Contacts of the helix formed by residues 328 - 350 (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 VAL 328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASN* 3.9 27.4 - - + +
101A ASN* 4.1 22.7 - - + +
102A SER* 3.6 22.0 - - - +
325A ARG* 3.1 25.2 + - + +
327A ASP* 1.3 77.4 - - - +
329A GLU* 1.3 67.2 + - - +
330A GLU* 4.1 11.2 - - + +
331A TYR* 3.0 33.9 + - + +
332A GLN* 3.1 13.1 + - - +
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP 3.6 3.6 + - - -
328A VAL* 1.3 74.4 - - - +
330A GLU* 1.3 58.0 + - - +
332A GLN* 3.1 20.1 + - - +
333A ASN* 2.9 45.3 + - - +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 6.3 0.7 - - + -
111A HIS* 3.4 23.5 - - + +
113A GLY* 6.0 5.4 - - - -
290A TYR* 3.6 30.0 - - + +
328A VAL* 3.3 10.8 - - + +
329A GLU* 1.3 80.2 - - - +
331A TYR* 1.3 56.8 + - - +
333A ASN* 3.4 22.8 + - - +
334A LEU* 3.1 24.9 + - - +
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Residues in contact with TYR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN 4.2 12.6 - - - -
105A TRP* 3.0 9.0 + - - -
287A ARG* 4.5 2.0 - - - -
288A LEU* 3.3 25.3 - - - +
289A ASP* 2.4 44.4 + - + -
290A TYR* 3.7 24.9 - + - -
324A SER* 3.6 13.7 - - - +
325A ARG* 3.0 52.1 + - + +
326A GLN* 5.0 2.2 - - - -
328A VAL* 3.0 28.2 + - + +
330A GLU* 1.3 73.2 - - - +
332A GLN* 1.3 60.7 + - - +
334A LEU* 3.3 6.5 + - - +
335A ARG* 3.0 28.4 + - - +
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Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 2.9 29.2 + - - +
327A ASP* 3.6 17.8 + - - +
328A VAL 3.1 8.6 + - - +
329A GLU* 3.1 20.0 + - - +
331A TYR* 1.3 76.5 - - - +
333A ASN* 1.3 65.6 + - - +
335A ARG* 3.2 9.8 + - - +
336A ALA* 3.1 22.2 + - - +
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Residues in contact with ASN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 2.9 35.8 + - - +
330A GLU* 3.5 31.5 + - - +
332A GLN* 1.3 77.8 - - - +
334A LEU* 1.3 64.6 + - - +
336A ALA* 3.2 8.9 + - - +
337A VAL* 3.1 26.8 + - + +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.2 13.7 - - + +
289A ASP* 3.2 20.2 - - - +
290A TYR* 3.2 45.8 - - + +
294A ILE* 5.3 2.0 - - + -
295A PRO* 4.1 20.9 - - + -
330A GLU* 3.1 14.4 + - - +
331A TYR* 3.3 6.0 + - - +
333A ASN* 1.3 79.7 - - - +
335A ARG* 1.3 61.9 + - - +
337A VAL* 3.2 9.0 + - + +
338A VAL* 3.0 36.7 + - + +
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 3.8 27.5 - - + +
326A GLN* 4.2 17.2 - - - +
331A TYR 3.0 14.3 + - - +
332A GLN* 3.5 12.8 - - - +
333A ASN 3.2 0.4 - - - -
334A LEU* 1.3 76.3 - - - +
336A ALA* 1.3 56.3 + - - +
338A VAL* 3.9 1.4 - - - +
339A ASN* 2.9 56.7 + - - +
359A PHE* 6.3 0.2 - - - -
361A HIS* 3.4 40.0 + - - +
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Residues in contact with ALA 336 (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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332A GLN 3.1 9.1 + - - +
333A ASN* 3.2 10.7 + - - +
335A ARG* 1.3 79.6 - - - +
337A VAL* 1.3 61.9 + - + +
339A ASN* 3.5 9.5 + - - +
340A GLU* 3.2 23.6 + - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 4.4 23.1 - - + -
333A ASN* 3.1 16.5 + - + +
334A LEU* 3.2 14.1 + - + +
336A ALA* 1.3 74.4 - - + +
338A VAL* 1.3 64.5 + - - +
340A GLU* 3.2 7.7 + - - +
341A LEU* 3.1 26.4 + - + +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.1 16.6 - - + -
294A ILE* 3.9 33.4 - - + -
295A PRO* 4.3 6.7 - - + -
298A LEU* 4.2 3.1 - - + -
334A LEU* 3.0 36.2 + - + +
335A ARG 3.9 2.7 - - - +
337A VAL* 1.3 73.1 - - - +
339A ASN* 1.3 65.7 + - - +
341A LEU* 3.2 7.6 + - - +
342A VAL* 2.9 29.2 + - + +
359A PHE* 3.8 30.1 - - + -
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Residues in contact with ASN 339 (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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335A ARG* 2.9 49.7 + - - +
336A ALA* 3.8 8.6 - - - +
338A VAL* 1.3 75.7 - - - +
340A GLU* 1.3 57.6 + - - +
