Contacts of the helix formed by residues 327 - 335 (chain A) in PDB entry 5M6E
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 CYS 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ASN 4.4 1.6 - - - -
302A HIS* 4.2 1.1 - - - -
303A CYS* 3.7 23.7 - - + +
320A HIS* 3.6 1.3 - - - +
324A TYR 3.3 16.9 + - - +
325A PRO 3.3 2.3 - - - +
326A GLY* 1.3 75.6 - - - +
328A LYS* 1.3 66.4 + - - +
329A TYR* 3.4 20.0 - - - -
330A LEU* 3.4 20.2 + - + +
331A LEU* 3.2 19.9 + - - +
339A ILE* 5.6 0.2 - - - +
401A ZN 2.4 36.3 - - - -
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Residues in contact with LYS 328 (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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252A ASN 4.9 1.0 + - - -
253A SER* 2.8 29.3 + - - +
254A THR 3.3 26.0 + - - +
255A ASN* 3.4 33.2 - - - +
302A HIS* 3.8 10.3 + - + +
326A GLY* 3.3 10.6 + - - +
327A CYS* 1.3 70.9 - - - +
329A TYR* 1.3 59.9 + - - +
331A LEU* 3.3 25.8 + - + +
332A GLU* 2.9 28.9 + - - +
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Residues in contact with TYR 329 (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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263A ALA 6.0 0.4 - - - -
268A ARG* 3.7 13.1 + - - -
286A ARG 3.0 17.7 + - - -
287A ALA 4.4 2.2 - - - -
288A GLY* 3.6 21.3 - - - -
300A CYS* 4.8 0.7 - - - -
301A PHE* 3.6 31.6 - + - -
302A HIS* 3.5 32.1 + + + -
317A TRP* 3.5 21.5 - + - -
320A HIS* 4.4 7.0 - + - -
327A CYS* 3.4 3.9 - - - -
328A LYS* 1.3 76.4 - - - +
330A LEU* 1.3 64.6 + - - +
332A GLU* 3.1 17.1 + - - +
333A GLN* 3.0 51.7 + - + +
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Residues in contact with LEU 330 (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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317A TRP* 3.8 35.4 - - + +
320A HIS* 4.3 6.7 - - + +
321A ALA* 3.7 39.5 - - + +
324A TYR 3.5 24.0 - - - +
325A PRO* 4.2 12.1 - - + +
327A CYS* 3.4 17.8 + - + +
329A TYR* 1.3 80.6 - - - +
331A LEU* 1.3 56.8 + - - +
334A LYS* 3.0 40.2 + - + +
338A TYR* 4.8 1.6 - - + -
339A ILE* 3.7 20.8 - - + +
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Residues in contact with LEU 331 (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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327A CYS 3.2 10.5 + - - +
328A LYS* 3.7 28.7 - - + +
329A TYR 3.3 0.4 - - - -
330A LEU* 1.3 78.8 - - - +
332A GLU* 1.3 63.3 + - - +
335A GLY* 3.1 20.5 + - - -
336A GLN* 3.6 49.6 - - + +
339A ILE* 3.7 10.8 - - + -
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Residues in contact with GLU 332 (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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328A LYS 2.9 14.0 + - - +
329A TYR* 3.1 19.0 + - - +
331A LEU* 1.3 79.3 - - - +
333A GLN* 1.3 83.6 + - - +
335A GLY* 4.6 1.4 + - - -
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Residues in contact with GLN 333 (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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317A TRP* 3.5 28.4 - - + -
329A TYR* 3.0 48.9 + - + +
330A LEU 4.1 0.2 - - - +
332A GLU* 1.3 112.6 + - - +
334A LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 334 (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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317A TRP* 3.7 55.5 - - + +
330A LEU* 3.0 16.6 + - + +
333A GLN* 1.3 84.9 - - + +
335A GLY* 1.3 61.4 + - - +
337A GLU* 5.1 1.6 - - - +
338A TYR* 3.4 66.4 + - + +
339A ILE* 4.7 0.4 - - + -
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Residues in contact with GLY 335 (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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330A LEU 4.0 1.0 + - - -
331A LEU* 3.1 19.7 + - - -
332A GLU 4.6 1.0 + - - -
333A GLN 3.9 0.4 - - - -
334A LYS* 1.3 79.7 - - - +
336A GLN* 1.3 64.5 + - - -
337A GLU* 3.3 11.2 + - - -
338A TYR 4.1 0.4 - - - -
339A ILE* 3.0 29.3 + - - +
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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