Contacts of the helix formed by residues 252 - 255 (chain A) in PDB entry 1Q2L
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 PHE 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.7 7.2 - - + -
51A ASN* 2.9 17.2 + - - -
53A MET* 3.6 26.6 - - + +
55A VAL* 4.7 5.2 - - + -
68A SER* 3.7 21.5 - - - -
69A ALA 4.4 2.2 - - - -
70A LEU* 4.2 16.6 - - + -
142A VAL* 3.6 20.0 - - + -
145A LEU* 4.0 24.9 - - + -
146A ALA* 3.8 21.8 - - + -
233A ALA* 3.9 21.5 - - + -
235A ILE* 3.9 20.2 - - + -
248A ALA* 3.1 9.3 + - - +
251A THR* 1.3 86.4 + - - +
253A GLY* 1.3 58.9 + - - +
255A VAL* 3.1 18.4 + - + +
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 6.0 0.4 - - - -
49A LEU* 3.7 11.0 - - - +
50A ASP 6.0 0.2 - - - -
51A ASN* 3.2 22.7 + - - +
248A ALA 3.0 10.5 + - - -
249A ALA* 3.2 20.6 + - - -
251A THR 3.0 2.0 - - - -
252A PHE* 1.3 78.2 - - - +
254A ARG* 1.3 58.5 + - - +
255A VAL 3.9 1.2 - - - +
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Residues in contact with ARG 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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99A LYS* 5.3 8.9 - - - +
100A LYS* 4.4 22.6 - - - +
143A ASP* 4.6 8.4 + - - -
146A ALA* 5.4 0.4 - - - -
147A ASP* 2.7 34.4 + - - +
150A ALA* 4.1 14.9 - - + +
151A GLU* 4.9 10.3 + - - +
249A ALA 5.0 1.1 - - - +
250A ASP 3.3 24.2 - - - +
251A THR* 3.0 15.8 + - - +
253A GLY* 1.3 77.2 - - - +
255A VAL* 1.3 64.2 + - - +
256A PRO* 3.2 8.5 - - - +
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Residues in contact with VAL 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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51A ASN* 2.9 28.7 + - - +
53A MET* 3.9 12.6 - - + -
146A ALA* 3.9 22.9 - - - +
149A ILE* 4.2 15.0 - - + +
150A ALA* 3.8 6.7 - - + -
226A TYR 4.7 2.7 - - - +
228A ALA* 3.4 17.3 - - + +
231A MET* 3.9 22.9 - - + -
251A THR 4.8 0.2 - - - +
252A PHE* 3.1 25.0 + - + +
253A GLY 3.9 0.7 - - - +
254A ARG* 1.3 75.9 - - - +
256A PRO* 1.3 80.6 - - + +
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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