Contacts of the strand formed by residues 146 - 151 (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 GLN 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LYS 3.2 4.8 + - - +
123B LYS* 3.4 36.8 + - + +
124B VAL 3.1 24.8 + - - +
144B ILE* 3.6 4.2 - - - +
145B GLU* 1.3 83.0 - - + +
147B ILE* 1.3 67.1 + - - +
148B ASP* 3.2 23.0 - - - +
175B ARG* 3.5 13.9 - - - +
177B ASN* 4.1 14.7 + - + +
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Residues in contact with ILE 147 (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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124B VAL 3.3 7.9 - - - +
126B VAL* 4.2 5.8 - - + -
135B LEU* 3.4 30.3 - - + +
138B VAL* 3.7 19.7 - - + -
139B ALA* 3.6 40.2 - - + +
144B ILE* 3.5 22.0 - - + -
146B GLN* 1.3 72.7 - - - +
148B ASP* 1.3 62.4 + - - +
173B ASP* 4.8 0.2 - - - +
175B ARG* 2.8 21.7 + - + +
176B VAL* 3.3 18.7 - - + +
177B ASN* 2.6 33.6 + - - -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 4.4 4.5 - - - +
124B VAL 2.7 14.4 + - - +
125B LEU* 3.6 21.3 - - + -
126B VAL* 2.7 36.6 + - - +
146B GLN* 3.2 30.1 - - - +
147B ILE* 1.3 73.9 - - - +
149B MSE 1.3 57.8 + - - +
177B ASN* 3.7 18.4 + - - +
186B PHE* 3.4 13.3 - - + -
195B TYR* 2.7 28.8 + - + +
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Residues in contact with MSE 149 (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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125B LEU* 4.9 0.9 - - - -
126B VAL* 3.3 18.8 - - + +
128B GLY 4.9 0.2 - - - -
129B GLY* 3.2 51.6 - - - +
130B GLY* 4.2 0.9 - - - +
135B LEU* 3.4 39.5 - - + -
148B ASP* 1.3 74.1 - - - +
150B CYS* 1.3 64.0 + - - +
151B GLU* 5.1 4.9 - - + -
157B VAL* 5.5 0.2 - - + -
171B TYR* 3.3 28.5 - - + +
176B VAL* 5.0 1.1 - - + -
177B ASN 3.0 12.3 + - - +
178B LEU* 3.7 24.0 - - + -
179B VAL* 2.7 37.4 + - - +
186B PHE* 5.6 1.1 - - - -
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Residues in contact with CYS 150 (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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125B LEU* 4.7 0.9 - - + -
126B VAL 3.0 13.0 + - - +
127B ILE* 3.9 16.7 - - + +
128B GLY* 3.0 21.9 + - - -
149B MSE 1.3 76.4 - - - +
151B GLU* 1.3 59.9 + - - +
152B ILE 4.0 1.2 + - - -
179B VAL* 3.4 7.4 - - - -
181B GLY* 3.8 18.5 - - - +
182B ASP 3.8 2.2 - - - -
183B GLY* 3.7 20.6 + - - -
186B PHE* 3.6 42.6 - - + -
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Residues in contact with GLU 151 (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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128B GLY* 3.9 13.3 - - - -
129B GLY 4.9 5.8 - - - +
130B GLY* 3.4 28.9 + - - +
149B MSE 4.0 4.8 - - + -
150B CYS* 1.3 73.4 - - - +
152B ILE* 1.3 82.2 + - - +
153B ASP* 3.2 32.4 + - - +
156B VAL* 4.0 13.0 - - - +
157B VAL* 3.7 22.9 - - + -
178B LEU* 5.0 4.7 - - + -
179B VAL 2.9 9.4 + - - +
180B ILE* 3.1 13.7 - - + +
181B GLY 3.1 16.5 + - - -
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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