Contacts of the helix formed by residues 312 - 327 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B MET 4.2 0.8 + - - -
311B VAL* 1.3 76.8 - - - +
313B ALA* 1.3 67.2 + - - +
314B ASP* 4.2 6.7 - - + +
315B LEU* 2.9 37.7 + - + +
316B PHE* 3.6 3.6 + - - +
349B PRO* 4.5 15.4 - - + +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B VAL 3.4 2.4 + - - -
312B GLU* 1.3 72.2 - - - +
314B ASP* 1.3 58.3 + - - +
316B PHE* 3.4 8.0 + - - +
317B ASP* 2.7 27.3 - - - +
349B PRO* 5.4 1.2 - - - +
359B PHE* 3.0 30.6 + - - +
360B CYS* 4.7 5.6 - - - +
361B PHE 4.9 2.9 - - - +
363B SER* 4.0 7.9 - - - -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLY* 5.1 12.3 - - - -
312B GLU* 3.1 6.8 - - + +
313B ALA* 1.3 78.5 - - - +
315B LEU* 1.3 53.1 + - - +
317B ASP* 3.1 8.2 + - - +
318B LYS* 2.6 40.0 + - + +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LEU* 4.8 3.8 - - + -
269B HIS* 3.2 35.2 - - + +
274B ILE* 5.9 1.8 - - + -
276B SER* 4.2 9.0 - - - +
277B GLY* 3.7 27.1 - - - +
311B VAL* 4.3 16.6 - - + -
312B GLU* 2.9 33.2 + - + +
314B ASP* 1.3 77.3 - - - +
316B PHE* 1.3 52.2 + - - +
318B LYS* 3.2 3.5 - - + -
319B LEU* 2.3 66.9 + - + +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B VAL* 5.3 8.2 - - + +
312B GLU 3.6 3.2 + - - +
313B ALA 3.4 9.0 + - - +
314B ASP 3.3 0.6 - - - -
315B LEU* 1.3 78.3 - - - +
317B ASP* 1.3 57.7 + - - +
319B LEU* 3.0 5.8 + - - +
320B GLU* 2.6 37.6 + - - +
333B PHE* 5.3 0.5 - - - -
360B CYS 4.4 14.1 - - - +
363B SER* 4.3 3.6 - - - +
365B SER* 4.1 11.7 - - - +
366B TRP* 5.1 5.8 - - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA 2.7 19.0 - - - +
314B ASP* 3.1 6.2 + - - +
316B PHE* 1.3 70.7 - - - +
318B LYS* 1.3 61.6 + - - +
320B GLU* 3.3 2.5 + - - +
321B ALA* 2.8 33.0 + - - +
363B SER* 2.8 19.7 - - - -
364B LYS* 2.6 37.4 + - + +
365B SER* 3.2 14.3 + - - -
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE* 6.6 0.4 - - + -
277B GLY* 4.7 16.2 - - - +
281B LEU* 5.7 5.0 - - + +
284B CYS* 6.1 4.9 - - + -
314B ASP* 2.6 25.7 + - + +
315B LEU* 3.4 7.4 - - + +
317B ASP* 1.3 72.8 - - - +
319B LEU* 1.3 59.7 + - + +
321B ALA* 3.3 5.7 + - - +
322B VAL* 2.9 36.3 + - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 4.1 33.2 - - + -
269B HIS* 6.4 0.9 - - + -
271B PHE* 6.3 0.4 - - + -
272B ALA* 4.1 19.3 - - + -
274B ILE* 4.6 20.2 - - + -
297B TRP* 3.8 14.1 - - + -
315B LEU* 2.3 62.0 + - + +
316B PHE* 3.0 5.6 + - - +
318B LYS* 1.3 71.0 - - + +
320B GLU* 1.3 61.9 + - - +
322B VAL* 3.8 4.0 - - + +
323B ALA* 3.0 28.1 + - - +
333B PHE* 3.4 14.3 - - + -
