Contacts of the helix formed by residues 295 - 302 (chain A) in PDB entry 4X61
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A PRO 3.5 4.1 + - - +
294A PRO* 1.3 76.3 - - - +
296A ALA* 1.3 64.9 + - - +
297A TYR* 3.1 14.1 + - - +
298A GLU* 2.7 71.0 + - - +
299A LEU* 3.1 11.9 + - - +
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Residues in contact with ALA 296 (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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295A ASN* 1.3 75.5 - - - +
297A TYR* 1.3 62.6 + - - +
299A LEU* 3.5 15.8 + - - +
300A PHE* 3.7 20.8 - - - -
331A PRO* 5.5 5.4 - - + -
575A GLY* 4.0 21.2 - - - +
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Residues in contact with TYR 297 (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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295A ASN* 3.1 12.2 + - - +
296A ALA* 1.3 78.1 - - - +
298A GLU* 1.3 63.6 - - + +
299A LEU 3.2 1.0 + - - -
300A PHE* 3.3 5.0 + - - +
301A ALA* 2.9 43.8 + - + +
505A ARG* 2.9 35.0 + - - -
572A HIS* 3.8 24.2 + + - -
575A GLY* 3.9 18.3 - - - +
576A MET 3.3 33.7 - - - -
577A PHE* 3.9 15.7 - - + +
579A TRP 4.0 7.8 + - - -
580A PHE* 3.4 21.8 - + - -
581A PRO* 4.4 0.2 - - - +
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Residues in contact with GLU 298 (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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259A LYS* 4.1 20.4 + - - -
292A PRO 5.6 1.0 - - - +
293A PRO 5.1 0.3 - - - +
294A PRO* 3.7 18.0 - - + +
295A ASN* 2.7 52.0 + - - +
297A TYR* 1.3 78.7 - - + +
299A LEU* 1.3 62.3 + - - +
301A ALA* 4.0 9.0 - - + -
302A LYS* 3.3 26.2 + - - +
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Residues in contact with LEU 299 (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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294A PRO* 3.8 28.9 - - + +
295A ASN 3.1 14.6 + - - +
296A ALA* 3.7 14.4 - - - +
297A TYR 3.2 0.4 - - - -
298A GLU* 1.3 79.7 - - - +
300A PHE* 1.3 68.2 + - + +
302A LYS* 4.0 10.7 + - - +
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Residues in contact with PHE 300 (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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296A ALA* 3.7 13.0 - - + -
297A TYR 3.3 4.2 + - - +
299A LEU* 1.3 83.1 - - + +
301A ALA* 1.3 63.3 + - - +
302A LYS 3.3 3.7 + - - +
304A TYR* 3.6 21.0 - - - -
326A VAL* 5.4 5.4 - - + -
329A LYS* 4.7 22.0 - - + -
331A PRO* 5.8 2.2 - - + -
577A PHE* 3.5 63.9 - + + -
702A 3XV 3.8 11.7 - - - +
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Residues in contact with ALA 301 (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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297A TYR* 2.9 42.2 + - + +
298A GLU* 4.2 5.8 - - + -
300A PHE* 1.3 76.3 - - - +
302A LYS* 1.3 63.6 - - - +
304A TYR* 3.0 24.6 + - - +
305A GLU* 4.1 5.6 + - - +
505A ARG* 4.3 9.7 - - + +
577A PHE* 5.2 0.6 - - + +
580A PHE* 4.0 22.0 - - + -
702A 3XV 4.6 0.2 - - - -
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Residues in contact with LYS 302 (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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261A GLU* 2.7 31.5 + - - -
294A PRO* 6.1 3.6 - - + -
298A GLU 3.3 20.2 + - - +
299A LEU* 4.2 9.4 - - - +
300A PHE 3.3 7.3 - - - +
301A ALA* 1.3 77.7 - - - +
303A GLY* 1.3 60.7 + - - +
304A TYR* 4.5 2.9 - - - -
305A GLU* 3.8 22.6 + - - +
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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