Contacts of the helix formed by residues 120 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ILE* 2.8 31.1 + - + +
119A LEU* 1.3 87.8 - - + +
121A ASP* 1.3 72.2 + - - +
122A LEU 3.4 0.9 - - - -
123A ASP* 3.3 2.6 + - - +
124A MET* 2.9 47.7 + - + +
170A PHE* 6.2 0.9 - - + -
296A PHE* 4.3 23.8 - - + -
8001A I3E 5.0 4.3 - - + -
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 4.1 13.2 - - + +
112A LYS* 2.8 45.4 + - - +
116A ILE* 3.2 18.6 + - - +
117A SER* 3.5 11.9 - - - +
120A VAL* 1.3 83.1 - - - +
122A LEU* 1.3 64.3 + - + +
124A MET* 3.3 6.0 + - - +
125A VAL* 2.9 35.5 + - + +
170A PHE* 3.4 19.9 - - - +
172A LEU* 5.7 0.2 - - + -
173A LEU* 4.6 11.4 - - + +
296A PHE* 5.2 0.7 - - - -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.7 29.8 - - + -
99A ARG* 4.0 33.2 - - + +
102A LEU* 4.0 16.4 - - + -
103A ALA* 3.9 19.1 - - + +
106A GLU* 5.3 0.9 - - + -
117A SER* 3.0 24.0 + - - +
118A TYR 3.7 9.2 - - - +
121A ASP* 1.3 77.7 - - + +
123A ASP* 1.3 66.9 + - - +
125A VAL* 3.3 7.1 + - + +
126A LEU* 3.0 31.6 + - + +
172A LEU* 3.7 26.7 - - + -
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Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.7 22.6 + - - +
118A TYR 3.9 1.0 + - - -
119A LEU 3.4 24.7 - - - +
120A VAL 3.3 3.4 + - - +
122A LEU* 1.3 79.8 - - - +
124A MET* 1.3 61.1 + - - +
126A LEU* 3.3 9.1 + - - +
127A LYS* 2.9 65.1 + - - +
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Residues in contact with MET 124 (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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120A VAL* 2.9 44.4 + - + +
121A ASP* 3.8 2.0 - - - +
123A ASP* 1.3 75.9 - - - +
125A VAL* 1.3 61.1 + - - +
127A LYS* 3.9 8.8 - - + +
128A CYS* 2.9 32.1 + - - +
173A LEU* 3.7 31.3 - - + +
177A TRP* 4.7 6.0 + - + +
459A PHE* 3.9 33.0 - - + +
460A GLY 6.5 0.2 - - - -
8001A I3E 3.9 23.3 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.9 36.6 - - + -
121A ASP 2.9 20.3 + - - +
122A LEU* 3.5 12.6 - - + +
124A MET* 1.3 76.6 - - - +
126A LEU* 1.3 61.6 + - - +
128A CYS* 3.8 1.4 - - - +
129A LEU* 3.1 27.5 + - + +
172A LEU* 3.6 21.5 - - + +
173A LEU* 3.6 32.5 - - - +
176A ALA* 4.0 16.8 - - + +
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Residues in contact with LEU 126 (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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92A ALA* 3.1 39.9 - - + +
95A ILE* 4.0 14.6 - - + -
96A GLU* 3.7 39.9 - - + +
99A ARG* 4.5 19.1 - - + +
122A LEU* 3.0 25.4 + - + +
123A ASP* 3.6 8.1 - - - +
125A VAL* 1.3 75.8 - - - +
127A LYS* 1.3 59.3 + - + +
129A LEU* 4.1 1.3 - - - +
130A ARG* 3.0 50.6 + - - +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 2.9 51.3 + - - +
124A MET* 3.9 9.0 - - + +
125A VAL 3.3 0.2 - - - -
126A LEU* 1.3 76.7 - - + +
128A CYS* 1.3 57.0 + - - +
130A ARG* 3.8 4.6 - - - +
131A TYR* 2.8 31.8 + - - +
461A ALA* 4.0 8.4 - - + +
147B ASP* 3.5 28.3 + - - +
80C ASP* 5.5 1.8 + - - -
82C SER* 5.2 6.5 - - - +
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Residues in contact with CYS 128 (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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124A MET 2.9 19.9 + - - +
125A VAL 3.8 3.8 - - - +
127A LYS* 1.3 73.8 - - - +
129A LEU* 1.3 65.7 - - - +
131A TYR* 3.3 0.3 + - - +
132A TYR* 3.0 44.5 + - - -
176A ALA* 3.4 34.8 - - + -
177A TRP* 3.7 26.0 - - + +
180A GLY* 5.0 0.2 - - - -
461A ALA* 4.1 14.1 - - + +
477A LEU* 4.4 2.9 - - + -
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Residues in contact with LEU 129 (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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88A LEU* 4.1 31.2 - - + +
91A LEU* 4.2 20.4 - - + -
92A ALA* 4.1 18.6 - - + -
95A ILE* 3.5 31.6 - - + -
125A VAL* 3.1 25.4 + - + +
126A LEU* 5.2 0.2 - - - -
128A CYS* 1.3 77.0 - - - +
130A ARG* 1.3 58.1 + - - +
