Contacts of the helix formed by residues 440 - 456 (chain B) in PDB entry 5YGP
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 MET 440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ALA* 3.9 21.1 - - + -
385B ARG* 4.6 9.0 - - - +
416B TYR* 3.4 23.8 - - + -
419B LEU* 3.3 31.0 - - + -
423B ARG* 4.6 8.1 - - - -
436B ALA 3.2 23.3 - - - +
437B LEU* 3.0 24.7 + - - +
439B ARG* 1.3 77.0 - - - +
441B GLY* 1.3 63.0 + - - +
443B GLU* 4.4 4.0 + - - +
444B GLY* 3.5 13.3 + - - -
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PRO* 4.2 17.9 - - - -
438B GLU 4.9 1.8 + - - -
439B ARG* 3.4 5.1 + - - +
440B MET* 1.3 78.0 - - - +
442B LEU* 1.3 66.8 + - - -
443B GLU 3.3 0.2 - - - -
444B GLY 3.1 1.0 + - - -
445B CYS* 3.1 25.5 + - - -
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 4.6 3.8 - - + -
383A PRO* 4.0 11.9 - - + +
386A ARG* 3.4 50.9 - - + +
389A GLU* 3.9 10.5 - - + +
390A PHE* 3.6 43.3 - - + +
393A THR* 4.5 13.2 - - + +
441B GLY* 1.3 71.8 - - - -
443B GLU* 1.3 73.0 + - + +
445B CYS* 3.2 3.7 + - + -
446B VAL* 3.0 30.8 + - + +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 6.0 0.3 + - - -
440B MET 4.4 3.6 + - - +
441B GLY 3.3 0.8 - - - -
442B LEU* 1.3 90.3 - - + +
444B GLY* 1.3 60.4 + - - +
446B VAL* 3.5 5.3 + - - +
447B GLU* 3.1 25.6 + - - +
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Residues in contact with GLY 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LEU* 3.2 36.5 - - - +
440B MET* 3.5 16.4 + - - -
441B GLY 3.1 6.2 + - - -
443B GLU* 1.3 80.9 - - - +
445B CYS* 1.3 55.0 + - - +
447B GLU* 3.5 2.6 + - - +
448B ASP* 2.8 28.1 + - - +
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Residues in contact with CYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 5.1 4.9 - - + +
381A ALA* 3.9 10.5 - - - -
382A VAL* 3.9 33.0 - - + -
383A PRO* 4.6 1.1 - - - -
390A PHE* 3.5 23.6 - - + -
438B GLU* 3.6 28.9 - - - -
441B GLY 3.1 14.7 + - - +
442B LEU* 3.2 8.0 + - - +
444B GLY* 1.3 73.5 - - - +
446B VAL* 1.3 60.2 + - - +
448B ASP* 3.2 9.1 + - - +
449B LEU* 3.0 23.7 + - - +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PHE* 3.5 24.5 - - + -
393A THR* 3.9 28.5 - - + -
394A LEU* 4.2 8.5 - - + +
442B LEU* 3.0 28.9 + - + +
443B GLU* 3.9 6.5 - - - +
445B CYS* 1.3 73.7 - - - +
447B GLU* 1.3 66.2 + - - +
448B ASP 3.3 0.2 + - - -
449B LEU* 3.3 2.1 + - - +
450B ARG* 3.0 62.3 + - - +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 4.1 3.1 - - - +
422B TRP* 4.5 5.4 - - + -
423B ARG* 2.6 55.3 + - - +
437B LEU* 3.4 18.6 - - + +
443B GLU 3.1 17.8 + - - +
444B GLY* 3.8 4.5 - - - +
446B VAL* 1.3 77.8 - - - +
448B ASP* 1.3 55.6 + - - +
450B ARG* 4.0 8.1 - - - +
451B SER* 2.4 40.1 + - - +
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Residues in contact with ASP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 3.2 13.3 - - - +
434B TYR* 3.4 26.4 - - - +
437B LEU* 3.7 15.9 - - + +
438B GLU* 3.0 30.5 - - + +
444B GLY 2.8 18.8 + - - +
