Contacts of the helix formed by residues 120 - 136 (chain J) in PDB entry 1ZUM
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 VAL 120 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J ILE* 2.8 42.5 + - + +
118J TYR 3.5 0.2 - - - -
119J LEU* 1.3 80.8 - - + +
121J ASP* 1.3 62.0 + - - +
122J LEU 3.5 0.2 - - - -
123J ASP* 3.3 2.2 + - - +
124J MET* 2.8 63.1 + - + +
296J PHE* 4.4 19.1 - - + -
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Residues in contact with ASP 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J GLU* 4.5 11.9 - - + +
112J LYS* 2.6 44.8 + - - +
116J ILE* 3.2 20.1 + - - +
117J SER* 3.5 10.8 - - - +
120J VAL* 1.3 78.1 - - - +
122J LEU* 1.3 64.2 + - + +
124J MET* 3.1 11.0 + - - +
125J VAL* 2.8 36.0 + - + +
170J PHE* 3.5 18.9 - - - +
172J LEU* 5.6 1.1 - - + -
173J LEU* 4.4 7.3 + - + +
296J PHE* 5.4 0.3 - - - -
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Residues in contact with LEU 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ILE* 4.4 16.2 - - + -
99J ARG* 3.3 52.9 - - + +
102J LEU* 3.6 14.6 - - + -
103J ALA* 3.8 18.2 - - + -
106J GLU* 5.2 1.8 - - + -
117J SER* 2.9 33.9 + - - +
118J TYR* 3.9 4.3 - - - +
121J ASP* 1.3 77.0 - - + +
123J ASP* 1.3 63.9 + - - +
125J VAL* 3.1 5.9 + - + +
126J LEU* 3.0 30.4 + - + +
172J LEU* 3.7 25.6 - - + -
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Residues in contact with ASP 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J ARG* 3.7 22.3 + - - +
118J TYR 3.9 3.8 + - - -
119J LEU 3.2 24.7 - - - +
120J VAL 3.3 2.6 + - - +
121J ASP 3.3 0.6 - - - -
122J LEU* 1.3 78.2 - - - +
124J MET* 1.3 61.8 + - - +
126J LEU* 3.4 7.3 + - - +
127J LYS* 3.0 68.5 + - - +
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Residues in contact with MET 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 2.8 45.4 + - + +
121J ASP* 3.7 7.0 - - - +
123J ASP* 1.3 77.3 - - - +
125J VAL* 1.3 61.3 + - - +
127J LYS* 3.7 9.4 - - + +
128J CYS* 2.9 31.9 + - - +
170J PHE* 5.5 5.6 - - + -
173J LEU* 3.3 39.1 - - + +
177J TRP* 6.1 1.3 - - - -
296J PHE* 5.8 1.8 - - + -
459J PHE* 5.3 19.7 - - - +
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Residues in contact with VAL 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ILE* 4.2 33.2 - - + -
121J ASP 2.8 20.7 + - - +
122J LEU* 3.1 11.4 + - + +
124J MET* 1.3 76.1 - - - +
126J LEU* 1.3 61.7 + - + +
128J CYS* 3.3 2.4 + - - +
129J LEU* 3.1 27.2 + - + +
172J LEU* 3.7 46.0 - - + +
173J LEU* 3.7 12.3 - - - +
176J ALA* 4.0 15.0 - - + -
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ALA* 3.1 36.3 - - + +
95J ILE* 3.7 17.3 - - + -
96J GLU* 3.7 41.5 - - + +
99J ARG* 4.3 20.6 - - + +
122J LEU* 3.0 22.2 + - + +
123J ASP* 3.7 7.6 - - - +
125J VAL* 1.3 77.8 - - + +
127J LYS* 1.3 58.2 + - + +
129J LEU* 3.5 1.3 + - + +
130J ARG* 3.0 51.3 + - - +
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Residues in contact with LYS 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I ASP* 3.3 32.3 + - - +
123J ASP* 3.0 47.0 + - - +
124J MET* 3.9 8.5 - - + +
125J VAL 3.3 0.2 - - - -
126J LEU* 1.3 76.8 - - + +
128J CYS* 1.3 57.9 + - - +
130J ARG* 4.0 5.6 - - - +
131J TYR* 3.0 29.6 + - - +
461J ALA* 3.8 8.7 - - + +
80L ASP* 5.2 2.4 + - - -
82L SER* 5.5 2.9 - - - +
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Residues in contact with CYS 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J MET 2.9 18.8 + - - +
125J VAL 3.6 4.5 - - - +
127J LYS* 1.3 73.9 - - - +
129J LEU* 1.3 66.5 + - - +
131J TYR* 3.2 2.3 + - - +
132J TYR* 3.0 50.4 + - - -
176J ALA* 3.4 31.0 - - + -
177J TRP* 3.7 30.3 - - + +
461J ALA* 4.0 12.3 - - + +
477J LEU* 4.4 2.0 - - - -
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Residues in contact with LEU 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J LEU* 4.1 31.3 - - + +
