Contacts of the helix formed by residues 303 - 317 (chain F) in PDB entry 4R8A
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 ARG 303 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276F ASP* 3.3 41.0 + - - +
279F GLN* 3.5 25.0 + - - +
298F LEU* 2.8 32.8 + - + +
301F GLY* 3.5 13.9 - - - +
302F GLU* 1.3 74.7 - - - +
304F PHE* 1.3 63.4 + - - +
305F ALA 3.4 2.2 - - - -
306F GLU* 2.7 49.9 + - - +
307F ALA* 3.1 20.6 + - - +
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Residues in contact with PHE 304 (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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299F GLU* 3.8 27.4 - - + -
302F GLU* 3.6 42.2 - - + -
303F ARG* 1.3 69.1 - - - +
305F ALA* 1.3 61.2 + - - +
307F ALA* 3.2 7.2 + - - +
308F HIS* 2.8 31.9 + - - +
334F LEU* 3.7 17.6 - - + +
337F LYS* 3.5 58.3 - - + -
338F LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ARG 3.4 0.4 - - - -
304F PHE* 1.3 78.2 - - - +
306F GLU* 1.3 60.8 + - + +
308F HIS* 3.4 3.3 + - - +
309F ALA* 3.1 26.5 + - - +
338F LEU* 4.0 22.6 - - + +
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Residues in contact with GLU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F GLN* 5.7 0.5 + - - -
283F ARG* 5.8 3.1 + - - +
298F LEU* 3.8 15.8 - - + +
303F ARG* 2.7 60.8 + - - +
304F PHE 3.2 0.4 - - - -
305F ALA* 1.3 78.9 - - + +
307F ALA* 1.3 65.1 + - - +
309F ALA* 3.2 7.4 + - - +
310F LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ILE* 3.5 19.5 - - - +
298F LEU* 3.5 34.9 - - + +
299F GLU 4.1 0.4 - - - +
303F ARG 3.1 9.9 + - - +
304F PHE* 3.2 8.7 + - - +
306F GLU* 1.3 77.3 - - - +
308F HIS* 1.3 57.0 + - - +
310F LEU* 3.6 1.1 + - - +
311F ALA* 3.0 28.4 + - - +
334F LEU* 3.6 20.4 - - + -
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Residues in contact with HIS 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F PHE 2.8 16.2 + - - +
305F ALA 3.7 5.0 + - - +
307F ALA* 1.3 75.3 - - - +
309F ALA* 1.3 64.7 + - - +
311F ALA* 3.7 1.7 - - - +
312F ARG* 3.0 48.4 + - - +
331F LEU* 4.1 13.8 - - + +
334F LEU* 4.1 17.0 - - + +
335F GLN* 4.1 31.0 + - + +
338F LEU* 3.8 23.3 - - + +
340F LEU* 4.4 15.0 - - + +
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Residues in contact with ALA 309 (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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305F ALA 3.1 17.1 + - - +
306F GLU* 3.2 8.5 + - - +
308F HIS* 1.3 81.6 + - - +
310F LEU* 1.3 56.4 + - - +
312F ARG* 3.5 4.4 + - - +
313F GLU* 3.1 27.1 + - - +
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Residues in contact with LEU 310 (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 ARG* 3.7 45.1 - - - +
291F ARG* 4.1 18.2 - - + +
294F ALA* 4.0 12.3 - - + -
295F ILE* 3.7 24.5 - - + +
298F LEU* 4.4 9.4 - - + -
306F GLU 3.1 15.5 + - - +
307F ALA 4.1 4.3 - - - +
309F ALA* 1.3 75.5 - - - +
311F ALA* 1.3 56.1 + - - +
313F GLU* 3.2 28.6 + - - +
314F ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ILE* 3.7 19.2 - - + +
307F ALA 3.0 19.3 + - - +
308F HIS 3.7 4.5 - - - +
309F ALA 3.3 0.2 - - - -
310F LEU* 1.3 77.6 - - - +
312F ARG* 1.3 57.8 + - - +
314F ALA* 3.2 2.4 + - - +
315F SER* 2.8 31.4 + - - -
327F LEU* 3.6 10.7 - - + +
330F LEU* 5.6 0.2 - - + -
331F LEU* 4.1 17.5 - - + +
334F LEU* 3.9 17.0 - - + -
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Residues in contact with ARG 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F HIS* 3.0 37.0 + - + +
309F ALA* 3.9 6.1 - - - +
311F ALA* 1.3 75.0 - - - +
313F GLU* 1.3 63.5 + - - +
315F SER* 3.1 18.8 + - - +
316F CYS* 3.2 44.3 + - - -
331F LEU* 4.8 8.7 - - + +
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Residues in contact with GLU 313 (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 ARG* 5.6 0.2 + - - -
291F ARG* 4.5 14.7 + - - +
309F ALA 3.1 15.5 + - - +
310F LEU* 3.4 30.7 - - - +
312F ARG* 1.3 78.7 - - - +
314F ALA* 1.3 61.8 + - - +
316F CYS* 3.6 13.1 + - - +
317F ALA* 3.7 8.7 + - - +
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Residues in contact with ALA 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ARG* 3.5 38.3 - - - +
295F ILE* 4.3 3.4 - - + -
310F LEU 2.8 16.8 + - - +
311F ALA* 3.5 5.6 - - - +
313F GLU* 1.3 73.1 - - - +
315F SER* 1.3 57.6 + - - +
316F CYS 3.1 4.0 - - - -
317F ALA 3.0 6.1 + - - -
318F PRO* 2.9 30.0 - - - +
323F GLU* 4.5 0.2 - - - -
327F LEU* 3.8 22.0 - - + -
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Residues in contact with SER 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F ALA 2.8 22.7 + - - -
312F ARG* 3.1 16.8 + - - +
314F ALA* 1.3 72.4 - - - +
316F CYS* 1.3 60.8 + - - +
317F ALA 3.4 0.2 - - - -
318F PRO* 3.8 10.2 - - - +
324F ARG* 4.9 8.1 + - - -
327F LEU* 3.7 18.8 - - - +
331F LEU* 3.8 20.8 - - - +
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Residues in contact with CYS 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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312F ARG* 3.2 51.0 + - - +
313F GLU* 3.7 8.3 - - - +
314F ALA 3.1 0.8 - - - -
315F SER* 1.3 81.0 - - - +
317F ALA* 1.3 61.2 + - + +
318F PRO* 3.7 3.1 - - - +
324F ARG* 5.7 0.7 + - - -
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Residues in contact with ALA 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ARG* 3.3 22.1 + - - +
313F GLU 3.7 5.6 + - - +
314F ALA 3.0 5.1 + - - +
316F CYS* 1.3 83.3 - - + +
318F PRO* 1.3 67.5 - - - +
319F GLU* 4.7 0.2 - - - -
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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