Contacts of the helix formed by residues 122 - 135 (chain A) in PDB entry 1W6J
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 GLY 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 4.4 6.7 - - - -
25A TRP* 3.7 18.2 - - - -
38A TYR* 4.2 12.4 - - - -
120A PRO 3.4 0.2 + - - -
121A ALA* 1.3 70.5 - - - +
123A TYR* 1.3 64.2 + - - +
124A ARG 3.5 2.2 - - - -
125A GLU* 3.5 21.0 + - - +
126A GLU* 3.1 26.0 + - - +
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Residues in contact with TYR 123 (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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25A TRP* 3.8 13.0 - + - -
36A TRP* 2.6 32.6 + - - +
37A THR* 5.1 1.8 - - - -
119A LEU* 3.7 17.7 - - + -
120A PRO* 3.1 53.0 + - + +
121A ALA 3.7 7.4 - - - -
122A GLY* 1.3 77.8 - - - +
124A ARG* 1.3 58.0 + - - +
126A GLU* 3.2 0.9 + - - +
127A ILE* 2.9 36.4 + - - +
366A PRO* 3.6 26.4 + - + +
369A LEU* 3.7 28.6 + - + +
376A MET* 3.5 35.0 - - + -
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Residues in contact with ARG 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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119A LEU* 4.8 7.9 - - + +
120A PRO 4.5 1.6 + - - -
122A GLY 3.5 0.2 - - - -
123A TYR* 1.3 77.7 - - - +
125A GLU* 1.3 100.3 + - - +
127A ILE* 3.9 3.2 - - - +
128A VAL* 3.1 38.0 + - + +
164A LEU* 2.7 52.3 + - + +
165A GLY* 4.6 9.3 + - - -
166A VAL* 5.2 3.8 - - - +
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Residues in contact with GLU 125 (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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19A ALA* 3.6 20.7 - - + +
20A THR* 3.8 20.2 - - + -
122A GLY* 3.5 29.1 + - - +
123A TYR 3.3 0.2 - - - -
124A ARG* 1.3 105.9 + - - +
126A GLU* 1.3 58.0 + - - +
128A VAL* 3.6 7.0 - - - +
129A ARG* 3.1 26.0 + - - +
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Residues in contact with GLU 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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18A PRO* 4.0 2.1 - - - +
19A ALA* 3.0 21.7 + - - -
20A THR* 2.6 32.1 + - + +
22A LEU* 4.5 0.2 - - - +
25A TRP* 3.8 4.7 - - + -
122A GLY 3.1 17.7 + - - +
123A TYR* 4.0 1.1 - - - +
125A GLU* 1.3 76.5 - - - +
127A ILE* 1.3 60.8 + - - +
129A ARG* 2.9 44.3 + - - +
130A TYR 2.9 23.7 + - - -
371A MET* 3.7 30.4 - - - +
375A GLY* 3.5 4.5 - - - -
376A MET* 3.2 18.4 + - + -
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Residues in contact with ILE 127 (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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105A LEU* 4.1 34.8 - - + -
108A LEU* 5.5 0.9 - - + -
109A LEU* 4.3 9.9 - - + -
119A LEU* 3.5 32.1 - - + -
123A TYR 2.9 21.2 + - - +
124A ARG* 3.9 4.0 - - - +
126A GLU* 1.3 73.4 - - - +
128A VAL* 1.3 66.2 + - - +
130A TYR* 3.2 3.1 + - - +
131A LEU* 3.0 27.5 + - + +
164A LEU* 3.7 20.6 - - + -
369A LEU* 4.7 4.9 - - + -
376A MET* 3.5 34.1 - - + +
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Residues in contact with VAL 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 ARG* 3.1 29.9 + - + +
125A GLU* 3.6 7.2 - - - +
127A ILE* 1.3 75.2 - - - +
129A ARG* 1.3 63.8 + - - +
131A LEU* 3.4 1.9 + - - +
132A ARG* 3.0 52.6 + - - +
161A LEU* 4.0 18.7 - - + +
164A LEU* 3.7 34.8 - - + +
166A VAL* 4.5 9.0 - - + -
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Residues in contact with ARG 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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16A THR* 2.9 30.9 + - - -
17A GLU 3.3 21.4 + - - +
18A PRO* 3.7 23.0 - - - +
19A ALA* 4.1 11.0 - - + +
