Contacts of the strand formed by residues 146 - 151 (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 GLN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LYS 3.2 2.3 + - - +
123A LYS* 3.6 23.0 - - + +
124A VAL 3.1 23.6 + - - +
144A ILE* 3.8 0.8 - - - +
145A GLU* 1.3 82.4 - - + +
147A ILE* 1.3 68.3 + - - +
148A ASP* 2.8 26.8 + - - +
175A ARG* 2.9 23.6 - - - +
176A VAL 4.7 0.2 - - - -
177A ASN* 3.0 22.6 - - + +
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Residues in contact with ILE 147 (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 VAL* 3.1 17.5 - - + +
126A VAL* 3.3 34.8 - - + -
135A LEU* 3.5 31.4 - - + +
138A VAL* 3.4 28.3 - - + -
139A ALA* 4.7 6.5 - - + +
144A ILE* 3.8 17.9 - - + -
146A GLN* 1.3 78.6 - - - +
148A ASP* 1.3 60.3 + - - +
149A MSE 3.3 2.2 + - - +
173A ASP* 5.6 1.1 - - - -
175A ARG* 3.0 10.7 + - + +
176A VAL* 4.0 12.1 - - + +
177A ASN* 2.7 34.1 + - - +
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Residues in contact with ASP 148 (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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123A LYS* 3.8 11.2 + - - -
124A VAL 3.0 10.1 + - - -
125A LEU* 3.6 19.6 - - + +
126A VAL 3.3 10.1 - - - +
146A GLN* 2.8 32.1 + - - -
147A ILE* 1.3 72.2 - - - +
149A MSE 1.3 51.4 + - - +
150A CYS* 2.6 25.1 + - - +
177A ASN* 2.9 19.4 + - - +
179A VAL* 5.7 0.9 - - + -
186A PHE* 4.2 12.0 - - + -
195A TYR* 2.5 33.7 + - + +
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Residues in contact with MSE 149 (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* 3.6 15.7 - - + -
129A GLY* 3.7 32.1 - - - +
132A GLY* 3.4 14.6 - - - +
134A VAL* 6.4 0.2 - - + -
135A LEU* 3.1 51.1 - - + +
147A ILE* 3.3 4.8 + - - +
148A ASP* 1.3 69.0 - - - +
150A CYS* 1.3 58.1 + - - +
151A GLU* 4.7 3.6 - - - -
171A TYR* 3.3 30.1 - - + -
176A VAL* 4.1 18.4 - - + -
177A ASN 3.3 4.0 + - - -
178A LEU* 3.1 22.6 - - + +
179A VAL* 3.0 25.2 + - - -
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Residues in contact with CYS 150 (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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125A LEU* 4.6 0.4 - - + -
126A VAL 2.7 11.3 + - - +
127A ILE* 3.5 15.2 - - + +
128A GLY 3.1 21.3 + - - -
129A GLY 5.2 0.7 - - - -
148A ASP 2.6 13.0 + - - +
149A MSE 1.3 70.0 - - - +
151A GLU* 1.3 56.9 + - - +
179A VAL* 3.7 12.3 - - + +
181A GLY 4.3 4.5 - - - -
182A ASP 3.7 11.9 - - - -
183A GLY* 4.2 8.0 - - - -
186A PHE* 3.4 51.1 - - + -
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Residues in contact with GLU 151 (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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76A GLN* 6.2 0.2 - - - -
92A LEU* 6.1 0.3 - - - +
128A GLY* 3.5 17.4 - - - +
129A GLY 3.9 11.2 - - - +
130A GLY* 3.1 34.7 + - - -
149A MSE 3.7 4.7 + - - -
150A CYS* 1.3 74.9 - - - +
152A ILE* 1.3 83.7 + - - +
153A ASP* 3.9 13.9 - - - +
156A VAL* 4.5 3.9 - - - +
157A VAL* 3.5 32.3 - - + -
178A LEU* 4.6 9.2 - - + -
179A VAL 3.0 8.3 + - - +
180A ILE* 3.2 6.5 - - + -
181A GLY 2.9 23.7 + - - +
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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