Contacts of the helix formed by residues 302 - 306 (chain A) in PDB entry 5JMO
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 SER 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A HIS 5.1 0.2 - - - -
301A ASP* 1.3 79.8 + - - +
303A CYS* 1.3 57.9 + - - +
304A ASN* 3.3 20.3 + - - +
305A CYS* 3.0 26.7 + - - +
306A ASP* 4.3 1.0 + - - +
331A GLU* 3.4 3.4 - - - +
332A ALA 3.7 13.3 + - - -
333A CYS* 4.1 1.6 - - - +
515A LEU 4.4 2.8 + - - -
516A LEU* 4.0 19.6 - - - +
517A ALA* 4.7 10.7 + - - -
519A ARG* 3.7 19.1 - - - +
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Residues in contact with CYS 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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293A SER* 3.2 30.3 - - - +
302A SER* 1.3 69.9 + - - +
304A ASN* 1.3 58.2 + - - +
305A CYS 3.2 0.8 + - - -
306A ASP* 3.6 10.2 + - - +
309A THR* 2.9 24.9 + - - +
310A ASN* 4.2 0.3 - - - +
331A GLU* 3.2 37.0 + - - +
332A ALA 3.7 1.2 + - - -
333A CYS* 2.0 44.2 - - - -
335A SER* 3.8 5.5 + - - -
336A THR* 3.6 9.4 - - - -
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Residues in contact with ASN 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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302A SER* 3.0 8.1 + - - +
303A CYS* 1.3 74.4 - - - +
305A CYS* 1.3 59.1 + - - +
306A ASP 3.2 6.9 + - - -
310A ASN* 3.5 21.0 + - - +
333A CYS* 3.2 12.5 - - - +
334A SER* 2.8 26.9 + - - +
335A SER* 2.9 29.1 + - - -
515A LEU* 2.9 33.7 + - - +
531A TRP* 3.0 23.2 + - - -
533A PHE* 4.2 8.6 - - + +
534A MET 3.5 9.3 + - - +
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Residues in contact with CYS 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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256A PRO* 5.0 1.6 - - - +
262A THR 3.5 18.2 - - - +
263A VAL* 3.5 13.4 - - + -
264A ASP 3.2 25.3 + - - +
301A ASP* 4.7 0.4 - - - +
302A SER* 3.0 13.8 + - - +
304A ASN* 1.3 77.7 - - - +
306A ASP* 1.3 57.3 + - - +
516A LEU* 3.6 27.8 - - - -
519A ARG* 3.5 30.5 - - - +
528A PHE* 4.6 9.0 - - - -
531A TRP* 3.8 10.0 - - - +
533A PHE* 5.1 1.3 - - - -
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Residues in contact with ASP 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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256A PRO* 3.5 19.7 - - + +
264A ASP 3.6 2.9 - - - -
293A SER 4.5 1.4 - - - +
303A CYS* 3.8 9.2 - - - +
304A ASN 3.2 1.4 - - - -
305A CYS* 1.3 79.1 - - - +
307A GLY* 1.3 59.4 + - - +
308A TYR* 2.9 22.0 + - - +
309A THR* 3.1 22.2 + - - +
310A ASN* 3.0 30.5 + - - +
531A TRP* 4.3 0.2 - - - -
605A CA 4.6 9.2 - - - -
5G AR7 2.9 39.4 + - - +
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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