91J LEU* 3.9 21.3 - - + -
92J ALA* 4.2 16.8 - - + -
95J ILE* 3.7 30.1 - - + -
125J VAL* 3.1 22.7 + - + +
126J LEU* 4.1 2.5 - - - +
128J CYS* 1.3 75.6 - - - +
130J ARG* 1.3 58.9 + - - +
132J TYR* 3.5 3.8 + - - +
133J ALA* 3.0 29.7 + - - +
176J ALA* 4.3 16.6 - - + +
179J LEU* 4.9 4.3 - - + -
180J GLY* 4.3 20.6 - - - +
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Residues in contact with ARG 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J ASN* 3.7 22.9 + - - +
92J ALA* 3.7 31.2 + - + +
93J ASP* 3.0 26.9 + - - +
96J GLU* 2.8 30.3 + - - -
126J LEU* 3.0 39.4 + - - +
127J LYS* 4.2 5.1 - - - +
129J LEU* 1.3 73.0 - - - +
131J TYR* 1.3 66.9 + - - +
133J ALA* 3.6 3.1 + - - +
134J GLY* 3.5 13.3 + - - -
86L ARG* 3.6 48.1 - - - +
134L GLY* 6.1 0.3 - - - -
138L LYS* 4.9 0.9 + - - -
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Residues in contact with TYR 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J LYS 3.0 20.4 + - - +
128J CYS 3.2 4.0 + - - +
130J ARG* 1.3 78.0 - - - +
132J TYR* 1.3 77.4 + + - +
134J GLY 3.1 15.2 + - - -
135J TRP* 2.9 35.1 + + - -
461J ALA* 3.4 29.2 - - + -
462J GLN* 3.5 34.1 + - + +
478J GLY* 3.5 22.9 - - - -
479J GLU 3.7 1.6 + - - -
137L ASP* 3.6 22.2 - - - +
138L LYS* 3.1 48.3 + - + +
140L HIS* 4.6 5.0 + - - -
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Residues in contact with TYR 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J LEU* 3.9 3.6 - - + -
128J CYS* 3.0 40.9 + - - +
129J LEU 4.1 2.5 - - - +
131J TYR* 1.3 96.4 - + - +
133J ALA* 1.3 65.4 + - - +
135J TRP* 3.0 16.2 + + - +
136J ALA 3.3 8.8 + - - -
177J TRP 5.2 1.1 - - - -
180J GLY* 3.5 29.4 - - - +
181J PRO* 3.7 36.8 - - + +
184J ALA* 3.4 10.5 - - + +
477J LEU* 2.8 49.3 + - + -
478J GLY 3.1 13.3 + - - -
481J GLY* 4.4 3.3 - - - -
482J LEU* 4.0 17.7 - - + -
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Residues in contact with ALA 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J GLY* 3.4 38.5 - - - +
88J LEU* 3.6 18.8 - - + +
89J ASN* 3.6 21.5 - - - +
129J LEU 3.0 17.9 + - - +
130J ARG 3.6 7.9 - - - +
131J TYR 3.2 0.4 - - - -
132J TYR* 1.3 77.4 - - - +
134J GLY* 1.3 61.2 + - - +
135J TRP 3.4 0.3 + - - -
136J ALA* 3.5 7.6 + - - +
137J ASP* 5.0 1.7 - - - +
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Residues in contact with GLY 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J ASN* 5.3 0.9 - - - +
130J ARG 3.5 4.9 + - - -
131J TYR 3.1 9.9 + - - -
133J ALA* 1.3 80.0 - - - +
135J TRP* 1.3 58.2 + - - +
136J ALA 3.4 0.2 - - - -
137J ASP* 3.7 0.4 - - - +
138J LYS* 2.8 37.3 + - - +
134L GLY* 4.0 21.5 - - - -
138L LYS* 3.9 8.3 - - - -
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Residues in contact with TRP 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J TYR* 2.9 41.6 + + - -
132J TYR* 3.0 18.3 + + - +
134J GLY* 1.3 74.5 - - - +
136J ALA* 1.3 65.3 + - - +
137J ASP 3.2 3.1 - - - -
138J LYS* 3.0 51.3 + - + -
139J TYR* 3.6 17.2 + + - +
184J ALA* 4.8 1.8 - - + -
479J GLU* 3.4 47.9 - - + +
482J LEU* 3.6 34.9 - - + +
135L TRP* 4.8 9.2 - + - -
138L LYS* 3.4 43.7 - - + +
140L HIS* 4.2 5.4 - + - -
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J ALA* 3.3 34.4 - - - +
82J SER* 5.2 0.4 - - - -
84J ARG* 3.4 13.8 + - + -
85J GLY* 3.7 13.7 - - - +
132J TYR 3.3 5.1 + - - +
133J ALA* 3.5 14.8 - - - +
134J GLY 3.4 1.2 - - - -
135J TRP* 1.3 76.9 - - - +
137J ASP* 1.3 58.5 + - - +
138J LYS 3.9 0.3 + - - -
139J TYR* 5.0 3.1 + - - +
184J ALA* 3.4 27.2 - - - +
145K PRO* 5.0 1.4 - - - +
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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
------------------------------------------------------------
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