Contacts of the helix formed by residues 120 - 136 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 2.7 44.1 + - + +
118B TYR 3.4 0.2 - - - -
119B LEU* 1.3 80.7 - - + +
121B ASP* 1.3 69.8 + - - +
122B LEU 3.4 0.2 - - - -
123B ASP* 3.3 2.3 + - - +
124B MET* 2.9 55.1 + - + +
296B PHE* 4.3 18.8 - - + -
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Residues in contact with ASP 121 (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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106B GLU* 4.3 13.2 - - - +
112B LYS* 2.7 40.2 + - - +
116B ILE* 3.1 25.8 + - - +
117B SER* 3.6 10.1 - - - +
120B VAL* 1.3 76.3 - - - +
122B LEU* 1.3 65.3 + - + +
124B MET* 3.2 12.2 + - - +
125B VAL* 2.9 33.6 + - + +
170B PHE* 3.5 18.8 - - - +
172B LEU* 5.5 0.4 - - + -
173B LEU* 4.7 7.9 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.7 30.3 - - + -
99B ARG* 3.9 34.1 - - + +
102B LEU* 4.2 14.4 - - + -
103B ALA* 3.9 19.3 - - + +
106B GLU* 5.2 0.9 - - + -
117B SER* 2.9 26.0 + - - +
118B TYR 3.7 9.4 - - - +
121B ASP* 1.3 78.8 - - + +
123B ASP* 1.3 63.0 + - - +
125B VAL* 3.3 6.0 + - + +
126B LEU* 3.0 31.8 + - + +
172B LEU* 3.7 28.9 - - + -
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Residues in contact with ASP 123 (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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99B ARG* 3.8 19.2 + - - +
118B TYR 3.9 3.0 + - - -
119B LEU 3.2 25.3 - - - +
120B VAL* 3.3 2.6 + - - +
122B LEU* 1.3 78.7 - - - +
124B MET* 1.3 61.4 + - - +
126B LEU* 3.4 9.9 + - - +
127B LYS* 3.0 62.2 + - - +
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Residues in contact with MET 124 (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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120B VAL* 2.9 48.6 + - + +
121B ASP* 3.7 8.5 - - - +
123B ASP* 1.3 78.1 - - - +
125B VAL* 1.3 61.1 + - - +
127B LYS* 3.8 8.8 - - + +
128B CYS* 2.9 31.2 + - - +
170B PHE* 5.4 6.1 - - + -
173B LEU* 3.3 39.4 - - + +
177B TRP* 6.2 0.7 - - - -
296B PHE* 5.5 2.2 - - + -
459B PHE* 5.3 20.4 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.1 23.6 - - + -
121B ASP 2.9 18.8 + - - +
122B LEU* 3.3 11.6 + - + +
124B MET* 1.3 76.7 - - - +
126B LEU* 1.3 63.8 + - - +
128B CYS* 3.2 2.3 + - - +
129B LEU* 3.0 42.2 + - + +
172B LEU* 3.6 45.8 - - + +
173B LEU* 3.6 10.1 - - - +
176B ALA* 4.0 12.7 - - + +
204B VAL* 6.3 0.2 - - + -
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Residues in contact with LEU 126 (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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92B ALA* 3.2 36.1 - - + +
95B ILE* 3.8 16.4 - - + -
96B GLU* 3.7 40.8 - - + +
99B ARG* 4.4 21.1 - - + +
122B LEU* 3.0 22.1 + - + +
123B ASP* 3.6 10.1 - - - +
124B MET 3.3 0.2 - - - -
125B VAL* 1.3 77.7 - - + +
127B LYS* 1.3 59.3 + - + +
129B LEU* 3.5 1.5 + - - +
130B ARG* 3.0 49.8 + - - +
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Residues in contact with LYS 127 (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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147A ASP* 3.5 30.4 + - - +
123B ASP* 3.0 47.3 + - - +
124B MET* 3.9 8.5 - - + +
126B LEU* 1.3 77.9 - - + +
128B CYS* 1.3 59.1 + - - +
130B ARG* 4.2 4.6 - - - +
131B TYR* 2.9 31.9 + - - +
461B ALA* 4.0 8.6 - - + +
80D ASP* 5.4 1.8 + - - -
82D SER* 5.3 5.6 - - - +
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Residues in contact with CYS 128 (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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124B MET 2.9 17.6 + - - +
125B VAL* 3.2 4.7 + - - +
127B LYS* 1.3 74.2 - - - +
129B LEU* 1.3 65.6 + - - +
131B TYR* 3.2 1.9 + - - +
132B TYR* 3.0 47.5 + - - -
176B ALA* 3.5 29.4 - - + -
177B TRP* 3.7 31.4 - - + +
461B ALA* 3.9 13.4 - - + +
477B LEU* 4.5 3.1 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.1 23.2 - - + +
91B LEU* 4.0 19.7 - - + -
92B ALA* 4.2 16.6 - - + -
95B ILE* 3.5 32.3 - - + -
