Contacts of the helix formed by residues 319 - 334 (chain B) in PDB entry 2HD1
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 SER 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ASN* 4.2 2.2 - - - +
317B ASP 3.6 2.0 + - - -
318B ILE* 1.3 75.8 - - - +
320B PRO* 1.3 70.8 - - - +
321B LEU 3.3 3.1 + - - -
322B GLU* 3.4 16.8 + - - -
323B ASN* 3.0 25.2 + - - -
361B LEU* 4.6 8.7 + - - -
364B ASP* 2.6 33.3 + - - +
367B ARG* 4.6 10.6 - - - +
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Residues in contact with PRO 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASN* 3.2 25.8 - - + +
304B GLN* 4.3 16.2 - - + -
305B ILE* 4.4 10.8 - - + -
311B LEU* 3.8 33.7 - - + +
312B ALA* 4.1 4.5 - - - +
315B TYR* 3.6 17.5 - - + -
317B ASP 3.8 11.2 - - - +
318B ILE 2.8 9.2 - - - +
319B SER* 1.3 90.2 - - - +
321B LEU* 1.3 60.6 + - - +
324B HIS* 3.1 23.9 + - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B HIS* 3.6 24.0 - - + +
297B PRO* 3.4 36.3 - - + -
299B TYR 3.5 19.3 - - - +
300B ASN* 3.7 14.8 - - + -
301B ASN* 2.8 33.1 + - - +
304B GLN* 4.2 6.1 - - + -
311B LEU* 4.0 13.9 - - + -
320B PRO* 1.3 72.2 - - - +
322B GLU* 1.3 67.5 + - - +
324B HIS* 3.0 7.6 + - + +
325B HIS* 2.8 42.2 + - + +
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Residues in contact with GLU 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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102B MG 4.0 14.2 - - - -
301B ASN* 2.9 27.5 + - - -
319B SER* 3.4 8.5 + - - +
321B LEU* 1.3 78.7 - - - +
323B ASN* 1.3 65.2 + - - +
325B HIS* 3.4 12.2 + - + -
326B CYS* 3.1 24.6 + - - +
360B ILE* 3.6 29.7 - - - +
361B LEU* 3.9 17.3 - - + +
363B THR* 3.6 11.5 - - - +
364B ASP* 3.4 34.0 + - + +
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Residues in contact with ASN 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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315A TYR* 4.6 5.2 - - - +
316A ASN* 3.0 29.8 + - - +
318A ILE* 4.7 5.3 - - - +
315B TYR* 3.5 34.1 + - + +
318B ILE* 2.8 36.8 + - - +
319B SER* 3.0 16.1 + - - +
320B PRO 3.9 0.2 - - - +
322B GLU* 1.3 76.3 - - - +
324B HIS* 1.3 57.3 + - - +
327B ALA* 3.0 26.0 + - - +
361B LEU* 3.6 21.1 - - - +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 5.5 0.6 + - - -
294B LEU 4.2 2.0 - - - -
295B ASP* 2.9 42.8 + - + -
297B PRO* 5.7 0.9 - - + -
311B LEU* 3.7 36.8 - - + +
314B ARG* 4.1 12.6 + - - -
315B TYR* 3.9 10.5 + - + -
320B PRO 3.1 14.3 + - - +
321B LEU* 3.0 10.0 + - - +
323B ASN* 1.3 76.2 - - - +
325B HIS* 1.3 70.7 + + - +
327B ALA* 3.0 4.1 + - + +
328B VAL* 2.9 45.0 + - + +
331B GLN* 5.9 1.6 - - - -
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Residues in contact with HIS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B MG 4.1 4.9 - - - -
291B CYS 3.9 2.9 - - - +
292B HIS 3.0 32.8 - - - +
293B ASP* 3.4 15.5 + - - -
294B LEU* 2.7 43.4 + - - +
295B ASP 4.6 0.9 - - - -
296B HIS* 3.7 33.7 - + + -
321B LEU* 2.8 46.0 + - + +
322B GLU* 3.4 18.1 + - + +
324B HIS* 1.3 73.7 - + - +
326B CYS* 1.3 58.7 + - - +
328B VAL* 3.3 2.8 + - - +
329B ALA* 2.9 28.8 + - - +
360B ILE* 4.1 2.0 - - + -
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Residues in contact with CYS 326 (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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316A ASN* 3.3 21.3 - - - +
322B GLU 3.1 15.1 + - - +
323B ASN 3.8 0.2 - - - +
325B HIS* 1.3 80.6 - - - +
327B ALA* 1.3 60.3 + - - +
329B ALA* 3.3 1.8 + - - +
330B PHE* 3.2 42.3 + - - -
357B ILE* 3.4 48.0 - - - +
