Contacts of the helix formed by residues 312 - 328 (chain A) in PDB entry 5FHH
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 GLU 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A MET 3.2 5.5 + - - -
311A VAL* 1.3 91.8 - - - +
313A ALA* 1.3 66.3 + - - +
314A ASP* 4.4 6.5 - - + +
315A LEU* 3.8 14.5 - - + +
316A PHE* 3.7 7.6 + - - +
349A PRO* 4.4 11.7 - - + -
357A PRO* 4.5 7.2 - - + +
358A ARG* 3.6 6.3 - - + +
360A CYS* 4.4 2.2 - - - +
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Residues in contact with ALA 313 (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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312A GLU* 1.3 71.7 - - - +
314A ASP* 1.3 59.9 + - - +
316A PHE* 2.7 32.1 + - - +
317A ASP* 3.4 3.6 + - - +
358A ARG* 2.7 36.8 + - + +
359A PHE 3.2 16.6 - - - +
360A CYS* 4.0 6.7 - - - +
362A GLN* 4.6 2.0 - - + -
363A SER* 3.7 22.0 - - - +
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.6 4.7 - - + +
313A ALA* 1.3 82.1 - - - +
315A LEU* 1.3 63.0 + - - +
316A PHE 3.3 0.2 + - - -
317A ASP* 3.4 6.4 + - - +
318A LYS* 3.0 40.2 + - + +
358A ARG* 5.0 6.2 - - - +
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Residues in contact with LEU 315 (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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268A LEU* 4.2 18.4 - - + -
269A HIS* 6.0 1.3 - - - +
274A ILE* 6.5 1.1 - - + -
276A SER* 4.7 31.0 - - - +
311A VAL* 3.7 26.5 - - + -
312A GLU* 3.8 23.0 + - + +
313A ALA 3.1 1.0 - - - -
314A ASP* 1.3 78.4 - - - +
316A PHE* 1.3 51.4 + - - +
318A LYS* 3.6 9.3 - - + +
319A LEU* 2.6 59.5 + - + +
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Residues in contact with PHE 316 (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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305A ILE* 5.3 7.4 - - + -
308A ILE* 5.4 4.9 - - + -
311A VAL* 4.8 8.5 - - + +
312A GLU 3.7 6.1 + - - +
313A ALA 2.7 20.0 + - - +
315A LEU* 1.3 74.7 - - - +
317A ASP* 1.3 49.8 + - - +
319A LEU* 3.1 12.3 + - + +
320A GLU* 2.4 36.2 + - - +
333A PHE* 4.7 19.9 - + - -
338A LEU* 4.4 13.5 - - + -
340A ILE* 4.9 15.7 - - + -
360A CYS* 4.3 10.5 - - + -
363A SER* 3.2 22.7 - - - +
365A SER* 3.8 15.5 - - - -
366A TRP* 3.5 27.6 - + - -
369A CYS* 3.9 29.4 - - - -
371A PRO* 6.3 1.1 - - + -
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Residues in contact with ASP 317 (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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313A ALA 3.4 4.5 + - - +
314A ASP* 3.4 7.9 + - - +
316A PHE* 1.3 78.2 - - - +
318A LYS* 1.3 59.4 + - + +
320A GLU* 2.9 14.1 + - - +
321A ALA* 2.9 18.0 + - - +
363A SER* 4.7 6.9 - - - -
364A LYS* 5.4 7.0 - - + +
365A SER* 3.5 23.1 + - - +
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Residues in contact with LYS 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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276A SER* 2.9 32.4 + - - +
277A GLY 2.2 31.6 + - - +
278A GLN* 5.5 0.4 - - - +
279A ALA 3.8 18.6 - - - +
280A PRO* 5.2 4.5 - - + -
281A LEU* 5.3 9.9 - - + +
284A CYS* 4.9 13.2 - - - -
314A ASP* 3.0 32.1 + - + +
315A LEU* 3.8 7.0 - - + +
317A ASP* 1.3 77.7 - - + +
319A LEU* 1.3 61.9 + - - +
321A ALA* 4.6 2.2 - - - +
322A VAL* 3.0 28.7 + - - +
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Residues in contact with LEU 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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268A LEU* 3.5 39.7 - - + -
272A ALA* 3.7 26.5 - - + -
274A ILE* 5.0 2.5 - - + -
297A TRP* 4.2 19.3 - - + -
303A LEU* 6.6 0.2 - - + -
305A ILE* 5.7 3.1 - - + -
311A VAL* 6.0 1.1 - - + -
315A LEU* 2.6 36.3 + - + +
316A PHE* 3.3 13.0 - - + +
318A LYS* 1.3 73.4 - - - +
320A GLU* 1.3 57.5 + - - +
322A VAL* 3.5 10.0 + - + +
323A ALA* 3.0 27.7 + - - +
333A PHE* 3.8 13.1 - - + -
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Residues in contact with GLU 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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316A PHE* 2.4 19.2 + - + +