132A TYR* 3.8 3.6 - - - +
133A ALA* 2.9 30.4 + - - +
176A ALA* 4.2 18.2 - - + +
179A LEU* 4.9 4.9 - - + -
180A GLY* 4.3 17.5 - - - +
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASN* 3.4 24.3 + - - +
92A ALA* 3.8 27.3 + - + +
93A ASP* 3.0 26.3 + - - +
96A GLU* 2.7 32.3 + - - -
126A LEU* 3.0 39.7 + - - +
127A LYS* 4.0 5.2 - - - +
129A LEU* 1.3 76.7 - - - +
131A TYR* 1.3 64.5 + - - +
133A ALA* 3.5 3.6 + - - +
134A GLY* 3.5 13.3 + - - -
86C ARG* 3.5 50.3 - - - +
89C ASN* 6.2 0.2 - - - +
138C LYS* 4.9 0.9 + - - -
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Residues in contact with TYR 131 (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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127A LYS 2.8 19.4 + - - +
128A CYS 3.6 2.0 - - - +
130A ARG* 1.3 76.5 - - - +
132A TYR* 1.3 74.3 + + - +
134A GLY 3.1 8.7 + - - -
135A TRP* 2.8 34.0 + + - -
461A ALA* 3.2 36.3 - - + -
462A GLN* 3.4 29.7 + - + +
478A GLY* 3.1 25.0 - - - -
479A GLU 3.5 1.9 + - - -
137C ASP* 3.3 22.2 - - - +
138C LYS* 3.0 55.5 + - + +
140C HIS* 4.5 4.7 + - - -
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Residues in contact with TYR 132 (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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88A LEU* 4.2 3.4 - - + -
128A CYS* 3.0 32.7 + - - +
129A LEU 4.1 1.6 - - - +
131A TYR* 1.3 89.9 - + - +
133A ALA* 1.3 66.4 + - - +
135A TRP* 3.0 19.0 + + - +
136A ALA 3.5 0.9 + - - -
177A TRP 5.1 0.4 - - - -
180A GLY* 3.5 23.8 - - - +
181A PRO* 3.8 34.7 - - + +
184A ALA* 3.4 18.3 - - + +
477A LEU* 2.8 57.9 + - + -
478A GLY 3.0 11.8 + - - -
481A GLY* 3.8 5.4 - - - -
482A LEU* 3.7 26.7 - - + -
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Residues in contact with ALA 133 (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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85A GLY* 3.4 37.7 - - - +
88A LEU* 3.6 19.7 - - + +
89A ASN* 3.7 20.6 - - - +
129A LEU 2.9 17.9 + - - +
130A ARG 3.6 7.0 - - - +
132A TYR* 1.3 76.9 - - - +
134A GLY* 1.3 61.2 + - - +
135A TRP 3.4 0.5 + - - -
136A ALA* 3.4 9.0 + - - +
137A ASP* 5.0 1.9 - - - +
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Residues in contact with GLY 134 (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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89A ASN* 5.4 0.2 - - - +
130A ARG 3.5 4.3 + - - -
131A TYR 3.1 10.6 + - - -
133A ALA* 1.3 79.8 - - - +
135A TRP* 1.3 58.0 + - - +
136A ALA 3.3 0.7 + - - -
137A ASP* 3.7 0.4 - - - +
138A LYS* 2.8 36.3 + - - +
130C ARG 6.0 0.2 - - - -
134C GLY* 3.8 22.9 - - - -
138C LYS* 3.8 8.1 - - - -
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Residues in contact with TRP 135 (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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131A TYR* 2.8 41.5 + + - -
132A TYR* 3.0 24.9 + + + +
134A GLY* 1.3 76.2 - - - +
136A ALA* 1.3 65.8 + - - +
137A ASP 3.3 0.7 - - - -
138A LYS* 3.1 46.1 + - + -
139A TYR* 3.6 18.7 + + - +
184A ALA* 4.7 1.7 - - + +
185A THR* 6.0 1.1 - - - +
478A GLY 4.5 0.2 - - - -
479A GLU* 3.5 51.3 - - + +
482A LEU* 3.6 25.3 - - + +
135C TRP* 4.9 8.7 - + - -
138C LYS* 3.3 43.0 - - + +
140C HIS* 4.3 5.4 - + - -
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Residues in contact with ALA 136 (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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81A ALA* 3.4 24.3 - - - +
82A SER* 5.2 0.2 - - - -
84A ARG* 3.3 24.9 + - + -
85A GLY* 3.6 13.7 - - - +
132A TYR 3.5 2.4 + - - -
133A ALA* 3.4 17.2 + - - +
134A GLY 3.3 1.6 - - - -
135A TRP* 1.3 78.8 - - - +
137A ASP* 1.3 58.5 + - - +
138A LYS 3.8 0.2 + - - -
139A TYR* 4.9 2.8 + - - +
184A ALA* 3.4 26.7 - - - +
145D PRO* 4.8 1.9 - - - +
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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