360B ILE* 3.9 24.4 - - + +
361B LEU* 5.5 2.2 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 3.5 27.8 - - - +
314A ARG* 3.8 3.1 - - - +
316A ASN* 3.5 1.7 + - - +
315B TYR* 3.6 15.5 - - - +
323B ASN 3.0 18.7 + - - +
324B HIS* 3.0 8.7 + - - +
326B CYS* 1.3 72.7 - - - +
328B VAL* 1.3 62.1 + - - +
330B PHE* 3.3 2.0 + - - -
331B GLN* 2.9 46.1 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ASN* 4.3 16.4 - - + +
294B LEU* 3.9 19.1 - - + +
295B ASP* 4.2 9.6 - - + +
324B HIS* 2.9 48.9 + - + +
325B HIS 3.7 4.0 - - - +
327B ALA* 1.3 72.4 - - + +
329B ALA* 1.3 68.2 + - - +
331B GLN* 3.5 17.1 - - + +
332B ILE* 2.9 39.0 + - + +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TRP* 5.2 1.2 + - - -
291B CYS* 3.6 22.9 - - + -
294B LEU* 3.4 21.7 - - + +
325B HIS 2.9 13.6 + - - +
326B CYS* 3.4 13.7 - - - +
327B ALA 3.2 0.2 - - - -
328B VAL* 1.3 77.9 - - - +
330B PHE* 1.3 67.8 + - + +
332B ILE* 3.4 5.4 + - - +
333B LEU* 3.1 30.6 + - - +
356B MET* 4.8 3.4 - - + -
360B ILE* 4.7 2.5 - - + -
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Residues in contact with PHE 330 (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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313A VAL* 4.3 15.0 - - + +
316A ASN* 4.9 0.7 - - - -
326B CYS* 3.2 45.6 + - - +
327B ALA* 4.1 2.7 - - - +
329B ALA* 1.3 76.3 - - + +
331B GLN* 1.3 61.6 + - - +
332B ILE 3.2 1.1 - - - -
333B LEU* 3.7 21.9 - - + +
334B ALA* 3.0 28.9 + - - +
341B PHE* 4.9 1.3 - + - -
349B PHE* 4.2 19.5 - + - -
353B ARG* 3.1 65.7 - - + +
356B MET* 3.9 31.2 - - + -
357B ILE* 4.3 4.5 - - + -
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Residues in contact with GLN 331 (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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310A GLU 5.9 0.2 + - - -
313A VAL* 3.7 16.9 - - + +
314A ARG* 5.0 5.9 - - - +
324B HIS* 5.9 1.9 - - - -
327B ALA* 2.9 36.1 + - - +
328B VAL* 3.1 19.8 + - + +
330B PHE* 1.3 77.5 - - - +
332B ILE* 1.3 65.2 + - + +
334B ALA* 3.3 15.0 + - - +
335B GLU* 3.6 15.2 + - - +
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Residues in contact with ILE 332 (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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238B TRP* 3.8 26.7 - - + +
241B CYS* 3.7 27.1 - - + +
242B VAL* 4.1 12.1 - - + -
245B ASN* 3.4 39.0 - - + +
294B LEU* 4.1 12.1 - - + -
328B VAL* 2.9 24.9 + - + +
329B ALA 3.5 7.2 - - - +
331B GLN* 1.3 78.9 - - + +
333B LEU* 1.3 57.6 + - - +
335B GLU* 2.9 31.5 + - - +
338B CYS* 3.4 10.8 - - + +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TRP* 3.4 32.3 - - + +
287B THR* 5.1 2.0 - - + -
291B CYS* 5.9 0.9 - - - -
329B ALA* 3.1 18.7 + - + +
330B PHE* 3.9 29.2 - - + +
331B GLN 3.4 0.2 - - - -
332B ILE* 1.3 79.8 - - - +
334B ALA* 1.3 56.7 + - - +
335B GLU 3.2 0.9 - - - -
338B CYS 3.9 6.5 - - - +
339B ASN* 3.2 35.1 + - - +
340B ILE* 3.7 26.9 - - + +
341B PHE* 3.5 31.9 - - + -
349B PHE* 5.4 4.3 - - + -
356B MET* 4.6 8.7 - - + -
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Residues in contact with ALA 334 (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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313A VAL* 5.8 7.0 - - + -
330B PHE 3.0 17.8 + - - +
331B GLN* 3.6 11.0 - - - +
332B ILE 3.1 0.4 - - - -
333B LEU* 1.3 75.7 - - - +
335B GLU* 1.3 65.9 + - - +
336B PRO* 3.2 10.3 - - - +
339B ASN* 5.3 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
------------------------------------------------------------
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