Contacts of the helix formed by residues 429 - 443 (chain A) in PDB entry 6PUO
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 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ILE* 3.6 39.7 - - + +
190A PHE* 4.0 20.2 - - + +
193A GLY* 3.8 19.9 - - - -
194A LEU* 4.6 4.3 - - + +
419A PHE* 4.0 19.1 - - + -
428A ASP* 1.3 77.1 - - - +
430A ASP* 1.3 66.4 + - - +
432A ALA* 3.1 5.5 + - - +
433A ILE* 3.1 40.1 + - + +
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Residues in contact with ASP 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY* 3.9 9.7 + - - +
196A LYS* 3.3 25.9 + - - +
197A VAL* 3.7 33.6 - - + +
428A ASP* 3.3 20.9 - - - +
429A VAL* 1.3 74.9 - - - +
431A VAL* 1.3 72.9 + - - +
433A ILE* 3.2 6.0 + - - +
434A LEU* 3.0 38.6 + - + +
464A ARG* 3.8 13.3 + - - +
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Residues in contact with VAL 431 (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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427A GLN* 3.8 29.8 - - + -
428A ASP* 3.9 12.8 - - + +
430A ASP* 1.3 95.2 + - - +
432A ALA* 1.3 60.8 + - - +
434A LEU* 4.1 6.5 - - - +
435A GLN* 2.9 47.0 + - - +
464A ARG* 4.8 8.5 - - - +
466A ASP* 4.9 3.8 - - - +
467A ILE* 4.6 19.0 - - + +
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Residues in contact with ALA 432 (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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351A VAL* 4.9 5.8 - - + +
417A THR* 5.4 5.0 - - + +
419A PHE* 4.1 21.3 - - + +
428A ASP 3.8 12.1 - - - +
429A VAL 3.1 10.8 + - - +
431A VAL* 1.3 83.6 - - + +
433A ILE* 1.3 58.1 + - + +
435A GLN* 3.8 8.3 - - - +
436A ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 433 (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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169A LEU* 5.7 4.3 - - + -
171A ILE* 5.5 7.4 - - + -
194A LEU* 5.0 9.4 - - + -
197A VAL* 4.5 23.8 - - + -
326A VAL* 4.1 33.0 - - + +
328A VAL* 5.4 15.0 - - + -
351A VAL* 4.7 18.2 - - + -
429A VAL* 3.1 32.4 + - + +
430A ASP* 3.2 6.0 + - - +
432A ALA* 1.3 76.6 - - + +
434A LEU* 1.3 63.7 + - + +
436A ALA* 3.3 6.4 + - - +
437A LEU* 2.9 30.0 + - + +
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Residues in contact with LEU 434 (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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169A LEU* 4.7 10.3 - - + -
197A VAL* 4.4 21.5 - - + -
201A THR* 5.1 3.6 - - - +
430A ASP* 3.0 21.5 + - + +
431A VAL* 4.1 6.3 - - - +
433A ILE* 1.3 80.7 - - + +
435A GLN* 1.3 57.7 + - - +
437A LEU* 3.3 6.0 + - + +
438A LEU* 2.9 35.3 + - + +
462A TRP* 3.6 39.8 - - + -
464A ARG* 3.7 36.3 - - - +
467A ILE* 4.7 16.4 - - + -
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Residues in contact with GLN 435 (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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431A VAL* 2.9 35.4 + - - +
432A ALA* 3.9 6.3 - - - +
434A LEU* 1.3 72.8 - - - +
436A ALA* 1.3 60.3 + - - +
438A LEU* 3.8 6.3 - - - +
439A LYS* 2.9 31.4 + - - +
442A ARG* 4.9 1.6 + - - -
467A ILE* 5.4 9.3 - - + +
470A SER* 4.9 9.9 + - - -
471A GLU* 5.0 17.6 - - + +
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Residues in contact with ALA 436 (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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326A VAL* 5.8 0.7 - - + -
349A PRO* 4.6 10.0 - - + +
350A CYS 5.6 0.2 - - - +
351A VAL* 3.9 23.6 - - + -
414A GLN 5.5 0.3 - - - +
415A LEU 5.6 1.0 - - - +
417A THR* 4.0 20.0 - - + +
432A ALA 2.9 19.6 + - - +