125B VAL* 3.0 25.9 + - + +
126B LEU 4.1 2.5 - - - +
128B CYS* 1.3 77.6 - - - +
130B ARG* 1.3 58.2 + - - +
132B TYR* 3.4 4.1 + - - +
133B ALA* 2.9 28.5 + - - +
176B ALA* 4.1 29.4 - - + +
179B LEU* 4.9 4.7 - - + -
180B GLY* 4.3 13.5 - - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN* 3.6 24.8 + - - +
92B ALA* 3.6 29.8 + - + +
93B ASP* 2.9 27.5 + - - +
96B GLU* 2.7 31.1 + - - -
126B LEU* 3.0 37.3 + - - +
127B LYS* 4.2 4.7 - - - +
129B LEU* 1.3 74.0 - - - +
131B TYR* 1.3 66.9 + - - +
133B ALA* 3.5 3.5 + - - +
134B GLY* 3.4 13.2 + - - -
86D ARG* 3.5 50.2 - - - +
89D ASN* 6.2 0.9 - - - +
138D LYS* 4.8 0.7 + - - -
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Residues in contact with TYR 131 (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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127B LYS 2.9 20.6 + - - +
128B CYS 3.2 3.3 + - - +
130B ARG* 1.3 76.1 - - - +
132B TYR* 1.3 78.7 + + - +
134B GLY 3.1 5.5 + - - -
135B TRP* 2.8 35.8 + + - -
461B ALA* 3.3 31.6 - - + -
462B GLN* 3.4 32.8 + - + +
478B GLY* 3.5 21.8 - - - -
479B GLU 3.6 1.9 + - - -
137D ASP* 3.5 26.0 - - - +
138D LYS* 3.0 51.7 + - + +
140D HIS* 4.6 5.0 + - - -
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Residues in contact with TYR 132 (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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88B LEU* 4.1 4.0 - - + -
128B CYS* 3.0 39.0 + - - +
129B LEU 4.0 1.8 - - - +
131B TYR* 1.3 89.5 - + - +
133B ALA* 1.3 67.3 + - - +
134B GLY 3.0 2.0 - - - -
135B TRP* 2.9 18.8 + + + +
136B ALA 3.4 7.6 + - - -
180B GLY* 3.5 23.3 - - - +
181B PRO* 3.7 37.1 - - + +
184B ALA* 3.4 10.5 - - + +
461B ALA 4.5 0.2 - - - -
477B LEU* 2.9 43.5 + - + -
478B GLY 2.9 22.0 + - - -
481B GLY* 4.2 3.5 - - - -
482B LEU* 3.7 24.7 - - + -
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Residues in contact with ALA 133 (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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85B GLY* 3.4 36.8 - - - +
88B LEU* 3.5 21.5 - - + +
89B ASN* 3.6 21.3 - - - +
129B LEU 2.9 18.2 + - - +
130B ARG 3.5 8.3 - - - +
131B TYR 3.2 0.2 - - - -
132B TYR* 1.3 77.3 - - - +
134B GLY* 1.3 61.8 + - - +
136B ALA* 3.4 9.2 + - - +
137B ASP* 5.0 1.6 - - - +
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Residues in contact with GLY 134 (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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89B ASN* 5.4 0.6 - - - +
130B ARG 3.4 4.9 + - - -
131B TYR 3.1 9.1 + - - -
132B TYR 3.0 0.8 - - - -
133B ALA* 1.3 81.4 - - - +
135B TRP* 1.3 57.9 + - - +
136B ALA 3.3 0.6 + - - -
137B ASP* 3.6 0.9 - - - +
138B LYS* 2.8 34.7 + - - +
134D GLY* 3.8 22.7 - - - -
138D LYS* 3.7 9.9 - - - -
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Residues in contact with TRP 135 (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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131B TYR* 2.8 41.3 + + - -
132B TYR* 2.9 21.0 + + + +
134B GLY* 1.3 76.2 - - - +
136B ALA* 1.3 65.8 + - - +
137B ASP 3.1 3.3 + - - -
138B LYS* 3.1 45.9 + - + -
139B TYR* 3.7 16.0 + + - +
184B ALA* 4.7 2.2 - - + -
479B GLU* 3.2 49.4 - - + +
482B LEU* 3.5 35.1 - - + +
135D TRP* 4.9 7.2 - + - -
138D LYS* 3.4 43.8 - - + +
140D HIS* 4.1 7.6 - + - -
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Residues in contact with ALA 136 (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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81B ALA* 3.3 34.3 - - - +
82B SER* 5.1 0.2 - - - -
84B ARG* 3.5 14.6 + - + -
85B GLY* 3.7 13.9 - - - +
132B TYR 3.4 3.2 + - - -
133B ALA* 3.4 15.5 + - - +
134B GLY 3.3 1.8 - - - -
135B TRP* 1.3 78.5 - - - +
137B ASP* 1.3 59.4 + - - +
138B LYS 3.9 0.2 + - - -
139B TYR* 4.9 4.3 + - - +
184B ALA* 3.5 26.9 - - + +
145C PRO* 5.2 1.2 - - - +
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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