22A LEU* 4.2 14.1 - - - +
56A LEU 5.4 0.4 + - - -
125A GLU 3.1 18.5 + - - +
126A GLU* 2.9 33.3 + - - +
127A ILE 3.2 0.4 - - - -
128A VAL* 1.3 79.3 - - - +
130A TYR* 1.3 50.9 + - - +
132A ARG* 3.5 7.9 + - - +
133A SER* 2.5 39.7 + - - +
371A MET* 4.3 3.0 - - - +
372A GLY 4.4 2.4 + - - -
373A LEU 2.7 29.3 + - - -
374A ASP 3.4 1.8 + - - -
375A GLY* 3.4 20.1 - - - +
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Residues in contact with TYR 130 (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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100A GLY 4.5 6.4 + - - -
101A PRO 4.9 2.2 + - - -
102A LEU* 3.8 13.4 - - + +
105A LEU* 3.9 18.4 - - + -
126A GLU 2.9 9.2 + - - +
127A ILE 3.5 3.4 - - - +
129A ARG* 1.3 73.5 - - - +
131A LEU* 1.3 72.5 + - + +
133A SER* 2.9 3.5 + - - -
134A VAL* 2.9 41.9 + - + +
145A ILE* 3.6 24.7 - - + +
374A ASP* 3.1 50.1 + - - +
375A GLY 4.4 0.7 - - - -
376A MET 3.3 28.9 - - - +
377A LYS* 3.5 41.5 + - + +
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Residues in contact with LEU 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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102A LEU* 5.4 2.9 - - + -
105A LEU* 3.9 23.1 - - + -
109A LEU* 4.7 2.2 - - + -
127A ILE* 3.0 31.1 + - + +
128A VAL 3.9 3.1 - - - +
130A TYR* 1.3 84.7 - - + +
132A ARG* 1.3 61.2 + - - +
134A VAL* 4.1 6.3 - - + -
135A GLN 3.1 5.5 + - - -
141A TRP* 3.0 31.0 + - + +
157A ASN* 3.2 27.1 - - + +
160A SER* 3.8 28.3 - - - -
161A LEU* 4.0 26.7 - - + -
164A LEU* 4.3 3.1 - - + -
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Residues in contact with ARG 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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128A VAL* 3.0 35.8 + - + +
129A ARG* 3.7 7.2 - - - +
131A LEU* 1.3 76.1 - - - +
133A SER* 1.3 62.3 + - - +
134A VAL 3.4 0.2 + - - -
135A GLN* 3.5 24.7 + - - +
141A TRP* 5.1 0.9 - - - -
161A LEU* 4.9 12.2 - - + +
166A VAL* 3.8 25.6 - - - +
170A ASP* 3.0 36.3 + - - -
172A ASP* 2.9 34.5 + - + +
173A LEU* 5.9 0.2 - - - +
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Residues in contact with SER 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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9A ARG* 3.6 21.0 + - - -
16A THR* 2.9 40.9 + - - +
129A ARG* 2.5 25.7 + - - +
130A TYR 2.9 5.6 + - - -
132A ARG* 1.3 78.0 - - - +
134A VAL* 1.3 59.3 + - - +
374A ASP* 3.2 20.0 + - - -
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Residues in contact with VAL 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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9A ARG* 3.1 16.6 + - - +
102A LEU* 4.1 13.1 - - + +
130A TYR* 2.9 60.5 + - + +
131A LEU* 3.9 4.3 - - + +
133A SER* 1.3 76.3 - - - +
135A GLN* 1.3 70.8 + - - +
136A LEU* 3.2 7.8 + - - +
141A TRP* 3.8 24.3 - - + +
145A ILE* 4.4 17.0 - - + -
374A ASP* 3.7 13.0 - - - +
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Residues in contact with GLN 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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9A ARG* 2.9 21.3 + - - -
131A LEU 3.1 7.0 + - - +
132A ARG* 3.5 16.8 + - - +
133A SER 4.1 1.2 - - - +
134A VAL* 1.3 74.3 - - - +
136A LEU* 1.3 67.1 + - - +
139A GLY* 2.8 37.4 + - - +
140A GLY 3.7 0.9 - - - -
141A TRP* 3.2 38.8 - - + +
161A LEU* 5.7 0.3 - - - +
172A ASP* 2.9 52.9 + - - +
175A ARG* 3.8 12.9 + - - +
176A ALA* 3.9 0.2 - - - +
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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
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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