Contacts of the helix formed by residues 132 - 140 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY 3.1 8.7 + - - -
131B ASP* 1.3 76.8 - - - +
133B GLY* 1.3 58.9 + - - +
134B VAL 3.2 2.7 - - - -
135B LEU* 2.9 13.3 + - - +
136B ARG 2.8 26.7 + - - -
167B VAL 3.3 14.3 - - - +
168B ALA* 4.3 0.4 - - - -
170B GLY* 3.7 1.6 - - - -
171B TYR* 3.4 23.9 + - - -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLN* 3.1 25.8 - - - +
131B ASP* 2.9 18.9 + - - -
132B GLY* 1.3 78.0 - - - +
134B VAL* 1.3 61.5 + - - +
136B ARG* 3.3 5.3 + - - +
137B GLU* 3.0 26.5 + - - +
167B VAL* 3.6 12.7 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 5.1 0.4 - - + -
107B GLN* 3.9 12.3 - - + +
110B ILE* 4.0 18.6 - - + -
111B THR* 3.5 16.8 - - - +
126B VAL* 3.9 20.4 - - + -
129B GLY* 5.3 8.7 + - - +
131B ASP* 4.3 1.4 + - - +
132B GLY 3.2 1.0 - - - +
133B GLY* 1.3 75.7 - - - +
135B LEU* 1.3 57.7 + - - +
137B GLU* 3.1 4.0 + - - +
138B VAL* 2.8 34.1 + - + +
199B ILE* 3.6 28.7 - - + -
201B ASP* 3.6 26.0 - - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 4.3 9.2 - - + -
129B GLY 5.9 0.2 + - - -
132B GLY* 2.9 11.4 + - - +
134B VAL* 1.3 75.2 - - + +
136B ARG* 1.3 67.3 + - - +
138B VAL* 3.1 4.0 + - - +
139B ALA* 2.8 26.2 + - - +
147B ILE* 3.4 31.6 - - + +
149B MSE 3.4 44.6 - - + -
170B GLY* 3.5 14.4 - - - +
171B TYR* 3.5 30.5 - - + -
176B VAL* 3.7 22.7 - - + -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU* 5.7 0.2 - - - +
104B CYS* 4.8 11.3 - - - +
107B GLN* 2.6 32.0 + - - +
108B GLU* 5.5 0.2 - - - +
132B GLY 2.8 14.6 + - - +
133B GLY* 3.5 5.7 + - - +
135B LEU* 1.3 73.2 - - - +
137B GLU* 1.3 94.0 + - - +
139B ALA* 3.3 14.4 + - - +
140B ARG* 3.3 14.2 + - - +
166B ASP* 3.3 23.2 + - - +
167B VAL* 4.0 7.4 - - - +
169B ILE* 4.2 19.7 - - + -
170B GLY* 3.7 16.9 - - - +
308B LYS* 4.8 15.8 - - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLN* 3.6 19.7 - - + +
108B GLU* 3.7 6.8 - - - +
111B THR* 3.3 20.2 - - + +
112B HIS* 2.6 40.2 + - - +
133B GLY 3.0 17.4 + - - +
134B VAL 3.3 8.3 - - - +
136B ARG* 1.3 113.4 + - - +
138B VAL* 1.3 61.8 + - - +
140B ARG* 3.1 24.6 + - - +
141B HIS* 3.8 0.7 - - - -
307B LEU* 2.9 27.6 - - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR* 3.5 20.2 - - + -
115B LEU* 3.8 15.9 - - + -
124B VAL* 4.2 10.8 - - + -
126B VAL* 4.2 8.3 - - + -
134B VAL* 2.8 27.2 + - + +
135B LEU* 3.6 5.2 - - - +
137B GLU* 1.3 71.3 - - - +
139B ALA* 1.3 59.0 + - - +
141B HIS* 2.8 31.4 + - - +
144B ILE* 4.1 12.6 - - + +
147B ILE* 3.7 28.5 - - + -
199B ILE* 3.6 21.8 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU 2.8 20.5 + - - +
136B ARG* 3.3 9.6 + - - +
138B VAL* 1.3 71.6 - - - +
140B ARG* 1.3 60.1 + - - +
141B HIS* 3.0 3.9 + - - -
142B ALA* 4.5 0.5 + - - -
144B ILE* 5.6 0.2 - - - -
147B ILE* 3.6 10.0 - - + +
170B GLY 5.7 0.2 - - - +
173B ASP* 3.2 20.2 - - + +
175B ARG* 2.8 41.9 + - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B HIS* 3.9 18.4 - - + -
136B ARG* 3.3 11.2 + - - +
137B GLU* 3.1 21.3 + - - +
138B VAL 2.9 1.0 + - - -
139B ALA* 1.3 76.3 - - - +
141B HIS* 1.3 57.3 + - + +
142B ALA* 3.4 6.3 + - - +
296B ILE* 4.2 24.0 - - + +
305B GLY 2.6 33.5 + - - +
306B PRO* 3.5 12.3 + - - +
307B LEU* 2.9 44.1 - - - +
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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