Contacts of the helix formed by residues 293 - 308 (chain A) in PDB entry 5HVO
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 GLY 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A TYR 3.9 6.7 + - - -
291A ILE 3.2 4.4 + - - -
292A LYS* 1.3 78.8 - - - +
294A ILE* 1.3 64.5 + - - +
295A PRO* 3.4 4.2 - - - +
296A GLN* 3.2 20.2 + - - +
297A LYS* 3.1 8.0 + - - +
382A SER* 3.1 34.2 + - - -
384A THR* 4.1 9.0 - - - -
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Residues in contact with ILE 294 (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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286A ASP* 4.5 1.1 - - + -
287A ARG 4.4 2.7 - - - +
288A LEU* 3.8 35.7 - - + -
289A ASP 4.6 5.5 + - - +
292A LYS* 4.2 22.7 - - + +
293A GLY* 1.3 73.5 - - - +
295A PRO* 1.3 74.6 - - + +
297A LYS* 3.2 12.0 + - + +
298A LEU* 3.0 32.1 + - + +
319A GLN* 4.2 37.9 - - + +
321A ALA* 5.2 2.5 - - + -
334A LEU* 5.3 1.3 - - + -
338A VAL* 3.9 27.1 - - + -
359A PHE* 5.9 0.4 - - + -
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Residues in contact with PRO 295 (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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290A TYR* 6.0 1.6 - - - +
293A GLY* 3.6 3.6 - - - +
294A ILE* 1.3 94.9 - - + +
296A GLN* 1.3 67.9 + - - +
298A LEU* 3.2 2.2 + - + +
299A HIS* 2.9 32.1 + - + +
334A LEU* 4.1 24.0 - - + -
337A VAL* 4.4 14.1 - - + -
338A VAL* 4.3 10.1 - - + -
341A LEU* 3.6 22.9 - - + -
115B ILE* 4.3 18.2 - - + -
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Residues in contact with GLN 296 (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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293A GLY* 3.2 23.3 - - - +
295A PRO* 1.3 80.1 - - - +
297A LYS* 1.3 58.4 + - - +
299A HIS* 3.5 2.4 + - - +
300A ALA* 3.0 30.0 + - - +
382A SER* 4.1 6.5 - - - +
384A THR* 3.4 17.5 - - + +
426A PRO* 3.5 34.7 - - + +
427A TRP* 3.2 40.3 - - - +
429A THR* 5.0 2.1 - - - +
432A LEU* 3.8 3.6 - - + +
115B ILE* 3.7 31.2 - - + +
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Residues in contact with LYS 297 (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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284A SER* 3.3 19.2 + - - +
286A ASP* 2.9 34.6 + - - -
292A LYS 4.5 2.8 + - - -
293A GLY 3.1 4.5 + - - +
294A ILE* 3.4 13.6 - - - +
296A GLN* 1.3 80.9 - - - +
298A LEU* 1.3 64.2 + - + +
301A LEU* 3.2 13.0 + - - +
317A LEU* 3.9 18.7 - - + +
319A GLN* 3.0 22.4 + - - +
380A VAL* 3.7 16.2 + - + -
382A SER* 3.3 33.2 + - - +
432A LEU* 4.0 2.5 - - - -
436A TYR* 2.8 30.9 + - - +
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Residues in contact with LEU 298 (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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294A ILE* 3.0 32.8 + - + +
295A PRO* 3.8 3.4 - - + +
297A LYS* 1.3 77.0 - - + +
299A HIS* 1.3 66.5 + - - +
301A LEU* 3.2 8.3 + - + +
302A GLU 3.1 17.3 + - - -
317A LEU* 3.9 26.0 - - + -
319A GLN* 5.4 4.3 - - + +
338A VAL* 4.2 3.6 - - + -
341A LEU* 3.9 23.1 - - + -
342A VAL* 3.8 28.9 - - + +
345A ILE* 3.2 23.8 - - + +
357A ILE* 4.0 21.1 - - + -
359A PHE* 6.1 0.2 - - + -
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Residues in contact with HIS 299 (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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295A PRO* 2.9 23.1 + - + +
296A GLN* 3.8 5.8 - - - +
298A LEU* 1.3 74.3 - - - +
300A ALA* 1.3 63.8 + - - +
302A GLU* 3.3 23.8 + - - +
303A VAL* 3.0 26.2 + - - +
341A LEU* 3.6 31.0 - - + +
344A ARG* 3.9 8.2 + - - -
345A ILE* 4.6 0.2 - - - -
429A THR* 3.9 5.2 - - + +
115B ILE* 3.7 26.5 - - + +
116B VAL* 3.4 30.1 - - + +
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Residues in contact with ALA 300 (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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296A GLN 3.0 9.0 + - - +
298A LEU 3.3 0.2 - - - -
299A HIS* 1.3 75.6 - - - +
301A LEU* 1.3 58.3 + - - +
303A VAL* 3.2 1.4 + - - -
304A PHE* 2.8 31.2 + - - +
429A THR* 3.7 20.5 - - + +