317A ASP 2.9 8.1 + - - +
319A LEU* 1.3 70.8 - - - +
321A ALA* 1.3 66.5 + - - +
323A ALA* 2.9 15.6 + - - +
324A ARG* 3.2 28.2 + - - +
333A PHE* 3.4 19.2 - - + -
365A SER* 3.2 28.9 - - - +
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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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281A LEU* 4.9 16.2 - - + -
317A ASP 2.9 15.0 + - - +
318A LYS* 4.8 2.0 - - - +
320A GLU* 1.3 74.0 - - - +
322A VAL* 1.3 53.7 + - - +
324A ARG* 3.0 28.3 + - - +
325A ALA* 2.7 38.6 + - + +
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Residues in contact with VAL 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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272A ALA* 5.5 0.9 - - - +
274A ILE* 4.2 9.9 - - + -
281A LEU* 4.8 5.4 - - + +
284A CYS* 3.8 25.1 - - + -
285A VAL* 4.0 24.0 - - + +
288A ALA* 3.5 28.0 - - + -
297A TRP* 3.2 17.6 + - + -
318A LYS 3.0 24.0 + - - +
319A LEU* 3.6 10.8 - - + +
320A GLU 3.1 0.4 - - - -
321A ALA* 1.3 77.3 - - - +
323A ALA* 1.3 63.9 + - - +
326A VAL* 3.3 17.7 + - - +
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Residues in contact with ALA 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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297A TRP* 2.2 55.6 + - + -
319A LEU 3.0 10.1 + - - +
320A GLU 2.9 10.8 + - - +
322A VAL* 1.3 71.7 - - - +
324A ARG* 1.3 61.1 + - - +
327A ARG* 3.4 19.4 + - - +
333A PHE* 3.7 27.6 - - + +
334A GLY* 4.4 1.6 - - - -
336A ILE* 4.3 2.7 - - + -
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Residues in contact with ARG 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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320A GLU* 3.2 24.5 + - - +
321A ALA* 3.0 33.0 + - - +
323A ALA* 1.3 75.3 - - - +
325A ALA* 1.3 57.1 + - - +
327A ARG 3.3 1.6 + - - -
328A GLN* 2.7 35.5 + - - -
329A GLN 3.4 19.6 - - - +
330A ASN* 4.3 13.5 - - - +
331A LYS 3.4 19.7 - - - -
332A PRO 3.3 16.7 + - - +
334A GLY* 3.5 23.6 - - - +
365A SER* 5.1 3.6 + - - -
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Residues in contact with ALA 325 (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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285A VAL* 3.5 28.3 - - + -
289A GLN* 4.6 5.7 + - - -
321A ALA* 2.7 21.3 + - + +
322A VAL 4.1 0.4 - - - +
324A ARG* 1.3 74.5 - - - +
326A VAL* 1.3 62.9 + - - +
328A GLN* 3.4 22.6 + - - +
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Residues in contact with VAL 326 (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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285A VAL* 4.4 2.9 - - + -
288A ALA* 4.1 19.5 - - + +
289A GLN* 3.4 42.9 + - + +
294A ARG* 4.6 11.0 - - + -
297A TRP* 2.9 42.6 - - + -
298A LEU* 4.6 11.6 - - + +
322A VAL 3.3 9.4 + - - +
325A ALA* 1.3 78.5 - - - +
327A ARG* 1.3 60.4 + - - +
328A GLN* 3.3 5.2 + - - +
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Residues in contact with ARG 327 (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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297A TRP* 3.5 22.1 + - + +
298A LEU* 3.6 20.7 + - - +
299A ASN 5.0 0.2 - - - -
300A CYS* 2.3 50.7 + - - -
301A GLN* 4.3 9.7 - - - +
323A ALA 3.4 19.2 + - - +
324A ARG 3.3 2.5 + - - +
326A VAL* 1.3 74.8 - - - +
328A GLN* 1.3 64.1 + - - +
329A GLN* 2.9 34.6 + - + +
334A GLY* 3.0 29.7 + - - +
335A GLY 4.5 5.7 + - - -
336A ILE* 3.6 15.5 - - - +
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Residues in contact with GLN 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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324A ARG 2.7 15.2 + - - -
325A ALA* 3.8 15.5 + - - +
326A VAL 3.1 6.3 - - - +
327A ARG* 1.3 73.9 - - - +
329A GLN* 1.3 61.9 + - - -
330A ASN* 3.1 11.6 + - - +
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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