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE 2.6 21.0 + - - +
317B ASP* 3.7 6.7 - - - +
319B LEU* 1.3 73.3 - - - +
321B ALA* 1.3 64.9 + - - +
323B ALA* 3.1 2.8 + - - +
324B ARG* 2.8 37.7 + - - +
330B ASN 5.1 2.6 - - - +
331B LYS 4.7 0.7 - - - +
332B PRO* 4.1 3.0 - - + +
333B PHE* 3.2 48.0 + - + +
365B SER* 4.4 15.7 - - - -
368B ARG* 3.9 21.1 - - + +
369B CYS* 5.3 4.0 - - + -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B LEU* 4.2 24.4 - - + +
285B VAL* 4.7 2.7 - - - +
317B ASP 2.8 22.1 + - - +
318B LYS* 3.6 6.5 - - - +
320B GLU* 1.3 79.2 + - - +
322B VAL* 1.3 67.4 + - + +
324B ARG* 4.2 2.8 - - - +
325B ALA* 3.3 22.5 + - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE* 4.2 24.0 - - + -
281B LEU* 5.5 3.4 - - + -
284B CYS* 4.4 8.1 - - + -
285B VAL* 4.1 20.4 - - + +
288B ALA* 3.6 31.0 - - + -
297B TRP* 4.3 15.3 - - + -
318B LYS* 2.9 27.3 + - + +
319B LEU* 3.8 8.1 - - + +
321B ALA* 1.3 75.2 - - - +
323B ALA* 1.3 64.9 + - - +
325B ALA* 3.1 3.6 + - - +
326B VAL* 3.0 33.4 + - + +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TRP* 3.3 31.5 - - + -
319B LEU 3.0 19.6 + - - +
320B GLU 3.1 4.9 + - - +
322B VAL* 1.3 77.5 - - - +
324B ARG* 1.3 64.5 + - - +
325B ALA 3.2 0.2 + - - -
326B VAL* 3.3 8.2 + - - +
327B ARG* 3.4 16.6 + - - +
333B PHE* 3.5 30.5 - - + +
334B GLY* 4.3 3.7 - - - -
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLU* 2.8 31.3 + - - +
321B ALA* 4.2 3.8 - - - +
323B ALA* 1.3 74.5 - - - +
325B ALA* 1.3 61.5 + - - +
328B GLN* 3.7 1.2 + - - -
329B GLN 2.8 44.1 + - - +
330B ASN* 4.3 10.8 - - + +
331B LYS 4.6 1.3 - - - +
334B GLY 3.9 10.7 - - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B VAL* 4.3 20.9 - - + -
289B GLN* 5.6 0.7 + - - -
321B ALA 3.3 14.7 + - - +
322B VAL 3.1 3.8 + - - +
324B ARG* 1.3 78.4 - - - +
326B VAL* 1.3 64.7 + - - +
328B GLN* 3.7 8.7 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.1 16.6 - - + +
288B ALA* 4.3 9.9 - - + +
289B GLN* 3.9 34.9 + - + +
294B ARG* 4.5 15.0 - - + +
297B TRP* 4.8 18.2 - - + -
298B LEU* 5.9 2.2 - - + +
322B VAL* 3.0 37.1 + - + +
323B ALA* 3.3 3.8 + - - +
325B ALA* 1.3 77.9 - - - +
327B ARG* 1.3 60.2 - - + +
328B GLN* 3.3 2.5 + - - +
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TRP* 5.4 9.9 - - + +
298B LEU* 5.6 8.1 - - - +
323B ALA 3.4 13.7 + - - +
325B ALA 3.4 0.4 - - - -
326B VAL* 1.3 78.0 - - + +
328B GLN* 1.3 69.6 + - - +
329B GLN* 3.3 8.5 + - + +
334B GLY* 5.0 12.3 - - - +
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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