Contacts of the helix formed by residues 407 - 420 (chain A) in PDB entry 6U37
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 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A SER* 3.7 33.0 - - - +
230A GLY* 4.1 2.7 - - - +
236A TRP* 5.0 1.1 - - + +
295A PHE* 3.7 29.6 - - + -
330A VAL* 3.8 7.9 - - + -
334A GLU* 3.4 41.5 - - + +
403A GLY* 2.9 12.6 + - - +
405A HIS 3.8 0.6 - - - -
406A ASN* 1.3 84.3 - - + +
408A VAL* 1.3 66.8 + - - +
409A CYS 3.4 1.6 - - - -
410A PRO* 3.3 3.0 - - - +
411A VAL* 2.9 28.6 + - - +
447A HIS* 4.6 1.3 - - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 4.1 24.5 - - + -
331A VAL 5.3 0.9 - - - +
334A GLU* 4.0 22.4 - - + -
403A GLY* 2.9 16.4 + - - +
404A ASP* 3.7 19.3 - - - +
407A VAL* 1.3 71.6 - - - +
409A CYS* 1.3 58.6 + - - +
411A VAL* 3.3 2.8 + - - +
412A ALA* 2.8 27.2 + - - +
524A LEU* 4.0 27.4 - - + +
525A ARG* 4.2 26.0 - - + +
529A CYS* 4.2 3.1 - - - -
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Residues in contact with CYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 3.1 28.1 + - - +
408A VAL* 1.3 73.8 - - - +
410A PRO* 1.3 63.1 - - + +
412A ALA* 4.3 0.7 - - - +
413A GLN* 2.8 31.9 + - - +
529A CYS* 2.0 59.9 - - + -
532A TRP* 3.7 20.9 - - + -
533A ASN* 3.4 16.3 + - - +
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Residues in contact with PRO 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 3.9 9.2 - - + +
233A ASN* 2.9 32.9 + - - +
234A GLY* 3.9 26.2 - - - +
235A PRO* 4.1 1.8 - - + -
404A ASP 3.4 13.5 - - - +
405A HIS 3.6 13.9 - - - +
406A ASN 3.6 16.8 - - - +
407A VAL 3.3 11.0 - - - +
409A CYS* 1.3 90.9 - - + +
411A VAL* 1.3 60.3 + - - +
413A GLN* 4.6 1.8 - - + +
414A LEU* 3.1 14.0 + - - +
533A ASN* 4.7 1.8 - - - +
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 5.5 0.7 - - + +
229A SER 5.1 0.2 - - - +
230A GLY* 3.4 42.4 - - - +
231A ALA* 4.0 6.1 - - + -
328A VAL* 4.1 29.1 - - + +
329A GLY* 4.4 6.7 - - - +
330A VAL* 4.3 19.1 - - + -
407A VAL 2.9 22.6 + - - +
408A VAL 3.6 4.3 - - - +
410A PRO* 1.3 73.5 - - - +
412A ALA* 1.3 63.1 + - - +
414A LEU* 3.2 4.4 + - + +
415A ALA* 2.8 28.2 + - - +
524A LEU* 5.0 8.3 - - + -
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Residues in contact with ALA 412 (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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408A VAL 2.8 20.8 + - - +
409A CYS* 3.9 6.5 - - - +
411A VAL* 1.3 73.5 - - - +
413A GLN* 1.3 63.6 + - - +
415A ALA* 3.4 2.6 + - - +
416A GLY* 3.0 21.8 + - - -
503A TYR* 4.0 8.9 + - - +
524A LEU* 4.0 39.5 - - + +
529A CYS* 4.6 7.2 - - + -
533A ASN* 5.1 1.1 - - - +
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Residues in contact with GLN 413 (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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233A ASN* 3.4 19.7 + - - +
313A GLU* 4.3 24.7 + - - +
316A ILE* 5.1 1.5 - - + +
317A ASN* 5.9 2.5 - - - +
409A CYS 2.8 17.9 + - - +
410A PRO* 4.0 4.0 - - - +
412A ALA* 1.3 77.0 - - - +
414A LEU* 1.3 61.7 + - - +
416A GLY* 4.1 0.5 - - - -
417A ARG* 3.3 31.4 + - + +
533A ASN* 3.6 45.1 + - - +
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Residues in contact with LEU 414 (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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210A GLY* 5.6 0.7 - - - -
