Contacts of the helix formed by residues 328 - 350 (chain B) in PDB entry 5HVM
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 VAL 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASN* 3.8 33.0 - - + +
102B ASN* 4.2 17.7 - - + +
103B SER* 3.8 18.6 - - - +
325B ARG* 3.1 19.0 + - + +
326B GLN 4.1 0.7 - - - +
327B ASP* 1.3 76.2 - - - +
329B GLU* 1.3 67.8 + - - +
330B GLU* 4.0 19.5 - - + +
331B TYR* 3.1 32.9 + - + +
332B GLN* 3.5 9.4 + - - -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP 3.5 3.7 + - - +
328B VAL* 1.3 75.9 - - - +
330B GLU* 1.3 64.3 + - + +
332B GLN* 3.2 25.2 + - - +
333B ASN* 3.1 45.7 + - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 4.3 15.8 - - - +
107B PRO* 4.9 0.2 - - - +
115B GLU* 2.8 52.1 - - + +
290B TYR* 3.6 32.4 + - + -
328B VAL* 3.3 17.7 + - + +
329B GLU* 1.3 77.4 - - + +
331B TYR* 1.3 57.7 + - + +
333B ASN* 3.4 12.5 + - - +
334B LEU* 2.9 28.9 + - - +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN 5.1 3.8 + - - -
106B TRP* 3.3 10.7 + - - -
288B LEU* 3.4 24.2 - - - +
289B ASP* 2.8 40.5 + - + -
290B TYR* 3.3 27.3 - + - -
324B SER* 3.4 16.8 - - - +
325B ARG* 3.2 47.3 + - + +
326B GLN* 4.9 3.1 - - - -
328B VAL* 3.1 32.9 + - + +
330B GLU* 1.3 78.5 - - + +
332B GLN* 1.3 58.8 + - - +
334B LEU* 3.8 8.0 - - + +
335B ARG* 2.9 29.8 + - - +
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLN* 2.9 26.7 + - - +
327B ASP* 3.2 20.6 + - - +
328B VAL 3.5 1.0 + - - +
329B GLU* 3.2 27.2 + - + +
331B TYR* 1.3 74.5 - - - +
333B ASN* 1.3 70.3 + - - +
335B ARG* 3.3 9.0 + - - +
336B ALA* 3.1 21.8 + - - +
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Residues in contact with ASN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 3.1 36.2 + - - +
330B GLU* 3.6 13.6 - - - +
332B GLN* 1.3 77.8 - - - +
334B LEU* 1.3 58.6 - - - +
336B ALA* 3.2 7.9 + - - +
337B VAL* 2.9 34.5 + - + +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 3.9 16.6 - - + +
289B ASP* 3.4 42.8 - - - +
290B TYR* 3.4 21.5 - - + +
294B VAL* 6.4 0.4 - - + -
295B PRO* 4.3 26.5 - - + -
330B GLU 2.9 17.7 + - - +
331B TYR* 3.8 7.4 - - + +
333B ASN* 1.3 77.1 - - - +
335B ARG* 1.3 63.9 + - - +
337B VAL* 3.3 9.1 + - + +
338B VAL* 2.9 29.8 + - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 3.5 53.5 + - - +
348A LYS* 5.5 7.7 - - - +
288B LEU* 3.9 25.7 - - + +
326B GLN* 4.0 17.2 + - - -
331B TYR 2.9 18.2 + - - +
332B GLN* 3.5 8.7 - - - +
333B ASN 3.2 0.4 - - - -
334B LEU* 1.3 78.3 - - - +
336B ALA* 1.3 57.3 + - - +
338B VAL* 3.8 1.4 - - - +
339B ASN* 2.9 48.4 + - - +
361B HIS* 3.6 34.4 + - + +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 3.7 27.9 - - + +
332B GLN 3.1 12.7 + - - +
333B ASN* 3.2 9.2 + - - +
335B ARG* 1.3 77.9 - - - +
337B VAL* 1.3 57.3 + - + +
339B ASN* 3.4 1.3 + - - +
340B GLU* 2.9 31.2 + - - +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 4.6 19.7 - - + -
333B ASN* 2.9 22.5 + - + +
334B LEU* 3.7 11.2 - - + +
336B ALA* 1.3 76.8 - - + +
338B VAL* 1.3 63.9 + - - +
340B GLU* 3.6 6.3 + - - +
341B LEU* 3.1 30.7 + - + +
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.1 17.5 - - + -
294B VAL* 3.8 33.0 - - + -
295B PRO* 4.3 17.7 - - + -
298B LEU* 4.4 2.9 - - + -
334B LEU* 2.9 24.1 + - + +
335B ARG* 3.9 2.5 - - - +
337B VAL* 1.3 76.4 - - - +
339B ASN* 1.3 63.7 + - - +
341B LEU* 3.2 7.6 + - - +
342B VAL* 3.0 28.1 + - + +
359B PHE* 3.7 31.2 - - + -
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Residues in contact with ASN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ASN 3.3 6.8 - - - +
340A GLU* 3.5 32.3 + - + +
343A GLY* 3.4 12.8 - - - +
344A ARG* 3.6 22.5 - - - +
335B ARG* 2.9 45.2 + - - +
336B ALA 3.6 4.3 - - - +
338B VAL* 1.3 76.4 - - - +
340B GLU* 1.3 60.7 + - - +
342B VAL* 3.3 3.2 + - - +
343B GLY 3.1 17.3 + - - -
359B PHE* 3.2 30.3 - - - -
361B HIS* 5.6 0.3 - - - +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 3.6 37.2 - - + +
339A ASN* 3.5 23.9 + - + +
340A GLU* 3.8 15.4 - - + +
336B ALA 2.9 18.4 + - - +
337B VAL* 3.7 6.3 - - - +
339B ASN* 1.3 75.1 - - - +
341B LEU* 1.3 70.9 + - - +
