU* 1.3 59.2 + - + +
121B CYS 3.1 1.6 + - - -
124B PHE* 3.5 6.8 - - + -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.3 25.6 + - + -
232A FAD 5.7 1.2 - - - +
91B VAL* 5.2 2.7 - - + -
99B PHE* 6.3 0.7 - - + -
115B TRP* 4.4 23.3 - - + -
116B MET* 3.3 30.9 + - + +
117B ASP 4.9 2.8 - - - +
118B ARG 3.5 1.1 - - - -
119B VAL* 1.3 77.7 - - + +
121B CYS* 1.3 62.1 + - - +
124B PHE* 4.6 6.5 - - + -
125B ALA* 3.7 24.9 - - + -
126B PHE* 3.8 4.3 - - - -
137B LEU* 4.1 17.0 - - + -
175B THR* 3.9 28.0 - - + -
176B LEU* 5.8 2.7 - - + -
179B CYS* 4.4 8.5 - - + -
181B PHE* 4.9 8.3 - - + -
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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