342A VAL* 3.7 5.9 - - - +
343A GLY* 2.9 25.8 + - - -
359A PHE* 3.6 25.7 - - - -
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA 3.2 14.5 + - - +
337A VAL* 3.7 6.2 - - - +
339A ASN* 1.3 76.1 - - - +
341A LEU* 1.3 69.7 + - - +
343A GLY* 3.4 0.9 + - - -
344A ARG* 2.8 49.3 + - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 3.6 39.0 - - + +
298A LEU* 3.9 17.3 - - + -
299A HIS* 3.6 28.5 - - + +
337A VAL* 3.1 17.2 + - + +
338A VAL* 3.6 7.9 - - - +
340A GLU* 1.3 80.3 - - - +
342A VAL* 1.3 60.5 + - - +
344A ARG* 3.5 31.6 - - - +
345A ILE* 2.9 49.2 + - + +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.8 17.9 - - + -
338A VAL* 2.9 21.9 + - + +
339A ASN* 3.7 5.6 - - - +
341A LEU* 1.3 74.8 - - - +
343A GLY* 1.3 65.3 + - - +
345A ILE* 4.4 0.2 - - - +
346A ASN* 3.1 42.7 + - - +
357A ILE* 4.4 15.9 - - + -
359A PHE* 3.9 47.8 - - + -
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Residues in contact with GLY 343 (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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339A ASN 2.9 15.3 + - - -
340A GLU* 3.7 3.1 - - - -
342A VAL* 1.3 79.5 - - - +
344A ARG* 1.3 61.2 + - - +
346A ASN* 4.2 3.3 - - - +
347A GLY* 3.1 20.3 + - - -
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Residues in contact with ARG 344 (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* 3.9 8.9 + - - -
302A GLU* 2.9 43.4 + - - -
340A GLU* 2.8 41.6 + - - +
341A LEU* 3.5 29.6 - - - +
343A GLY* 1.3 73.3 - - - +
345A ILE* 1.3 62.0 + - - +
347A GLY* 3.2 2.1 + - - -
348A LYS* 3.0 39.1 + - + +
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Residues in contact with ILE 345 (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* 3.2 39.9 - - + +
299A HIS 4.3 0.2 - - - +
301A LEU* 4.8 9.4 - - + -
302A GLU* 4.2 19.1 - - + +
341A LEU* 2.9 38.0 + - + +
344A ARG* 1.3 88.4 - - - +
346A ASN* 1.3 64.4 + - - +
348A LYS* 3.2 7.3 + - - +
349A PHE* 3.1 39.8 + - + +
356A PRO* 4.3 3.7 - - + +
357A ILE* 3.6 20.6 - - + -
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Residues in contact with ASN 346 (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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342A VAL* 3.1 32.6 + - - +
343A GLY* 4.2 2.9 - - - +
345A ILE* 1.3 75.7 - - - +
347A GLY* 1.3 56.3 + - - +
350A GLY* 2.7 33.4 + - - -
355A MET* 3.7 25.0 - - - +
356A PRO* 3.0 11.7 - - - +
357A ILE* 2.7 52.6 + - - +
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Residues in contact with GLY 347 (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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343A GLY 3.1 16.3 + - - -
344A ARG 3.6 4.5 - - - -
345A ILE 3.2 0.2 - - - -
346A ASN* 1.3 77.1 - - - +
348A LYS* 1.3 62.2 + - - +
350A GLY 4.4 4.3 + - - +
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Residues in contact with LYS 348 (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* 2.8 26.8 + - - +
306A GLN* 2.9 25.3 + - - -
344A ARG* 3.0 22.5 + - + +
345A ILE* 3.5 10.8 - - - +
346A ASN 3.2 0.2 - - - -
347A GLY* 1.3 80.9 - - - +
349A PHE* 1.3 83.1 + - + +
350A GLY 4.9 0.9 - - - +
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Residues in contact with PHE 349 (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* 3.9 27.4 - - + -
305A LEU* 3.8 40.6 - - + -
306A GLN* 3.9 24.5 - - + -
312A VAL* 4.0 29.5 - - + +
345A ILE* 3.1 21.3 + - + -
348A LYS* 1.3 100.7 - - + +
350A GLY* 1.3 66.6 + - - +
351A THR* 3.8 5.9 + - - +
354A TYR* 3.9 13.5 - - - -
356A PRO* 3.5 19.5 - - + -
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASN 2.7 26.6 + - - -
347A GLY 4.3 3.3 - - - +
348A LYS 3.6 2.5 - - - +
349A PHE* 1.3 77.0 - - - +
351A THR* 1.3 63.1 + - - +
354A TYR 3.1 13.2 - - - -
355A MET* 3.7 11.7 - - - -
356A PRO* 4.1 4.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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