Contacts of the helix formed by residues 315 - 324 (chain F) in PDB entry 4EC4
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283F GLN* 4.5 1.9 - - - +
313F SER 3.3 6.5 + - - +
314F GLU* 1.3 69.7 - - - +
316F PRO* 1.4 75.8 - - - +
317F TRP* 3.2 16.4 + - - +
318F GLU* 3.5 40.8 + - - +
319F GLN* 3.4 19.6 + - - +
338F TYR* 4.0 6.4 + - - -
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Residues in contact with PRO 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F VAL* 4.4 5.2 - - + -
280F ASN* 5.5 1.1 - - + -
283F GLN* 3.7 36.3 - - + +
284F LEU* 3.6 41.5 - - + +
287F ALA* 4.4 6.5 - - + -
289F PHE* 3.8 7.8 - - + -
310F TRP* 3.8 13.4 - - + -
314F GLU 3.3 6.9 - - - +
315F ASP* 1.4 90.5 - - - +
317F TRP* 1.3 62.9 + - - +
319F GLN* 3.6 2.4 + - - +
320F HIS* 3.4 21.7 + - - +
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Residues in contact with TRP 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F GLN* 3.0 36.4 + - - +
286F ARG* 3.2 33.1 - - + +
287F ALA* 3.4 26.5 - - + +
315F ASP* 3.2 11.0 + - - +
316F PRO* 1.3 76.9 - - + +
318F GLU* 1.3 66.6 - - - +
320F HIS* 3.2 13.5 + - - +
321F ALA* 3.3 10.7 + - - +
329F TYR* 4.4 2.2 - + - -
330F LEU* 4.1 24.9 - - + +
333F GLN* 3.6 33.4 - - + -
334F LYS* 3.6 42.2 - - + -
338F TYR* 3.2 19.9 + + + +
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Residues in contact with GLU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F GLU* 5.3 1.4 - - - +
315F ASP* 3.5 36.9 + - - +
317F TRP* 1.3 76.8 - - - +
319F GLN* 1.3 72.0 + - - +
321F ALA* 3.2 7.3 + - - +
322F LYS* 2.9 25.1 + - + +
338F TYR* 3.0 14.1 + - - +
342F ILE* 3.8 25.7 - - + +
346F HIS* 3.4 25.4 + - - +
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Residues in contact with GLN 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A 0O6 3.0 30.8 - - - +
307F LEU* 3.8 21.0 - - + +
310F TRP* 3.7 18.8 - - + -
314F GLU* 3.5 31.2 + - - +
315F ASP 3.4 14.1 + - - +
316F PRO 4.1 0.9 - - - +
317F TRP 3.3 0.6 - - - -
318F GLU* 1.3 91.2 + - - +
320F HIS* 1.3 59.7 - - - +
322F LYS* 3.5 16.9 - - - +
323F TRP* 2.9 45.0 + - + +
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Residues in contact with HIS 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F ALA* 3.1 27.1 + - - +
289F PHE* 3.5 23.8 - + + -
300F CYS* 3.2 14.3 - - + +
303F CYS* 4.5 0.2 - - - -
307F LEU* 4.3 1.9 - - - +
316F PRO 3.4 11.6 + - - +
317F TRP* 3.2 12.9 + - - +
319F GLN* 1.3 77.0 - - - +
321F ALA* 1.3 61.8 + - - +
324F TYR* 3.2 35.6 + + + +
327F CYS* 3.9 8.7 - - + -
329F TYR* 4.1 8.2 - + - -
330F LEU* 3.4 23.6 - - + +
401F ZN 2.1 37.0 - - - -
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F TRP 3.3 1.4 + - - +
318F GLU 3.2 8.6 + - - +
319F GLN 3.2 0.2 - - - -
320F HIS* 1.3 77.5 - - - +
322F LYS* 1.3 67.3 + - - +
325F PRO* 3.3 19.1 - - - +
330F LEU* 3.5 18.3 - - + +
338F TYR* 4.0 18.2 - - + -
339F ILE* 4.1 13.7 - - + -
342F ILE* 3.9 21.3 - - + -
343F HIS* 3.4 11.4 + - - -
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Residues in contact with LYS 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.5 40.2 - - + +
402A 0O6 5.1 0.9 - - - -
403A P33 4.4 2.3 - - - +
318F GLU* 2.9 14.5 + - + +
319F GLN* 3.1 23.9 + - - +
321F ALA* 1.3 79.1 - - - +
323F TRP* 1.3 101.3 + - + +
325F PRO* 3.8 1.7 - - - +
342F ILE* 4.1 9.6 - - + +
343F HIS* 3.3 23.5 + - + -
346F HIS* 3.0 53.6 + - + +
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Residues in contact with TRP 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASN* 4.0 22.0 - - + -
250A PHE* 3.8 29.2 - + + -
402A 0O6 3.4 95.1 + + + -
403A P33 3.6 22.9 - - - +
307F LEU* 3.6 19.5 - - + -
319F GLN* 2.9 33.8 + - - +
322F LYS* 1.3 103.2 - - + +
324F TYR* 1.3 91.1 + - + +
325F PRO* 3.5 2.5 - - - -
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Residues in contact with TYR 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A 0O6 3.6 42.2 + + + +
403A P33 5.5 4.5 - - - -
251F PRO* 3.8 25.8 - - + -
289F PHE* 5.6 0.7 - + - -
303F CYS* 4.1 15.9 - - + -
305F GLY* 3.2 33.2 - - - -
306F GLY 2.8 27.2 + - - -
307F LEU* 3.7 22.4 - - + -
320F HIS* 3.2 33.6 + + + +
323F TRP* 1.3 99.8 - - + +
325F PRO* 1.3 64.9 - - - +
326F GLY 3.2 2.9 - - - -
327F CYS* 3.0 20.4 + - + +
330F LEU* 3.8 1.6 - - - +
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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