Contacts of the helix formed by residues 124 - 137 (chain W) in PDB entry 2Q4G
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 LEU 124 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96W LEU* 3.9 36.8 - - + +
97W THR 4.1 2.7 - - - +
98W GLY* 3.6 21.4 + - - +
101W CYS* 3.8 28.0 - - - -
119W LEU* 4.1 26.5 - - + -
122W ASN* 3.2 14.4 + - + +
123W LEU* 1.3 74.8 - - - +
125W GLY* 1.3 69.9 + - - +
128W GLY 3.7 5.7 + - - -
129W LEU* 4.7 6.5 - - + +
132W LEU* 5.5 1.6 - - + -
148W LEU* 4.2 5.8 - - + -
151W CYS* 3.4 32.0 + - + +
153W LEU* 4.6 4.7 - - + -
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Residues in contact with GLY 125 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123W LEU* 3.7 5.4 - - - -
124W LEU* 1.3 82.8 - - - +
126W ASP* 1.3 65.8 + - - -
127W ALA 3.5 1.1 - - - -
129W LEU* 3.2 18.4 + - - +
151W CYS 2.9 10.7 + - - -
152W SER* 3.4 23.5 - - - -
153W LEU* 3.5 3.8 - - - +
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Residues in contact with ASP 126 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125W GLY* 1.3 69.6 - - - -
127W ALA* 1.3 61.1 + - - +
129W LEU* 3.8 0.3 - - - +
130W GLN* 2.8 50.9 + - - +
152W SER 4.0 2.6 + - - +
153W LEU* 3.6 1.4 - - - -
154W SER* 2.6 40.6 + - - +
156W ALA* 3.6 16.5 - - + +
157W SER* 2.7 27.8 + - - +
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Residues in contact with ALA 127 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125W GLY 3.5 0.6 - - - -
126W ASP* 1.3 77.2 - - - +
128W GLY* 1.3 58.6 + - - +
130W GLN* 3.5 13.5 + - - +
131W LEU* 3.0 30.6 + - - +
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Residues in contact with GLY 128 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W GLY* 3.9 11.8 - - - -
101W CYS* 3.2 37.5 - - - +
124W LEU 3.7 12.5 + - - -
125W GLY 3.6 2.6 + - - -
126W ASP 3.3 0.4 - - - -
127W ALA* 1.3 78.6 - - - +
129W LEU* 1.3 63.1 + - - +
131W LEU* 3.2 4.0 + - - +
132W LEU* 2.9 18.0 + - - +
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Residues in contact with LEU 129 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101W CYS* 4.2 2.6 - - - -
124W LEU* 4.4 5.6 + - + +
125W GLY 3.2 17.8 + - - +
126W ASP 3.8 2.7 - - - +
128W GLY* 1.3 76.0 - - - +
130W GLN* 1.3 64.5 + - + +
132W LEU* 2.9 18.3 + - + +
133W CYS* 2.9 38.2 + - - -
136W LEU* 5.9 0.4 - - + -
148W LEU* 3.9 29.8 - - + -
153W LEU* 3.2 26.5 - - + -
157W SER* 2.8 42.4 - - - +
161W LEU* 4.3 7.2 - - + -
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Residues in contact with GLN 130 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126W ASP* 2.8 36.5 + - - +
127W ALA* 3.8 14.5 + - - +
129W LEU* 1.3 74.3 - - - +
131W LEU* 1.3 63.1 + - - +
133W CYS* 3.4 18.6 + - - +
134W GLU* 3.6 12.0 + - - +
156W ALA* 2.7 28.1 - - - +
157W SER* 5.0 2.9 - - - -
160W PRO* 3.7 26.0 - - + +
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Residues in contact with LEU 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W GLY 4.9 5.2 - - - +
101W CYS* 4.1 3.4 - - + -
102W GLY* 3.6 38.1 - - - +
105W SER* 3.1 17.9 + - - +
127W ALA 3.0 19.7 + - - +
128W GLY* 3.4 5.8 - - - +
130W GLN* 1.3 77.9 - - - +
132W LEU* 1.3 61.3 + - - +
134W GLU* 3.2 32.0 + - + +
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Residues in contact with LEU 132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101W CYS* 4.5 8.5 - - + +
104W LEU* 3.5 25.4 - - + -
105W SER* 3.8 16.1 + - - +
108W LEU* 3.4 30.7 - - + -
117W LEU* 5.0 1.8 - - + -
119W LEU* 3.5 29.4 - - + -
124W LEU* 5.5 2.7 - - + -
128W GLY 2.9 12.1 + - - +
129W LEU* 2.9 23.6 + - + +
131W LEU* 1.3 72.0 - - - +
133W CYS* 1.3 57.8 + - - +
134W GLU 2.9 2.5 - - - -
135W GLY* 2.6 27.2 + - - -
136W LEU* 3.0 24.3 + - + -
146W LEU* 5.3 1.8 - - + -
148W LEU* 4.9 1.8 - - + -
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Residues in contact with CYS 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129W LEU* 2.9 23.6 + - - -
130W GLN 3.5 10.3 - - - +
132W LEU* 1.3 75.8 - - - +
134W GLU* 1.3 56.5 - - + +
136W LEU* 3.3 12.8 + - - +
137W LEU* 3.0 38.5 + - + +
160W PRO* 3.7 45.3 - - + +
161W LEU* 3.8 23.3 - - - -
164W VAL* 4.0 5.3 - - + +
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Residues in contact with GLU 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105W SER* 4.5 1.1 - - - +
109W ARG* 3.4 24.4 + - - +
130W GLN 3.6 9.0 + - - +
131W LEU* 3.2 29.8 + - + +
132W LEU 2.8 0.8 + - - -
133W CYS* 1.3 76.8 - - - +
135W GLY* 1.3 62.6 + - - +
137W LEU* 3.5 22.6 + - + +
138W ASP 3.8 3.3 + - - -
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Residues in contact with GLY 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105W SER* 3.2 33.8 + - - -
108W LEU* 4.8 5.2 - - - -
109W ARG* 3.9 14.3 + - - +
132W LEU 2.6 15.0 + - - -
134W GLU* 1.3 76.2 - - - +
136W LEU* 1.3 60.8 + - - +
138W ASP* 3.1 21.1 + - - +
141W CYS* 3.9 5.4 - - - +
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Residues in contact with LEU 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108W LEU* 3.3 28.7 - - + +
117W LEU* 5.3 0.2 - - + -
129W LEU* 5.9 0.4 - - + -
132W LEU* 3.0 24.5 + - + +
133W CYS* 3.6 23.8 - - - +
135W GLY* 1.3 78.1 - - - +
137W LEU* 1.3 57.4 + - - +
138W ASP 3.1 0.9 + - - -
141W CYS* 3.3 15.1 - - - +
143W LEU* 3.4 26.7 - - + -
146W LEU* 3.9 24.5 - - + -
161W LEU* 5.1 2.0 - - + -
164W VAL* 4.0 24.9 - - + -
168W LYS* 2.9 32.5 + - - -
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Residues in contact with LEU 137 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133W CYS* 3.0 26.8 + - + +
134W GLU* 3.8 13.2 - - + +
135W GLY 3.2 0.6 - - - -
136W LEU* 1.3 74.0 - - - +
138W ASP* 1.3 63.9 + - - +
139W PRO* 3.5 5.2 - - - +
163W SER* 3.5 45.3 - - - +
164W VAL* 3.7 15.9 - - + -
167W ALA* 3.7 18.5 - - + +
168W LYS* 4.3 3.9 + - - +
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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
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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