Contacts of the helix formed by residues 390 - 398 (chain A) 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 LEU 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLY* 6.5 0.4 - - - -
41A GLY 6.2 1.8 - - - +
249A ILE* 3.9 23.3 - - + -
250A GLY* 4.1 16.4 - - - +
251A ILE* 3.8 26.5 - - + -
388A MET* 4.1 7.0 - - + -
389A ASN* 1.3 70.1 - - - +
391A VAL* 1.3 66.1 + - - +
392A ALA 3.1 2.5 - - - -
393A TYR* 3.0 23.3 + - + +
394A GLU* 2.9 32.3 + - - +
601A UDP 2.9 25.2 + - - +
602A VDM 3.6 23.1 - - + +
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Residues in contact with VAL 391 (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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285A VAL* 3.3 38.1 - - + +
286A ASP* 5.4 0.9 - - - +
373A TYR* 3.4 29.2 - - + +
379A CYS* 4.4 14.6 - - - -
381A VAL* 4.8 4.9 - - + -
389A ASN* 3.3 9.7 + - - +
390A LEU* 1.3 77.4 - - - +
392A ALA* 1.3 59.0 + - - +
394A GLU* 3.3 4.5 + - - +
395A TYR* 2.9 28.1 + - - +
601A UDP 3.5 38.3 + - - +
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Residues in contact with ALA 392 (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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381A VAL* 4.3 9.2 - - + +
389A ASN* 3.4 19.3 + - - +
390A LEU 3.1 0.4 - - - -
391A VAL* 1.3 80.6 - - - +
393A TYR* 1.3 62.2 + - - +
395A TYR* 3.4 4.7 + - - +
396A ILE* 3.2 27.1 + - - +
406A LEU* 4.0 23.6 - - + +
408A LEU* 4.3 9.9 - - + -
414A ALA* 4.8 0.9 - - + -
418A LEU* 3.9 20.6 - - + -
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Residues in contact with TYR 393 (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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249A ILE 4.0 15.4 + - - -
250A GLY* 4.3 4.0 - - - -
251A ILE* 3.3 41.3 - - + +
388A MET* 3.5 20.6 - - + +
389A ASN 3.7 14.4 - - - -
390A LEU* 3.0 11.4 + - + +
392A ALA* 1.3 74.2 - - - +
394A GLU* 1.3 59.1 + - - +
396A ILE* 3.1 5.6 + - - +
397A ALA* 2.8 27.9 + - - +
414A ALA* 4.0 21.5 - - + -
417A SER* 3.4 27.7 + - - -
418A LEU* 4.1 12.6 - - + -
457A TYR* 3.5 26.3 + + - -
458A VAL* 3.9 23.1 - - + +
461A TYR 4.4 5.2 - - - -
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Residues in contact with GLU 394 (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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251A ILE* 3.9 22.2 - - + +
256A PHE* 3.3 35.4 - - + -
369A LEU* 5.1 0.2 - - - -
373A TYR* 3.1 21.2 + - + -
390A LEU* 2.9 22.2 + - - +
391A VAL* 3.7 3.2 - - - +
393A TYR* 1.3 75.4 - - - +
395A TYR* 1.3 59.7 + - - +
397A ALA* 3.4 3.0 + - - +
398A SER* 2.9 29.8 + - - -
601A UDP 2.5 48.7 + - - -
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Residues in contact with TYR 395 (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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283A VAL* 4.3 0.7 - - + -
373A TYR* 3.6 47.5 - + + -
376A SER* 2.8 28.7 + - - -
377A ASP 3.4 9.9 - - - -
378A ALA* 3.4 0.5 - - - -
379A CYS* 3.3 40.2 - - + -
391A VAL 2.9 15.7 + - - +
392A ALA* 3.7 5.2 - - - +
393A TYR 3.2 0.2 - - - -
394A GLU* 1.3 74.1 - - - +
396A ILE* 1.3 74.4 + - + +
398A SER* 3.1 10.2 + - - -
399A GLN* 3.2 37.7 - - + +
404A GLY* 3.3 24.8 - - - -
405A VAL 3.7 13.7 - - - -
406A LEU* 4.4 6.1 - - + -
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Residues in contact with ILE 396 (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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392A ALA 3.2 13.0 + - - +
393A TYR 3.1 8.1 + - - +
395A TYR* 1.3 79.3 - - + +
397A ALA* 1.3 63.2 + - - +
398A SER 3.0 5.9 + - - -
399A GLN* 3.2 9.9 + - + -
404A GLY 5.2 2.9 - - - +
406A LEU* 4.2 20.4 - - + -
418A LEU* 4.9 1.1 - - + -
451A PHE* 3.4 26.0 - - + -
454A LEU* 3.4 56.3 - - + +
455A ASP* 4.0 11.6 - - - +
458A VAL* 3.5 29.6 - - + -
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Residues in contact with ALA 397 (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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251A ILE* 3.6 22.2 - - + -
253A PRO* 4.2 12.6 - - + +
256A PHE* 4.0 20.3 - - + +
257A GLN* 4.0 26.1 + - - +
260A LEU* 4.8 2.3 - - - +
393A TYR 2.8 15.2 + - - +
394A GLU 3.6 7.0 - - - +
395A TYR 3.3 0.2 - - - -
396A ILE* 1.3 77.0 - - - +
398A SER* 1.3 58.9 + - - +
399A GLN 3.5 0.6 + - - -
400A GLN* 4.3 6.4 - - - +
455A ASP* 5.5 2.2 - - - -
458A VAL* 4.5 5.6 - - + +
459A ASN* 5.6 0.9 - - - +
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Residues in contact with SER 398 (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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256A PHE* 3.6 20.4 - - - +
260A LEU* 3.8 27.7 - - - +
370A ILE* 4.6 5.0 - - - +
373A TYR* 3.7 28.6 - - - +
374A ALA* 4.0 10.6 - - - +
394A GLU 2.9 16.6 + - - -
395A TYR 3.1 4.6 + - - -
396A ILE 3.0 1.0 - - - -
397A ALA* 1.3 77.8 - - - +
399A GLN* 1.3 63.9 + - - +
400A GLN* 3.6 3.2 + - - -
401A LYS 5.3 0.7 + - - -
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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