Contacts of the strand formed by residues 122 - 126 (chain A) in PDB entry 2DH3
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 ALA 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY* 1.3 73.4 - - - -
123A LEU* 1.3 62.8 - - - +
154A LYS 4.5 5.1 + - - -
155A VAL* 3.6 19.5 - - + +
156A LYS* 3.4 21.1 + - - -
157A GLY 3.9 3.5 + - - -
357A PHE* 4.0 19.7 - - + -
363A PRO* 3.4 26.6 - - + +
365A PHE* 4.0 13.5 - - + -
422A PHE* 5.4 0.4 - - + -
426A SER* 4.8 4.6 + - - +
429A ARG* 5.1 2.2 - - - +
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Residues in contact with LEU 123 (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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117A TRP* 4.0 16.8 - - + -
118A TRP* 5.1 2.7 - - + -
121A GLY 5.3 1.1 - - - +
122A ALA* 1.3 78.7 - - - +
124A TYR* 1.3 59.5 - - - +
155A VAL* 4.9 0.4 - - - -
156A LYS* 6.0 0.4 - - + -
157A GLY* 3.3 29.4 - - - +
159A VAL* 4.5 6.7 - - + -
204A ILE* 4.1 10.1 - - + -
274A LEU* 4.4 11.2 - - + -
276A ILE* 4.3 21.8 - - + -
298A LEU* 4.8 4.7 - - + -
362A THR* 3.6 25.6 - - + -
363A PRO 2.9 10.6 + - - +
364A VAL* 3.5 22.4 - - + -
365A PHE* 2.9 32.4 + - - -
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Residues in contact with TYR 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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122A ALA 4.2 0.2 + - - -
123A LEU* 1.3 72.3 - - - +
125A ARG* 1.3 56.8 + - - +
126A ILE* 3.7 26.7 + - + -
132A PHE* 3.8 12.6 - + - -
149A TYR* 4.3 1.4 - - - -
150A LEU* 3.5 31.2 - - + -
153A LEU* 3.8 10.5 - - + -
155A VAL* 3.9 31.4 - - + -
157A GLY 3.1 7.8 + - - +
158A LEU* 3.2 7.1 - - + +
159A VAL* 2.6 32.6 + - - -
365A PHE* 3.6 8.3 - + + -
366A SER 4.6 3.8 - - - -
367A TYR* 3.5 32.3 - - + +
368A GLY 3.9 0.7 + - - -
370A GLU* 2.5 41.8 + - + -
388A MET* 4.2 1.4 - - - +
422A PHE* 5.4 5.4 - + - -
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Residues in contact with ARG 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 TYR* 1.3 72.0 - - - +
126A ILE* 1.3 61.1 + - - +
127A GLY 3.8 2.5 - - - +
159A VAL* 3.7 22.2 - - + +
245A GLN* 4.0 15.8 + - - +
300A THR* 4.4 7.3 - - - +
333A SER* 4.5 1.0 - - - -
335A SER* 3.1 27.1 + - - +
336A GLN* 3.2 26.8 + - - +
337A ALA* 3.9 5.6 - - - +
338A ARG 3.8 11.1 + - - -
364A VAL* 3.2 43.3 + - + +
365A PHE* 2.7 17.7 + - - +
366A SER* 3.1 33.1 + - - +
367A TYR* 2.8 35.0 + - - +
369A ASP* 5.3 0.4 + - - -
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Residues in contact with ILE 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 TYR* 3.7 32.8 - - + +
125A ARG* 1.3 75.5 - - - +
127A GLY* 1.3 61.4 + - - +
128A ASP 4.4 8.7 - - - +
129A LEU* 4.6 14.6 + - + +
132A PHE* 4.0 36.6 - - + -
143A LEU* 4.3 18.6 - - + -
150A LEU* 4.5 2.2 - - + -
158A LEU* 4.1 29.4 - - + -
159A VAL 2.8 20.4 + - - +
160A LEU* 3.9 5.8 - - + +
161A GLY 3.5 15.2 + - - -
367A TYR* 3.9 7.4 - - + -
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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