213A LEU* 6.1 3.6 - - + -
214A LEU* 6.3 0.2 - - + -
227A LEU* 3.7 30.5 - - + -
230A GLY 5.1 0.2 - - - +
231A ALA* 4.0 6.1 - - + -
232A PRO* 3.9 16.2 - - + -
233A ASN* 3.9 7.5 - - - +
316A ILE* 3.6 35.4 - - + -
328A VAL* 5.0 8.1 - - + -
410A PRO 3.1 18.3 + - - +
411A VAL* 3.2 5.4 + - + +
413A GLN* 1.3 75.2 - - - +
415A ALA* 1.3 60.0 + - - +
417A ARG* 3.3 1.9 + - - +
418A LEU* 2.9 61.8 + - + +
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Residues in contact with ALA 415 (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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328A VAL* 3.7 28.3 - - + -
411A VAL 2.8 19.8 + - - +
412A ALA* 3.9 3.8 - - - +
414A LEU* 1.3 74.8 - - - +
416A GLY* 1.3 61.8 + - - +
418A LEU* 3.5 4.7 + - - +
419A ALA* 3.1 25.8 + - - +
425A VAL* 3.9 8.9 - - + +
503A TYR* 3.6 26.6 - - + -
524A LEU* 5.1 2.5 - - + -
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Residues in contact with GLY 416 (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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412A ALA 3.0 16.0 + - - -
413A GLN* 4.1 1.3 - - - -
415A ALA* 1.3 79.1 - - - +
417A ARG* 1.3 62.9 + - - +
419A ALA* 3.5 0.3 + - - +
420A ALA* 3.1 26.5 + - - +
503A TYR* 3.7 13.4 - - - -
505A ALA* 3.7 17.1 - - - +
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Residues in contact with ARG 417 (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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316A ILE* 3.7 21.8 - - + +
317A ASN* 3.2 54.2 + - - +
321A PHE* 5.1 0.2 - - - -
413A GLN* 3.3 25.5 + - + +
414A LEU 3.9 0.4 - - - +
416A GLY* 1.3 74.9 - - - +
418A LEU* 1.3 66.4 + - - +
420A ALA* 3.7 4.7 + - - -
421A GLN* 2.4 66.4 + - - +
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Residues in contact with LEU 418 (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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213A LEU* 5.2 7.9 - - + -
316A ILE* 5.4 0.7 - - + -
321A PHE* 3.5 48.0 - - + +
324A LEU* 4.9 3.4 - - + -
326A VAL* 3.8 34.3 - - + -
328A VAL* 5.3 1.1 - - + -
414A LEU* 2.9 49.5 + - + +
415A ALA* 3.9 2.9 - - - +
417A ARG* 1.3 78.9 - - - +
419A ALA* 1.3 60.5 + - - +
421A GLN 3.4 6.8 + - - -
422A GLY 3.6 0.3 + - - -
423A ALA* 3.0 32.1 + - + +
425A VAL* 3.7 13.2 - - + -
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Residues in contact with ALA 419 (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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415A ALA 3.1 17.2 + - - +
416A GLY 4.1 2.9 - - - +
418A LEU* 1.3 77.9 - - - +
420A ALA* 1.3 58.2 + - - +
421A GLN 3.2 4.0 + - - -
422A GLY* 3.8 5.2 + - - -
423A ALA 3.2 17.2 - - - +
425A VAL* 3.7 6.2 - - + +
503A TYR 3.2 27.6 - - - +
504A THR* 3.9 15.5 - - + -
505A ALA 4.1 3.6 - - - +
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Residues in contact with ALA 420 (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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416A GLY 3.1 18.8 + - - +
417A ARG* 3.7 6.0 + - - +
418A LEU 3.4 0.2 - - - -
419A ALA* 1.3 74.6 - - - +
421A GLN* 1.3 66.1 + - + +
422A GLY 3.8 0.9 - - - -
505A ALA* 3.8 18.2 - - + +
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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