Contacts of the helix formed by residues 120 - 134 (chain E) in PDB entry 3SZ9
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E ILE* 2.8 38.7 + - + +
119E LEU* 1.3 85.5 - - + +
121E ASP* 1.3 72.9 + - - +
122E LEU 3.3 1.3 - - - -
123E ASP* 3.3 2.2 + - - +
124E MET* 2.9 49.5 + - + +
170E PHE* 6.0 0.4 - - + -
296E PHE* 4.3 21.5 - - + -
8001E I3E 4.8 5.4 - - + -
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Residues in contact with ASP 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E GLU* 4.4 12.6 - - + +
112E LYS* 2.7 46.7 + - - +
116E ILE* 3.2 20.6 + - - +
117E SER* 3.6 10.8 - - - +
120E VAL* 1.3 78.0 - - - +
122E LEU* 1.3 64.1 + - + +
124E MET* 3.4 5.7 + - - +
125E VAL* 2.9 34.2 + - + +
170E PHE* 3.5 20.8 - - - +
172E LEU* 5.6 0.7 - - + -
173E LEU* 4.6 10.5 - - + +
296E PHE* 5.2 0.2 - - - -
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ILE* 3.6 31.2 - - + -
99E ARG* 3.9 33.7 - - + +
102E LEU* 4.1 15.3 - - + -
103E ALA* 3.9 15.7 - - + -
106E GLU* 5.3 1.1 - - + -
117E SER* 3.0 28.5 + - - +
118E TYR 3.6 9.2 + - - +
120E VAL 3.3 0.2 - - - -
121E ASP* 1.3 78.6 - - + +
123E ASP* 1.3 65.2 + - - +
125E VAL* 3.3 6.8 + - + +
126E LEU* 3.0 31.2 + - + +
172E LEU* 3.8 26.7 - - + -
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Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ARG* 3.6 21.1 + - - +
118E TYR 3.9 2.8 + - - -
119E LEU 3.3 26.5 - - - +
120E VAL 3.3 2.8 + - - +
122E LEU* 1.3 78.6 - - - +
124E MET* 1.3 61.4 + - - +
126E LEU* 3.3 8.2 + - - +
127E LYS* 2.8 66.0 + - - +
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Residues in contact with MET 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL* 2.9 40.4 + - + +
121E ASP 3.9 1.8 - - - +
123E ASP* 1.3 79.2 - - - +
125E VAL* 1.3 66.2 + - - +
127E LYS* 4.0 8.6 - - + +
128E CYS* 2.9 26.7 + - - +
170E PHE* 6.4 0.2 - - - -
173E LEU* 3.7 30.9 - - + +
177E TRP* 5.0 3.8 - - + +
459E PHE* 3.7 36.1 - - + +
8001E I3E 3.8 23.8 - - + -
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Residues in contact with VAL 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ILE* 4.1 23.1 - - + -
121E ASP 2.9 22.2 + - - +
122E LEU* 3.5 10.5 - - + +
124E MET* 1.3 78.3 - - - +
126E LEU* 1.3 63.5 + - - +
128E CYS* 3.4 1.4 + - - +
129E LEU* 3.1 37.7 + - + +
172E LEU* 3.6 20.9 - - + +
173E LEU* 3.6 36.1 - - - +
176E ALA* 4.0 14.3 - - + +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ALA* 3.1 36.6 - - + +
95E ILE* 3.8 15.9 - - + -
96E GLU* 3.7 41.5 - - + +
99E ARG* 4.5 18.8 - - + +
122E LEU 3.0 24.4 + - - +
123E ASP* 3.6 8.3 - - - +
124E MET 3.2 0.2 - - - -
125E VAL* 1.3 78.9 - - + +
127E LYS* 1.3 64.0 + - + +
129E LEU* 3.4 3.4 + - - +
130E ARG* 3.0 45.1 + - - +
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Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ASP* 2.8 51.4 + - - +
124E MET* 4.0 9.9 - - + +
125E VAL 3.3 0.2 - - - -
126E LEU* 1.3 78.4 - - + +
128E CYS* 1.3 55.8 + - - +
130E ARG* 4.2 4.4 - - - +
131E TYR* 2.9 31.0 + - - +
461E ALA* 4.0 9.5 - - + +
462E GLN* 6.3 0.7 - - - +
147F ASP* 3.7 27.6 + - - +
80G ASP* 5.5 2.2 + - - -
82G SER* 5.4 6.3 - - - +
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Residues in contact with CYS 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E MET 2.9 19.7 + - - +
