Contacts of the strand formed by residues 123 - 127 (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 LYS 123 (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* 1.3 73.8 - - + +
124A VAL* 1.3 59.5 + - - +
145A GLU* 5.4 3.1 - - + +
146A GLN* 3.6 23.7 - - + +
148A ASP* 3.8 17.3 + - - +
194A SER* 3.0 39.5 - - - +
195A TYR* 3.6 26.5 - - + -
196A ASP* 2.6 44.5 + - - +
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Residues in contact with VAL 124 (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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115A LEU* 4.3 14.1 - - + -
121A PRO* 4.2 14.1 - - + -
123A LYS* 1.3 78.3 - - - +
125A LEU* 1.3 70.2 + - - +
126A VAL* 4.9 4.3 - - + -
138A VAL* 4.9 4.7 - - + -
144A ILE* 3.3 34.5 - - + -
146A GLN 3.1 7.2 + - - +
147A ILE* 3.1 18.2 - - + +
148A ASP* 3.0 21.8 + - - -
195A TYR* 4.0 5.3 - - - -
197A ALA* 3.4 27.8 - - + +
199A ILE* 4.4 10.3 - - + -
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Residues in contact with LEU 125 (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* 1.3 75.8 - - - +
126A VAL* 1.3 64.4 + - - +
127A ILE* 3.7 32.8 - - + -
148A ASP* 3.6 20.4 - - + +
150A CYS* 4.6 0.7 - - + -
186A PHE* 3.5 19.5 - - + -
187A LEU* 3.8 24.5 - - + -
195A TYR* 3.3 42.7 - - + +
197A ALA 2.9 11.8 + - - +
198A VAL* 4.0 14.6 - - + -
199A ILE* 3.1 26.2 + - - +
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Residues in contact with VAL 126 (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* 4.9 3.6 - - + -
125A LEU* 1.3 78.9 - - - +
127A ILE* 1.3 62.0 + - - +
128A GLY 4.0 0.3 + - - -
129A GLY* 4.4 21.7 + - - +
134A VAL* 4.6 17.7 - - + -
135A LEU* 4.6 5.2 - - + +
138A VAL* 4.5 16.2 - - + -
147A ILE* 3.3 30.1 - - + -
148A ASP 3.3 6.4 + - - +
149A MSE 4.2 16.8 - - + -
150A CYS* 2.7 32.9 + - - +
199A ILE* 3.7 14.1 - - + +
201A ASP* 5.3 2.0 - - + -
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Residues in contact with ILE 127 (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* 3.7 30.7 - - + -
126A VAL* 1.3 76.1 - - - +
128A GLY* 1.3 60.5 + - - +
129A GLY 3.6 0.7 - - - -
150A CYS* 3.5 17.7 - - + +
183A GLY* 4.2 28.9 - - - +
186A PHE* 5.5 1.8 - - + -
187A LEU* 4.3 16.6 - - + -
198A VAL* 5.1 3.8 - - + -
199A ILE 2.9 14.7 + - - +
200A VAL* 3.6 15.4 - - + -
201A ASP* 2.7 34.8 + - - +
202A SER* 5.7 0.7 - - - +
212A LEU* 4.9 13.5 - - + -
217A PHE* 4.3 9.6 - - + -
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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