433A ILE 3.6 4.5 - - - +
434A LEU 3.3 0.2 - - - -
435A GLN* 1.3 76.6 - - - +
437A LEU* 1.3 57.5 + - - +
439A LYS* 3.4 12.6 + - - +
440A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 437 (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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169A LEU* 3.8 28.5 - - + -
324A PRO* 3.8 21.5 - - + -
325A ILE 4.4 8.3 - - - +
326A VAL* 4.9 10.3 - - + +
349A PRO* 3.8 26.2 - - + +
433A ILE* 2.9 18.7 + - + +
434A LEU* 3.7 7.9 - - + +
435A GLN 3.3 0.2 - - - -
436A ALA* 1.3 78.6 - - - +
438A LEU* 1.3 56.6 + - + +
440A ALA* 3.4 1.6 + - + +
441A SER* 3.0 29.0 + - - -
458A LEU* 5.6 4.5 - - + -
462A TRP* 3.7 28.0 - - + -
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Residues in contact with LEU 438 (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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434A LEU 2.9 18.3 + - - +
435A GLN* 3.9 5.8 - - - +
437A LEU* 1.3 75.0 - - + +
439A LYS* 1.3 59.7 + - - +
441A SER* 3.3 4.9 + - - +
442A ARG* 2.9 38.7 + - - +
455A GLN* 3.8 47.1 - - + +
458A LEU* 4.9 13.7 - - + -
459A ALA* 5.4 2.9 - - + -
462A TRP* 4.7 17.5 - - + -
467A ILE* 3.7 17.9 - - + -
471A GLU* 3.3 28.5 - - - +
472A ILE* 4.9 5.2 - - + -
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Residues in contact with LYS 439 (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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413A ARG 4.3 5.9 + - - -
414A GLN* 3.3 40.7 + - - +
416A LEU 4.2 4.2 + - - -
417A THR* 3.2 28.1 + - - +
435A GLN 2.9 18.0 + - - +
436A ALA* 3.8 10.5 - - - +
437A LEU 3.3 0.2 - - - -
438A LEU* 1.3 76.7 - - - +
440A ALA* 1.3 61.8 + - - +
442A ARG* 3.2 25.4 + - - +
443A SER* 3.2 23.0 + - - -
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Residues in contact with ALA 440 (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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347A GLY 5.3 1.8 - - - +
349A PRO* 3.7 28.9 - - + -
414A GLN 5.2 3.8 - - - +
415A LEU* 4.0 28.2 - - + +
436A ALA 2.9 18.2 + - - +
437A LEU* 3.7 2.5 - - + +
439A LYS* 1.3 79.7 - - - +
441A SER* 1.3 61.0 + - - +
442A ARG 3.5 0.2 + - - -
443A SER* 3.7 6.7 + - - -
444A GLN* 3.6 16.3 + - - +
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Residues in contact with SER 441 (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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437A LEU* 3.0 18.9 + - - +
438A LEU* 3.8 7.6 - - - -
439A LYS 3.3 0.2 - - - -
440A ALA* 1.3 76.5 - - - +
442A ARG* 1.3 61.3 + - - +
444A GLN* 3.6 11.0 - - - +
451A ASN* 2.8 22.9 + - - -
454A HIS* 3.7 24.3 + - - -
455A GLN* 4.1 12.0 - - - +
458A LEU* 4.7 11.6 - - - +
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Residues in contact with ARG 442 (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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435A GLN 4.9 1.6 + - - -
438A LEU* 2.9 18.8 + - - +
439A LYS* 3.5 37.2 + - - +
440A ALA 3.2 0.4 - - - -
441A SER* 1.3 78.0 - - - +
443A SER* 1.3 62.8 + - - +
444A GLN 3.1 9.6 + - - +
446A HIS* 4.3 7.1 + - - -
451A ASN* 3.4 14.4 + - - +
452A TRP* 4.9 23.4 - - + +
455A GLN* 3.4 32.2 + - - +
471A GLU* 3.7 23.0 + - - -
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLN* 3.6 43.7 - - - +
415A LEU* 4.9 4.0 - - - +
439A LYS 3.2 5.5 + - - -
440A ALA* 3.7 9.2 + - - -
441A SER 3.4 0.2 - - - -
442A ARG* 1.3 77.7 - - - +
444A GLN* 1.3 64.0 + - - +
445A ASP* 3.7 1.9 + - - -
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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