Contacts of the helix formed by residues 250 - 255 (chain A) in PDB entry 3QJQ
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 ILE 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.7 26.0 - - + -
246A ILE* 3.2 13.8 + - + +
248A TYR 3.8 0.4 - - - -
249A THR* 1.3 93.1 - - - +
251A LEU* 1.3 66.5 + - - +
252A PRO* 3.4 1.7 - - - +
253A LYS* 3.2 15.5 + - - +
254A GLN* 3.2 26.3 - - - +
403A TRP* 3.7 40.4 - - + +
506A LEU* 4.6 7.0 - - + -
507A PRO* 3.6 30.1 - - + +
508A PHE* 4.0 15.7 - - + -
509A ALA 4.8 0.2 - - - +
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Residues in contact with LEU 251 (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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246A ILE* 3.1 13.8 + - + +
247A ILE* 3.4 37.2 - - + +
250A ILE* 1.3 76.0 - - - +
252A PRO* 1.4 71.3 - - + +
253A LYS 3.1 0.5 + - - -
254A GLN* 3.2 8.0 + - + -
255A ALA* 2.9 21.5 + - - +
316A VAL* 4.8 0.7 - - + -
320A LEU* 4.2 24.5 - - + -
345A ALA 4.2 2.9 - - - +
346A PHE* 4.0 34.1 - - + +
349A PRO* 4.0 31.9 - - + -
350A VAL* 4.3 6.1 - - + -
353A LEU* 5.3 1.1 - - + -
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Residues in contact with PRO 252 (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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247A ILE 3.0 26.2 - - - +
248A TYR* 3.4 23.6 - - - +
250A ILE 3.7 2.2 - - - +
251A LEU* 1.4 84.3 - - + +
253A LYS* 1.3 60.7 + - - +
255A ALA* 3.5 10.2 - - + +
257A GLY 2.8 28.9 + - - +
258A LYS 3.8 4.0 - - - +
259A LEU* 3.6 31.9 - - + +
316A VAL* 6.5 0.2 - - + -
319A SER* 4.3 16.2 - - - +
320A LEU* 5.8 2.2 - - + -
323A ALA* 4.8 0.8 - - + +
509A ALA* 3.9 7.4 - - + -
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Residues in contact with LYS 253 (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 3.6 + - - +
251A LEU 3.1 1.2 + - - -
252A PRO* 1.3 77.5 - - - +
254A GLN* 1.3 60.8 + - - +
256A GLY* 2.9 22.7 + - - -
257A GLY 3.8 9.2 - - - +
507A PRO* 3.4 40.4 - - + +
508A PHE 3.5 20.2 + - - +
509A ALA* 4.1 10.2 - - - +
510A GLU* 4.9 19.4 + - + +
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Residues in contact with GLN 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 22.9 - - - +
251A LEU* 3.2 8.4 + - + +
253A LYS* 1.3 75.0 - - + +
255A ALA* 1.3 58.3 + - - +
256A GLY* 3.1 1.7 + - - -
327A ARG* 5.1 1.7 + - - -
340A PRO* 3.0 24.1 - - - +
343A ASN* 4.3 21.5 + - - +
345A ALA* 3.7 14.1 - - - +
346A PHE* 5.0 9.9 - - + +
403A TRP* 3.2 37.4 + - - +
507A PRO* 3.7 26.9 - - + +
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Residues in contact with ALA 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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251A LEU 2.9 16.5 + - - +
252A PRO* 3.5 10.5 - - + +
253A LYS 3.1 0.4 - - - -
254A GLN* 1.3 78.7 - - - +
256A GLY* 1.3 54.0 + - - +
257A GLY 3.3 2.2 - - - -
320A LEU* 3.4 32.5 - - + -
323A ALA* 3.3 19.4 - - + +
327A ARG* 3.4 15.0 - - - +
339A LEU* 3.8 5.4 - - - +
340A PRO* 3.9 13.3 - - - +
346A PHE* 4.2 7.6 - - + -
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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