432A LEU* 3.3 49.1 - - + -
433A ALA* 3.5 5.0 - - - +
436A TYR* 3.5 9.0 - - + +
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Residues in contact with LEU 301 (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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282A MET* 5.6 4.0 - - - -
297A LYS 3.2 11.7 + - - +
298A LEU* 3.2 12.4 + - + +
300A ALA* 1.3 78.5 - - - +
302A GLU* 1.3 56.5 + - - +
304A PHE* 3.4 19.7 + - + +
305A LEU* 3.0 41.2 + - + +
315A VAL* 5.3 10.1 - - + -
317A LEU* 4.3 25.4 - - + +
345A ILE* 4.8 2.7 - - + -
356A PRO* 4.2 14.6 - - + +
357A ILE* 3.4 37.7 - - + -
436A TYR* 3.3 16.7 - - + -
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Residues in contact with GLU 302 (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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298A LEU 3.1 11.7 + - - +
299A HIS* 3.6 19.3 - - - +
300A ALA 3.2 0.4 - - - -
301A LEU* 1.3 77.9 - - - +
303A VAL* 1.3 58.6 + - + +
305A LEU 3.4 0.5 + - - -
306A GLN* 3.0 43.1 + - - +
344A ARG* 2.9 37.6 + - - -
345A ILE* 4.2 14.9 - - + +
348A LYS* 2.8 29.0 + - - +
349A PHE* 3.9 20.3 - - + -
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Residues in contact with VAL 303 (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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299A HIS 3.0 18.3 + - - +
300A ALA 3.6 6.5 - - - +
302A GLU* 1.3 73.7 - - + +
304A PHE* 1.3 66.9 + - - +
306A GLN* 3.4 16.2 + - - +
307A ASN* 3.0 28.0 + - - +
429A THR* 3.7 18.2 - - + -
430A GLU* 3.3 40.6 - - + +
433A ALA* 3.6 13.2 - - + -
116B VAL* 5.3 8.1 - - + -
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Residues in contact with PHE 304 (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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282A MET* 5.9 0.4 - - - -
300A ALA 2.8 20.7 + - - +
301A LEU* 3.6 11.0 - - + +
303A VAL* 1.3 73.6 - - - +
305A LEU* 1.3 68.8 + - + +
307A ASN* 3.2 5.4 + - - +
308A HIS* 2.8 45.3 + + + +
311A TRP* 3.7 26.7 - + + -
315A VAL* 4.0 28.0 - - + -
433A ALA* 3.6 24.9 - - + +
436A TYR* 3.8 25.1 - + + -
437A HIS* 3.6 32.8 - + + -
440A VAL* 4.5 6.7 - - + -
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Residues in contact with LEU 305 (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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301A LEU* 3.0 30.2 + - + +
302A GLU* 5.3 0.2 - - - -
304A PHE* 1.3 84.0 - - + +
306A GLN* 1.3 65.1 + - - +
308A HIS 3.4 17.9 - - - +
309A PRO* 3.4 8.3 - - - +
311A TRP* 4.1 2.9 - - + -
312A VAL* 3.9 30.3 - - + +
315A VAL* 4.0 24.9 - - + -
345A ILE* 5.6 0.2 - - + -
349A PHE* 3.8 45.7 - - + -
354A TYR* 4.7 2.9 - - - +
356A PRO* 3.9 24.2 - - + -
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Residues in contact with GLN 306 (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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302A GLU* 3.0 29.7 + - - +
303A VAL* 3.7 16.3 - - - +
304A PHE 3.3 0.2 - - - -
305A LEU* 1.3 77.5 - - - +
307A ASN* 1.3 65.3 + - - +
308A HIS 3.5 0.3 + - - -
309A PRO* 3.8 11.6 - - - +
348A LYS* 2.9 34.0 + - - -
349A PHE* 3.9 13.9 - - + -
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Residues in contact with ASN 307 (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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303A VAL* 3.0 28.5 + - - +
304A PHE* 3.5 6.0 - - - +
306A GLN* 1.3 78.3 - - - +
308A HIS* 1.3 81.9 + - + +
309A PRO* 3.5 6.3 - - - +
310A GLU* 4.1 1.2 - - - +
430A GLU* 3.3 27.3 + - - +
433A ALA* 4.7 4.0 - - - +
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Residues in contact with HIS 308 (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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304A PHE* 2.8 32.6 + + + +
305A LEU* 3.4 10.6 - - - +
306A GLN 3.3 0.2 - - - -
307A ASN* 1.3 98.5 + - + +
309A PRO* 1.3 60.8 - - - +
310A GLU* 3.0 29.6 + - - +
311A TRP* 2.9 30.5 + - + +
312A VAL 3.7 2.3 + - - -
437A HIS* 3.4 44.2 + + + +
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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