Contacts of the helix formed by residues 370 - 380 (chain A) in PDB entry 3U86
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 ASP 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLU* 3.0 20.0 + - + +
369A ASN* 1.3 80.1 - - + +
371A VAL* 1.3 59.7 + - + +
372A ILE 3.5 1.3 - - - -
373A PRO* 3.7 2.5 - - - -
374A ASN* 3.1 44.6 + - - +
46B LYS* 2.9 45.7 + - + +
47B LYS* 4.1 8.7 + - - -
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Residues in contact with VAL 371 (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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329A CYS* 3.6 30.1 - - - -
341A TRP* 3.9 11.4 - - + -
366A GLU* 2.7 30.9 + - + +
367A VAL* 3.8 9.0 - - - +
370A ASP* 1.3 74.5 - - + +
372A ILE* 1.3 62.7 + - - +
374A ASN* 4.1 3.0 - - - +
375A LEU* 3.1 27.3 + - + +
39B ALA* 4.3 13.2 - - + +
46B LYS* 4.0 31.6 - - + +
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Residues in contact with ILE 372 (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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338A LEU* 4.4 14.8 - - + -
341A TRP* 3.7 28.7 - - + -
367A VAL* 2.9 35.3 + - + +
368A ALA* 4.3 3.8 - - - +
371A VAL* 1.3 74.8 - - - +
373A PRO* 1.3 69.1 - - + +
375A LEU* 3.0 6.2 + - - +
376A LEU* 2.8 50.2 + - + +
413A LEU* 4.4 23.1 - - + -
416A PHE* 4.4 19.1 - - + -
417A TYR* 5.7 1.3 - - + +
443A SER* 4.3 5.8 - - - +
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Residues in contact with PRO 373 (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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368A ALA 3.1 24.0 - - - +
369A ASN 3.2 22.2 - - - +
370A ASP 3.7 9.2 - - - +
372A ILE* 1.3 93.2 - - + +
374A ASN* 1.3 65.3 + - - +
376A LEU* 3.8 5.0 - - + +
377A LYS* 3.0 29.1 + - - +
439A PHE* 4.2 13.7 - - + -
442A GLN* 4.0 18.6 - - - +
443A SER* 4.2 12.8 - - - +
446A ARG* 4.6 2.3 + - - -
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Residues in contact with ASN 374 (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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370A ASP* 3.1 33.9 + - - +
371A VAL* 4.4 3.8 - - - +
373A PRO* 1.3 82.0 - - - +
375A LEU* 1.3 60.1 + - - +
377A LYS* 3.9 27.9 - - + +
378A GLU* 3.5 19.9 + - - +
47B LYS* 6.1 2.6 - - - +
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Residues in contact with LEU 375 (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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329A CYS* 3.7 33.7 - - + +
332A ARG* 4.0 20.4 - - - +
334A VAL* 3.9 26.2 - - + +
337A ALA* 4.7 9.4 - - + -
338A LEU* 6.4 0.9 - - + -
341A TRP* 4.3 14.1 - - + -
371A VAL* 3.1 18.6 + - + +
372A ILE* 3.0 6.4 + - + +
374A ASN* 1.3 78.4 - - - +
376A LEU* 1.3 68.0 - - + +
378A GLU* 3.5 21.3 - - - +
379A ALA* 3.5 16.1 + - - +
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Residues in contact with LEU 376 (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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334A VAL* 6.2 3.6 - - + -
338A LEU* 5.0 15.7 - - + -
372A ILE* 2.8 32.2 + - + +
373A PRO* 3.8 4.3 - - + +
375A LEU* 1.3 74.3 - - + +
377A LYS* 1.3 57.5 + - - +
378A GLU 3.0 1.8 - - - -
379A ALA* 2.7 26.5 + - + +
380A ALA* 2.8 11.4 + - - +
404A LEU* 3.9 20.7 - - + +
413A LEU* 5.2 1.3 - - + -
443A SER* 3.6 46.7 - - - +
446A ARG* 3.7 21.3 - - + +
447A PHE* 4.4 16.4 - - + -
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Residues in contact with LYS 377 (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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373A PRO 3.0 13.2 + - - +
374A ASN* 3.9 36.8 - - - +
376A LEU* 1.3 78.2 - - - +
378A GLU* 1.3 62.9 + - - +
380A ALA* 3.4 10.0 - - - +
381A SER* 3.1 18.1 + - - +
446A ARG* 3.9 29.1 - - - +
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Residues in contact with GLU 378 (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 ARG* 2.9 47.7 + - - +
334A VAL* 5.2 2.9 - - - +
374A ASN 3.5 14.3 + - - +
375A LEU* 3.5 19.3 - - - +
376A LEU 3.0 0.6 - - - -
377A LYS* 1.3 84.8 - - + +
379A ALA* 1.3 59.9 + - - +
381A SER* 3.1 15.1 + - - -
382A LEU* 3.1 33.9 - - + +
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Residues in contact with ALA 379 (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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334A VAL* 4.9 14.8 - - + -
375A LEU 3.5 7.8 + - - +
376A LEU* 2.7 15.1 + - + +
378A GLU* 1.3 75.4 - - - +
380A ALA* 1.3 55.5 + - - +
381A SER 2.8 10.2 + - - -
382A LEU* 3.1 22.2 + - + +
383A LEU* 3.5 16.8 + - - +
402A SER* 4.8 4.9 + - - +
403A ALA* 5.6 4.0 - - + +
404A LEU* 3.8 19.0 - - + +
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Residues in contact with ALA 380 (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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376A LEU 2.8 10.7 + - - +
377A LYS* 3.4 15.0 - - - +
379A ALA* 1.3 73.5 - - - +
381A SER* 1.3 58.1 + - - +
383A LEU* 4.9 3.4 - - - -
384A GLU* 2.8 43.2 - - - +
404A LEU* 3.3 20.4 - - + +
446A ARG* 3.8 24.2 - - - +
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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