343B GLY 3.2 1.9 + - - -
344B ARG* 2.9 37.9 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 3.9 34.1 - - + +
298B LEU* 4.0 14.4 - - + -
299B HIS* 3.6 37.2 - - + +
302B GLU* 5.2 0.9 - - - +
337B VAL* 3.1 21.1 + - + +
338B VAL* 3.5 9.6 - - - +
340B GLU* 1.3 87.5 + - - +
342B VAL* 1.3 58.4 + - - +
344B ARG* 3.3 12.9 + - - +
345B ILE* 3.0 49.5 + - + +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 6.2 0.9 - - + -
343A GLY* 4.4 14.1 - - - -
346A ASN* 5.9 1.6 - - + +
355A MET* 5.3 3.8 - - + -
298B LEU* 4.0 17.0 - - + -
338B VAL* 3.0 21.1 + - + +
339B ASN 3.6 7.0 - - - +
340B GLU 3.2 0.2 - - - -
341B LEU* 1.3 77.2 - - - +
343B GLY* 1.3 62.8 + - - +
345B ILE* 4.4 0.2 - - - +
346B ASN* 3.1 42.1 + - - +
357B ILE* 4.2 16.3 - - + +
359B PHE* 4.0 42.4 - - + -
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ASN* 3.4 34.1 - - - +
342A VAL* 4.6 17.0 - - - -
343A GLY* 4.6 0.6 - - - -
359A PHE* 3.8 4.5 - - - -
339B ASN 3.1 10.9 + - - -
340B GLU 3.2 0.2 + - - -
342B VAL* 1.3 78.7 - - - +
344B ARG* 1.3 61.5 + - - +
346B ASN* 4.0 1.9 - - - +
347B GLY* 3.0 21.8 + - - -
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 3.6 44.6 + - - +
339A ASN* 3.6 16.5 - - - +
361A HIS* 5.8 0.3 - - - +
302B GLU* 4.0 25.2 + - - -
340B GLU* 2.9 28.7 + - - +
341B LEU* 3.3 17.7 + - - +
343B GLY* 1.3 77.4 - - - +
345B ILE* 1.3 63.8 + - - +
347B GLY* 3.7 0.9 - - - -
348B LYS* 3.0 28.4 + - + +
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Residues in contact with ILE 345 (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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298B LEU* 3.4 44.6 - - + +
301B LEU* 4.6 9.0 - - + -
302B GLU* 4.1 26.7 - - + +
341B LEU* 3.0 31.0 + - + +
344B ARG* 1.3 78.3 - - + +
346B ASN* 1.3 63.9 + - - +
348B LYS* 3.1 17.4 + - - +
349B PHE* 3.1 31.6 + - + +
356B PRO* 4.6 7.2 - - + -
357B ILE* 3.5 26.2 - - + -
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Residues in contact with ASN 346 (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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342A VAL* 6.1 3.5 - - + +
346A ASN* 4.9 6.1 - - - +
355A MET* 4.8 5.7 - - - +
359A PHE* 3.8 7.1 - - + +
342B VAL* 3.1 33.3 + - - +
343B GLY* 4.2 3.4 - - - +
345B ILE* 1.3 78.8 - - - +
347B GLY* 1.3 56.3 + - - +
350B GLY* 2.8 32.9 + - - -
355B MET* 3.8 23.4 - - - +
356B PRO* 3.2 14.5 - - - +
357B ILE* 3.0 47.5 + - - +
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Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.3 24.6 + - - -
360A LEU* 3.9 1.4 - - - -
361A HIS* 3.0 33.6 + - - +
362A LYS* 3.6 11.6 + - - -
343B GLY 3.0 18.7 + - - -
344B ARG* 3.7 1.6 - - - -
346B ASN* 1.3 75.4 - - - +
348B LYS* 1.3 60.2 + - - +
350B GLY 4.8 0.2 - - - +
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Residues in contact with LYS 348 (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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335A ARG* 6.1 3.6 - - - +
361A HIS* 5.1 3.6 - - - -
362A LYS* 2.7 24.9 + - - +
302B GLU* 3.7 22.7 + - - +
306B SER* 4.2 11.7 + - - -
344B ARG* 3.0 20.4 + - + +
345B ILE* 3.1 10.3 + - - +
347B GLY* 1.3 79.0 - - - +
349B PHE* 1.3 92.3 + - + +
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Residues in contact with PHE 349 (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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362A LYS* 3.8 2.2 + - - +
302B GLU* 3.9 20.4 - - + -
305B LEU* 3.8 42.0 - - + -
306B SER* 3.7 16.4 - - - -
312B VAL* 3.8 38.9 - - + +
345B ILE* 3.1 25.4 + - + +
348B LYS* 1.3 113.3 - - + +
350B GLY* 1.3 68.4 + - - +
351B THR* 3.8 6.4 + - - +
354B PHE* 4.7 3.1 - - - -
356B PRO* 4.1 14.6 - - + -
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.1 7.8 - - - +
362A LYS* 2.9 23.9 + - - +
346B ASN 2.8 20.4 + - - -
347B GLY 4.8 0.5 - - - +
348B LYS 3.6 0.2 - - - -
349B PHE* 1.3 81.9 - - - +
351B THR* 1.3 61.4 + - - +
354B PHE* 3.0 15.5 - - - -
355B MET* 4.2 5.8 - - - -
356B PRO* 4.1 7.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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