Contacts of the helix formed by residues 132 - 140 (chain A) in PDB entry 2Q41
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY* 4.1 3.0 + - - -
131A ASP* 1.3 84.8 + - - +
133A GLY* 1.3 57.7 + - - -
134A VAL 3.4 1.8 - - - -
135A LEU* 3.1 8.6 - - - +
136A ARG* 2.9 20.4 + - - +
149A MSE 3.4 26.0 - - - +
167A VAL 3.5 9.8 - - - +
170A GLY* 3.6 10.0 - - - -
171A TYR* 3.8 7.7 + - - -
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Residues in contact with GLY 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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107A GLN* 3.3 21.1 - - - -
131A ASP* 3.1 14.0 + - - -
132A GLY* 1.3 75.4 - - - +
134A VAL* 1.3 60.4 + - - +
135A LEU 3.0 1.3 - - - -
136A ARG* 2.8 15.6 + - - +
137A GLU* 2.8 33.4 + - - +
167A VAL* 3.8 9.2 + - - +
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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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106A TYR* 5.1 2.9 - - + -
107A GLN* 3.7 17.3 - - + +
110A ILE* 4.0 22.4 - - + -
111A THR* 3.1 18.6 - - - +
126A VAL* 4.6 16.6 - - + -
129A GLY* 5.6 2.7 - - - -
131A ASP* 3.8 8.5 + - - +
132A GLY 3.4 0.4 - - - -
133A GLY* 1.3 75.4 - - - +
135A LEU* 1.3 62.0 + - - +
137A GLU* 3.3 12.4 + - - +
138A VAL* 3.1 29.2 + - + +
149A MSE 6.4 0.2 - - + -
199A ILE* 4.4 14.6 - - + -
201A ASP* 4.1 25.6 - - + +
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Residues in contact with LEU 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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126A VAL* 4.6 6.2 - - + +
132A GLY* 3.1 12.2 - - - +
133A GLY 3.0 0.2 - - - -
134A VAL* 1.3 79.5 - - - +
136A ARG* 1.3 61.7 + - - +
138A VAL* 3.1 16.5 + - - +
139A ALA* 3.2 13.2 + - - +
147A ILE* 3.5 42.6 - - + +
149A MSE 3.1 40.8 - - + +
170A GLY* 3.3 28.7 - - - -
171A TYR* 3.3 7.4 - - - +
173A ASP* 5.6 0.6 - - + +
176A VAL* 3.4 25.8 - - + -
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Residues in contact with ARG 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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103A GLU* 4.3 15.5 + - - +
104A CYS* 5.6 4.2 - - - +
107A GLN* 2.6 30.0 + - - +
132A GLY 2.9 12.2 + - - +
133A GLY* 2.8 9.1 + - - +
135A LEU* 1.3 74.8 - - - +
137A GLU* 1.3 78.9 + - - +
139A ALA* 3.2 20.3 + - + +
140A ARG* 3.7 15.7 + - - +
166A ASP* 2.9 49.7 + - - +
167A VAL* 4.7 1.0 - - - +
169A ILE* 3.6 19.7 - - + -
170A GLY* 4.2 6.3 - - - -
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Residues in contact with GLU 137 (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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104A CYS* 5.6 0.8 - - - -
107A GLN* 2.7 51.8 - - + +
108A GLU* 3.5 18.3 - - - +
111A THR* 3.6 16.2 - - + +
112A HIS* 3.1 25.9 + - - +
133A GLY 2.8 15.3 + - - +
134A VAL* 3.3 9.0 - - - +
135A LEU 3.2 0.2 - - - -
136A ARG* 1.3 100.8 + - - +
138A VAL* 1.3 61.1 + - - +
140A ARG* 3.2 38.3 + - - +
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Residues in contact with VAL 138 (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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111A THR* 3.9 13.7 - - + +
115A LEU* 4.1 17.0 - - + -
124A VAL* 4.9 4.7 - - + -
126A VAL* 4.5 16.4 - - + -
134A VAL* 3.1 19.1 - - + +
135A LEU* 3.1 10.7 + - - +
137A GLU* 1.3 72.4 - - - +
139A ALA* 1.3 51.5 + - - +
140A ARG 2.7 17.2 + - - -
141A HIS* 2.8 25.6 + - - +
144A ILE* 3.9 23.6 - - + -
147A ILE* 3.4 28.0 - - + -
199A ILE* 4.8 5.6 - - + -
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Residues in contact with ALA 139 (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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135A LEU 3.2 8.5 + - - +
136A ARG* 3.2 14.3 + - + +
138A VAL* 1.3 77.2 - - - +
140A ARG* 1.3 61.1 + - - +
141A HIS 3.1 2.4 + - - +
142A ALA* 5.4 0.3 - - - -
144A ILE* 5.6 0.2 - - - -
147A ILE* 4.7 2.8 - - + +
170A GLY* 6.4 0.4 - - - -
173A ASP* 3.1 31.6 - - + +
175A ARG* 3.2 26.4 + - - +
304A ASN* 4.0 6.0 - - - +
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Residues in contact with ARG 140 (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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108A GLU* 4.6 6.2 + - - -
112A HIS* 3.5 17.0 + - + -
136A ARG* 3.7 13.3 + - - +
137A GLU* 3.2 45.4 + - - +
138A VAL 2.7 5.5 + - - -
139A ALA* 1.3 76.3 - - - +
141A HIS* 1.3 63.5 + - + +
142A ALA* 3.5 4.0 + - - +
296A ILE* 4.7 2.0 - - + -
300A SER 4.5 11.5 - - - +
301A SER* 4.3 16.8 + - - +
304A ASN* 3.0 23.2 + - - +
305A GLY* 2.8 36.5 + - - +
306A PRO 3.5 16.8 + - - -
307A LEU* 3.8 25.1 - - - +
308A LYS* 6.0 0.4 - - - +
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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