Contacts of the helix formed by residues 302 - 308 (chain A) in PDB entry 1CEZ
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 LYS 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLU* 2.6 43.6 + - - +
201A TRP* 3.5 37.0 - - + -
202A SER 5.9 0.9 - - - +
301A SER* 1.3 73.2 - - - +
303A LYS* 1.3 61.2 + - + +
305A LEU* 3.1 6.0 + - + +
306A MET* 2.9 56.7 + - + +
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Residues in contact with LYS 303 (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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300A HIS* 4.2 1.9 + - - -
301A SER* 3.1 24.6 + - - -
302A LYS* 1.3 79.6 - - + +
304A ALA* 1.3 61.7 + - - +
306A MET* 3.1 22.0 + - - +
307A ARG* 3.4 15.5 + - - +
738A GLU* 5.6 0.2 - - - -
740A LYS* 3.7 25.3 - - - +
764A ASN 5.7 2.2 + - - -
766A ASP* 3.9 16.0 + - - +
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Residues in contact with ALA 304 (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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299A THR* 3.7 15.2 - - + +
300A HIS* 3.6 10.1 - - - +
301A SER* 3.1 16.7 + - - +
303A LYS* 1.3 79.2 - - - +
305A LEU* 1.3 60.8 + - - +
307A ARG* 3.5 32.5 + - - +
308A TYR* 3.7 12.1 - - - -
736A TRP* 5.0 0.7 - - - -
738A GLU* 3.3 22.4 + - - +
1T T 4.8 4.0 - - - +
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Residues in contact with LEU 305 (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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200A ALA* 5.1 1.8 - - + +
201A TRP* 4.1 21.3 - - + +
281A ILE* 3.1 39.7 - - + +
282A THR* 4.2 17.9 - - + -
295A ALA* 4.3 6.7 - - + -
297A VAL* 3.8 37.2 - - + +
299A THR* 3.4 18.3 + - - +
301A SER 3.2 3.4 + - - +
302A LYS* 3.1 10.2 + - + +
304A ALA* 1.3 73.7 - - - +
306A MET* 1.3 71.8 + - - +
307A ARG 3.1 2.2 - - - -
308A TYR* 2.9 18.8 + - + -
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Residues in contact with MET 306 (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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281A ILE* 3.9 16.4 - - - -
302A LYS* 2.9 45.1 + - + +
303A LYS* 3.4 11.7 - - - +
305A LEU* 1.3 81.1 - - - +
307A ARG* 1.3 62.5 + - - +
309A GLU* 2.9 52.9 + - - +
310A ASP 4.7 0.3 + - - -
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Residues in contact with ARG 307 (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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303A LYS* 3.4 10.4 + - - +
304A ALA* 3.5 29.5 + - - +
305A LEU 3.0 0.6 + - - -
306A MET* 1.3 77.3 - - - +
308A TYR* 1.3 59.0 + - - +
309A GLU 3.3 0.2 - - - -
310A ASP 4.6 2.4 + - - -
311A VAL* 3.1 16.2 - - - +
736A TRP* 3.4 64.4 - - + +
738A GLU* 2.8 35.0 + - - +
740A LYS* 6.1 0.2 - - - +
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Residues in contact with TYR 308 (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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281A ILE* 4.3 11.5 - - + +
296A LEU* 5.6 2.7 - - + -
297A VAL* 4.1 25.9 - - + +
299A THR* 4.6 4.5 - - + -
304A ALA 3.7 13.0 - - - -
305A LEU* 2.9 20.9 + - + +
307A ARG* 1.3 76.5 - - - +
309A GLU* 1.3 66.1 + - - +
310A ASP 3.1 3.2 + - - -
311A VAL* 3.2 20.5 + - + +
313A MET* 4.3 17.7 - - + +
317A TYR* 4.9 8.1 + - - +
422A TRP* 3.9 6.9 + - - -
733A PHE* 3.6 30.9 - + - -
734A PRO* 2.6 48.0 + - + -
735A VAL* 3.6 5.2 - - - -
736A TRP* 3.2 26.4 + + - -
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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