445B CYS* 3.3 10.5 - - - +
446B VAL 3.1 0.4 - - - -
447B GLU* 1.3 76.8 - - - +
449B LEU* 1.3 63.3 + - - +
451B SER* 3.3 5.9 + - - -
452B ARG* 2.8 46.3 + - - +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA 5.5 0.4 - - - +
374A GLN* 3.7 41.7 - - + +
375A LEU* 3.9 20.0 - - + +
378A VAL* 4.4 9.0 - - + -
390A PHE* 4.2 7.9 - - + -
394A LEU* 3.6 35.7 - - + -
396A LEU* 4.3 5.8 - - + -
445B CYS 3.0 15.6 + - - +
446B VAL 3.3 2.9 + - - +
448B ASP* 1.3 76.3 + - - +
450B ARG* 1.3 61.1 + - - +
452B ARG* 2.9 9.2 + - - +
453B LEU* 2.8 56.6 + - + +
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Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A THR* 3.2 36.6 + - - +
394A LEU* 4.5 16.0 + - + +
446B VAL* 3.0 42.6 + - + +
447B GLU* 4.1 6.9 - - - +
449B LEU* 1.3 75.6 - - - +
451B SER* 1.3 60.7 + - - +
453B LEU* 4.0 12.0 - - + +
454B GLN* 3.1 24.4 + - - +
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Residues in contact with SER 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B TRP* 3.1 45.7 - - - -
434B TYR* 4.0 15.9 + - - -
437B LEU* 4.2 2.4 - - - +
447B GLU* 2.4 28.5 + - - +
448B ASP* 3.3 10.5 - - - -
449B LEU 3.1 0.2 - - - -
450B ARG* 1.3 75.0 - - - +
452B ARG* 1.3 63.2 + - - +
454B GLN* 3.4 7.7 + - - +
455B ARG* 3.0 22.2 + - - +
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Residues in contact with ARG 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN* 3.9 42.3 + - + +
377A ASP* 3.6 33.3 + - - +
378A VAL* 4.2 2.8 - - - +
434B TYR* 3.6 50.5 - - + +
438B GLU* 2.7 26.9 + - - -
448B ASP* 2.8 28.8 + - - +
449B LEU* 2.9 11.9 + - - +
451B SER* 1.3 75.1 - - - +
453B LEU* 1.3 64.5 + - - +
455B ARG* 3.1 14.4 + - - +
456B LEU* 3.3 16.9 + - - +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 3.8 40.6 - - + +
374A GLN* 4.4 7.6 - - + -
394A LEU* 5.9 0.7 - - + -
396A LEU* 4.3 23.6 - - + -
449B LEU* 2.8 43.7 + - + +
450B ARG* 4.0 11.0 - - + +
452B ARG* 1.3 76.6 - - - +
454B GLN* 1.3 61.2 + - - +
455B ARG 3.4 0.3 + - - -
456B LEU* 3.4 30.1 + - + +
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B TRP* 4.3 25.2 - - - +
450B ARG 3.1 19.1 + - - +
451B SER* 3.7 4.1 + - - +
452B ARG 3.3 0.2 - - - -
453B LEU* 1.3 77.7 - - - +
455B ARG* 1.3 63.5 + - - +
456B LEU 3.3 6.1 + - - +
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Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 3.4 43.1 - - + +
430B LEU* 3.4 39.3 - - - +
434B TYR* 3.9 14.1 + - - +
451B SER 3.0 12.9 + - - +
452B ARG* 3.1 15.2 + - - +
454B GLN* 1.3 80.4 - - - +
456B LEU* 1.3 62.8 - - + +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 4.4 25.6 - - + +
367A THR* 5.2 1.8 - - - +
370A ALA* 3.9 45.3 - - + +
371A ALA* 4.3 4.3 - - + +
374A GLN* 4.1 16.4 - - - +
452B ARG 3.3 12.0 + - - +
453B LEU* 3.6 34.7 - - + +
454B GLN 3.3 7.4 - - - +
455B ARG* 1.3 80.7 - - - +
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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