125E VAL 3.7 4.3 - - - +
127E LYS* 1.3 77.6 - - - +
129E LEU* 1.3 57.3 + - - +
131E TYR* 3.3 1.2 + - - +
132E TYR* 3.0 49.0 + - - -
176E ALA* 3.5 30.3 - - + -
177E TRP* 3.8 31.0 - - + +
461E ALA* 4.1 12.5 - - + +
477E LEU* 4.3 3.8 - - + -
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Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU* 4.1 31.3 - - + +
91E LEU* 4.1 19.7 - - + -
92E ALA* 4.2 16.2 - - + -
95E ILE* 3.5 33.0 - - + -
125E VAL* 3.1 22.5 + - + +
126E LEU* 4.1 2.9 - - - +
128E CYS* 1.3 71.7 - - - +
130E ARG* 1.3 61.3 + - - +
132E TYR* 3.5 3.2 + - - +
133E ALA* 2.8 30.9 + - - +
176E ALA* 4.3 19.3 - - + +
179E LEU* 4.9 4.7 - - + -
180E GLY* 4.3 16.4 - - - +
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Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ASN* 3.7 19.7 + - - +
92E ALA* 3.5 24.7 + - + +
93E ASP* 2.9 35.0 + - - +
96E GLU* 2.6 33.1 + - - -
126E LEU* 3.0 35.5 + - - +
127E LYS* 4.2 4.3 - - - +
129E LEU* 1.3 71.9 - - - +
131E TYR* 1.3 68.0 + - - +
133E ALA* 3.6 2.6 + - - +
134E GLY* 3.5 12.8 + - - -
86G ARG* 3.6 50.2 - - - +
89G ASN* 6.2 0.9 - - - +
134G GLY* 6.0 0.2 - - - -
138G LYS* 4.8 0.9 + - - -
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Residues in contact with TYR 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E LYS 2.9 21.8 + - - +
128E CYS 3.5 2.5 - - - +
130E ARG* 1.3 75.5 - - - +
132E TYR* 1.3 74.9 + + - +
134E GLY 3.0 9.0 + - - -
135E TRP* 3.0 32.6 + + - -
461E ALA* 3.1 39.0 - - + -
462E GLN* 3.7 28.8 + - + +
478E GLY* 3.3 23.8 - - - -
479E GLU 3.6 1.7 + - - -
137G ASP* 3.4 21.8 - - - +
138G LYS* 2.9 58.6 + - + +
140G HIS* 4.4 5.4 + - - -
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Residues in contact with TYR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.1 2.9 - - + -
128E CYS* 3.0 39.8 + - - +
129E LEU 4.2 1.6 - - - +
131E TYR* 1.3 85.2 - + - +
133E ALA* 1.3 67.4 + - - +
134E GLY 3.0 1.1 - - - -
135E TRP* 3.0 26.9 + + + +
136E ALA 3.5 0.3 + - - -
177E TRP 5.2 0.7 - - - -
180E GLY* 3.5 23.3 - - - +
181E PRO* 3.9 30.4 - - + +
184E ALA* 3.4 17.8 - - + +
477E LEU* 2.9 33.8 + - + -
478E GLY 2.8 28.6 + - - -
481E GLY* 3.8 6.1 - - - -
482E LEU* 3.6 28.7 - - + -
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Residues in contact with ALA 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E GLY* 3.4 37.0 - - - +
88E LEU* 3.7 18.7 - - + +
89E ASN* 3.4 27.6 - - - +
129E LEU 2.8 22.2 + - - +
130E ARG 3.6 3.8 - - - +
131E TYR 3.3 0.2 - - - -
132E TYR* 1.3 74.0 - - - +
134E GLY* 1.3 61.9 + - - +
135E TRP 3.3 0.3 + - - -
136E ALA* 3.4 9.4 + - - +
137E ASP* 5.0 1.7 - - - +
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ASN* 5.3 0.4 - - - +
130E ARG 3.5 4.6 + - - -
131E TYR 3.0 11.3 + - - -
132E TYR 3.0 1.2 - - - -
133E ALA* 1.3 80.6 - - - +
135E TRP* 1.3 57.9 + - - +
136E ALA 3.4 0.4 + - - -
137E ASP* 3.8 0.6 - - - +
138E LYS* 2.8 36.3 + - - +
134G GLY* 3.8 22.7 - - - -
138G LYS* 3.8 8.5 - - - -
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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
------------------------------------------------------------
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