Contacts of the helix formed by residues 253 - 261 (chain A) in PDB entry 2Q5H
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 ASN 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.4 13.9 - - + +
126A CYS* 3.0 26.5 - - - -
249A GLY* 2.6 23.3 + - - +
250A ILE 3.1 7.9 + - - +
251A PHE 3.1 0.8 - - - -
252A LEU* 1.3 80.4 - - - +
254A PHE* 1.3 63.8 + - - +
255A LYS 3.3 3.3 + - - -
256A ARG* 2.7 48.1 + - + +
257A LEU* 3.0 29.3 + - + +
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Residues in contact with PHE 254 (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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250A ILE 3.2 5.5 + - - +
251A PHE* 2.8 19.4 + - - +
252A LEU 3.4 1.4 + - - -
253A ASN* 1.3 77.1 - - - +
255A LYS* 1.3 63.2 + - + +
257A LEU* 3.7 4.8 - - - +
258A LEU* 2.9 41.3 + - + +
265A LEU* 5.6 0.2 - - + -
267A PHE* 3.6 30.3 - + - -
300A PHE* 3.8 37.5 - + - -
415A LEU* 3.6 19.5 - - + -
426A LEU* 4.0 23.1 - - + +
427A VAL 3.9 29.4 - - - -
428A ALA* 5.0 1.3 - - + -
518A PRO* 4.0 20.0 - - + -
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Residues in contact with LYS 255 (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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252A LEU 5.2 1.0 + - - +
253A ASN 3.3 0.4 - - - -
254A PHE* 1.3 80.4 - - + +
256A ARG* 1.3 69.3 + - + +
258A LEU* 3.2 6.0 + - - +
259A GLU* 2.9 27.3 + - - +
424A VAL* 4.1 18.8 - - + -
425A PRO* 3.7 32.6 + - + +
426A LEU* 3.8 14.1 - - + +
427A VAL 5.8 1.3 - - - +
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Residues in contact with ARG 256 (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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252A LEU 5.3 3.2 + - - +
253A ASN* 2.7 40.1 + - + +
255A LYS* 1.3 78.7 - - + +
257A LEU* 1.3 58.7 + - + +
259A GLU* 3.4 11.7 + - - +
260A PHE* 2.9 29.8 + - - +
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Residues in contact with LEU 257 (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 LEU* 3.8 26.4 - - + +
124A ILE* 3.5 31.9 - - + -
250A ILE* 4.2 17.7 - - + +
253A ASN* 3.0 26.1 + - + +
254A PHE* 3.7 3.8 - - - +
256A ARG* 1.3 76.1 - - + +
258A LEU* 1.3 64.6 + - - +
260A PHE* 3.2 9.3 + - + +
261A ASN* 3.0 23.4 + - - +
267A PHE* 4.0 15.9 - - + -
269A ALA* 3.4 29.4 - - + -
300A PHE* 5.4 0.2 - - + -
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Residues in contact with LEU 258 (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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254A PHE* 2.9 38.5 + - + +
255A LYS* 3.6 5.2 - - - +
257A LEU* 1.3 71.8 - - - +
259A GLU* 1.3 63.7 + - + +
261A ASN* 3.2 8.3 + - - +
263A GLY* 3.0 46.2 + - - +
264A LYS 3.4 24.2 - - - +
265A LEU* 4.7 4.7 - - + -
267A PHE* 3.7 23.5 - - + -
427A VAL 4.8 10.5 - - - +
428A ALA* 4.7 12.8 - - + -
429A GLU 5.8 1.3 - - - +
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Residues in contact with GLU 259 (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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255A LYS 2.9 16.4 + - - +
256A ARG* 3.6 10.4 - - - +
258A LEU* 1.3 79.7 - - + +
260A PHE* 1.3 57.9 + - - +
262A GLN* 2.7 29.5 + - - +
263A GLY* 3.5 4.7 + - - +
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Residues in contact with PHE 260 (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 LEU* 3.7 35.0 - - + -
256A ARG 2.9 18.5 + - - +
257A LEU* 3.2 13.4 + - + +
259A GLU* 1.3 77.9 - - - +
261A ASN* 1.3 56.7 + - - +
262A GLN* 3.2 11.1 + - - +
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Residues in contact with ASN 261 (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 LEU* 4.4 12.4 - - + +
257A LEU 3.0 12.4 + - - +
258A LEU 3.6 8.7 - - - +
259A GLU 3.0 0.8 - - - -
260A PHE* 1.3 75.5 - - - +
262A GLN* 1.3 68.5 + - - +
263A GLY 3.1 1.8 - - - -
264A LYS* 3.1 35.0 + - - +
266A PRO 3.6 5.9 + - - +
267A PHE* 3.5 29.6 - - + +
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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