Contacts of the helix formed by residues 315 - 324 (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 ASP 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A GLN* 4.6 11.0 + - - +
310A TRP* 4.0 1.3 - - - -
313A SER 3.8 3.5 + - - +
314A GLU* 1.3 71.7 - - - +
316A PRO* 1.3 76.5 - - - +
317A TRP* 3.1 15.1 + - - +
318A GLU* 3.0 52.4 + - + +
319A GLN* 2.9 26.1 + - - +
338A TYR* 4.1 1.2 + - - -
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Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.8 13.2 - - + -
283A GLN* 3.9 31.4 - - + +
284A LEU* 3.8 32.1 - - + +
287A ALA* 3.7 20.6 - - + -
289A PHE* 3.6 6.1 - - + -
310A TRP* 3.7 12.3 - - + -
314A GLU 3.8 6.5 - - - +
315A ASP* 1.3 92.5 - - - +
317A TRP* 1.3 56.5 + - + +
319A GLN* 3.5 1.2 + - - +
320A HIS* 3.0 29.1 + - - +
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Residues in contact with TRP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLN* 5.6 3.8 - - + -
286A ARG* 3.3 24.5 + - - +
287A ALA* 3.5 28.8 - - + +
315A ASP* 3.1 9.1 + - - +
316A PRO* 1.3 75.3 - - + +
318A GLU* 1.3 66.4 + - - +
320A HIS* 3.3 10.2 + - - +
321A ALA* 3.0 23.2 + - - +
329A TYR* 3.5 19.7 - + - -
330A LEU* 3.8 33.6 - - + +
333A GLN* 3.5 30.5 - - + -
334A LYS* 3.7 36.5 - - + +
338A TYR* 3.4 19.3 + - + +
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Residues in contact with GLU 318 (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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315A ASP* 3.0 38.4 + - + +
317A TRP* 1.3 76.2 - - - +
319A GLN* 1.3 61.3 + - - +
321A ALA* 3.3 4.0 + - - +
322A LYS* 2.8 27.7 + - - +
338A TYR* 3.4 14.1 + - - +
342A ILE* 3.6 26.4 - - + +
346A HIS* 3.7 24.1 + - + +
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Residues in contact with GLN 319 (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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307A LEU* 3.9 18.9 - - + +
310A TRP* 3.8 17.9 - - + -
314A GLU* 4.0 24.3 + - + +
315A ASP 2.9 20.9 + - - +
316A PRO 4.0 2.0 - - - +
318A GLU* 1.3 77.9 + - - +
320A HIS* 1.3 66.4 + - - +
322A LYS* 4.1 18.6 + - - +
323A TRP* 3.1 53.7 + - - +
346A HIS* 4.8 6.5 + - - -
404A 7HT 3.3 22.1 + - + -
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Residues in contact with HIS 320 (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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287A ALA 2.8 29.0 + - - -
289A PHE* 3.5 18.2 - + + -
300A CYS* 3.3 16.7 - - + +
303A CYS* 3.6 1.4 - - - -
307A LEU* 4.3 2.4 - - - +
316A PRO 3.0 18.1 + - - +
317A TRP* 3.4 21.0 - + + +
319A GLN* 1.3 76.6 - - - +
321A ALA* 1.3 56.7 + - - +
324A TYR* 2.9 47.8 + + + -
327A CYS* 3.6 10.7 - - + -
329A TYR* 4.4 7.9 - + - -
330A LEU* 4.4 5.8 - - + -
401A ZN 2.1 36.1 - - - -
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Residues in contact with ALA 321 (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 3.0 12.7 + - - +
318A GLU 3.6 7.0 - - - +
320A HIS* 1.3 74.3 - - - +
322A LYS* 1.3 65.6 + - - +
323A TRP 3.4 0.2 + - - -
325A PRO 3.5 10.9 - - - -
330A LEU* 3.7 26.3 - - + +
338A TYR* 4.7 5.4 - - + -
339A ILE* 4.7 5.8 - - + -
342A ILE* 3.8 20.4 - - + -
343A HIS* 3.0 27.2 - - + -
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Residues in contact with LYS 322 (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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318A GLU 2.8 20.0 + - - +
319A GLN* 3.2 19.5 + - - +
321A ALA* 1.3 74.7 - - - +
323A TRP* 1.3 96.1 + - + +
325A PRO* 4.0 6.2 - - - +
342A ILE* 4.6 0.6 - - - +
343A HIS* 4.7 5.9 + - - -
346A HIS* 3.8 46.6 + - + +
349A GLU* 5.7 0.4 + - - -
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Residues in contact with TRP 323 (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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307A LEU* 3.6 14.8 - - + -
319A GLN* 3.1 46.3 + - - +
322A LYS* 1.3 103.7 - - + +
324A TYR* 1.3 91.5 + - + +
325A PRO* 3.4 10.5 - - - +
404A 7HT 3.5 63.3 + + + +
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Residues in contact with TYR 324 (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 PRO* 4.3 23.8 - - + -
289A PHE* 5.5 1.1 - + - -
303A CYS* 3.8 20.0 - - + -
305A GLY* 3.5 28.0 - - - -
306A GLY 2.5 41.0 + - - -
307A LEU* 3.8 13.0 - - + -
320A HIS* 2.9 27.9 + + + +
323A TRP* 1.3 95.0 - - + +
325A PRO* 1.3 65.1 - - - +
326A GLY 3.2 4.5 + - - -
327A CYS* 3.3 15.3 + - + +
330A LEU* 3.5 4.3 - - - +
403A DMS 3.8 13.7 + - + +
404A 7HT 3.4 20.2 - - + +
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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