Contacts of the helix formed by residues 440 - 457 (chain B) in PDB entry 5YWB
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 ALA 440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B SER* 5.2 0.7 - - - +
306B ARG* 3.4 42.8 - - + +
307B ILE* 4.3 14.4 - - + -
310B ASP* 5.3 1.4 - - + +
436B PRO 3.8 1.7 + - - +
437B ASN 3.6 7.0 + - - +
438B LEU 2.9 0.8 - - - -
439B TRP* 1.3 79.8 - - - +
441B MET* 1.3 64.2 + - - +
442B PRO 3.4 2.0 - - - -
443B VAL* 3.2 10.3 - - + +
444B GLN* 3.1 26.8 + - - +
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Residues in contact with MET 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ASN 3.8 6.2 + - - +
438B LEU* 3.3 24.1 + - + +
440B ALA* 1.3 77.4 - - - +
442B PRO* 1.3 77.4 - - + +
444B GLN* 3.3 7.9 + - - +
445B ILE* 3.0 40.6 + - + +
589B PRO* 4.4 21.1 - - + +
590B LEU* 5.7 3.6 - - + -
593B LEU* 4.2 33.2 - - + -
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Residues in contact with PRO 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU 3.4 15.0 - - - +
439B TRP* 4.3 7.6 - - + +
440B ALA* 3.6 4.7 - - - +
441B MET* 1.3 100.1 - - + +
443B VAL* 1.3 63.2 + - + +
445B ILE* 3.0 13.8 - - + +
446B ILE* 3.0 34.3 + - + +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 3.7 45.3 - - + +
310B ASP* 5.6 3.6 - - + -
314B PHE* 5.9 0.4 - - + -
439B TRP 4.3 2.9 - - - +
440B ALA* 3.2 33.2 - - + +
442B PRO* 1.3 75.9 - - + +
444B GLN* 1.3 62.4 + - - +
446B ILE* 3.4 8.5 + - - +
447B VAL* 2.9 42.1 + - + +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG* 3.4 28.1 + - - -
310B ASP* 4.6 5.6 - - + +
314B PHE* 3.3 32.8 - - + -
440B ALA 3.1 20.5 + - - +
441B MET* 3.5 6.9 - - - +
442B PRO 3.2 0.2 - - - -
443B VAL* 1.3 78.4 - - - +
445B ILE* 1.3 64.2 + - + +
448B GLY* 2.9 24.4 + - - -
585B ILE* 2.9 45.3 + - - +
586B LEU* 4.6 3.0 - - + +
589B PRO* 3.4 23.9 - - + +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B MET* 3.0 25.9 + - + +
442B PRO* 3.0 21.8 - - + +
444B GLN* 1.3 81.0 - - + +
446B ILE* 1.3 84.7 + - + +
448B GLY* 3.2 1.8 + - - -
449B VAL* 3.0 24.4 + - + +
586B LEU* 3.5 32.5 - - + +
589B PRO* 5.5 3.8 - - + -
590B LEU* 5.8 6.1 - - + -
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Residues in contact with ILE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 3.0 29.1 + - + +
443B VAL* 3.8 7.4 - - - +
445B ILE* 1.3 89.1 - - + +
447B VAL* 1.3 65.9 + - + +
449B VAL* 3.2 14.1 - - + +
450B ILE* 3.0 26.2 + - + +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 5.4 9.4 - - + -
314B PHE* 3.4 31.4 - - + -
443B VAL* 2.9 30.7 + - + +
446B ILE* 1.3 78.5 - - + +
448B GLY* 1.3 63.5 + - - +
450B ILE* 3.2 14.8 - - + +
451B LEU* 2.9 27.9 + - + +
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Residues in contact with GLY 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 4.4 9.3 - - - -
444B GLN 2.9 14.9 + - - -
445B ILE* 3.2 5.1 + - - -
447B VAL* 1.3 75.4 - - - +
449B VAL* 1.3 57.4 + - - +
451B LEU* 3.3 5.7 + - - +
452B LEU* 3.0 34.0 + - - +
582B LEU* 4.7 13.4 - - - +
586B LEU* 6.0 8.1 - - - -
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ILE* 3.0 15.2 + - + +
446B ILE* 3.2 18.2 - - + +
448B GLY* 1.3 76.0 - - - +
450B ILE* 1.3 66.9 + - + +
452B LEU* 3.2 22.8 + - + +
453B TYR* 3.0 25.4 + - + +
460B ALA* 6.5 0.4 - - + -
464B ALA* 5.4 9.0 - - + -
467B ILE* 4.3 20.9 - - + -
586B LEU* 6.3 0.4 - - - +
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 3.0 16.4 + - + +
447B VAL* 3.2 32.5 - - + +
449B VAL* 1.3 79.3 - - + +
451B LEU* 1.3 61.0 + - + +
453B TYR* 4.2 9.0 + - + +
454B TYR* 3.7 34.1 - - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 3.9 29.4 - - + +
315B ALA* 5.5 0.9 - - - -
318B LEU* 5.2 22.0 - - + +
447B VAL* 2.9 22.6 + - + +
448B GLY 3.7 4.0 - - - +
449B VAL 3.1 0.2 - - - -
450B ILE* 1.3 79.6 - - + +
452B LEU* 1.3 64.3 + - - +
453B TYR 3.3 1.2 + - - -
454B TYR* 3.4 15.9 + - + +
455B ILE* 3.4 31.7 - - + +
582B LEU* 3.8 26.5 - - + -
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B GLY 3.0 20.5 + - - +
449B VAL* 3.2 31.6 + - + +
451B LEU* 1.3 73.6 - - - +
453B TYR* 1.3 65.3 + - - +
455B ILE* 3.7 5.3 - - - +
456B LEU* 2.9 36.2 + - + +
460B ALA* 4.6 21.1 - - + +
463B GLY* 5.7 4.5 - - - -
464B ALA* 5.6 5.2 - - + +
467B ILE* 4.8 11.0 - - + -
579B SER* 6.5 0.9 - - - -
582B LEU* 4.2 18.8 - - + +
586B LEU* 5.3 9.9 - - + -
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Residues in contact with TYR 453 (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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449B VAL* 3.0 16.6 + - + +
450B ILE* 4.3 8.7 - - + +
451B LEU 3.3 0.4 - - - -
452B LEU* 1.3 81.0 - - + +
454B TYR* 1.3 92.8 + + - +
455B ILE 2.9 1.9 + - - -
457B GLY* 2.9 48.2 + - - -
460B ALA* 4.5 14.1 - - + -
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Residues in contact with TYR 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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450B ILE* 3.7 33.0 - - + +
451B LEU* 3.4 12.2 + - + +
452B LEU 3.4 0.8 - - - -
453B TYR* 1.3 102.8 - + - +
455B ILE* 1.3 60.1 + - + +
457B GLY* 4.8 0.9 - - - -
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Residues in contact with ILE 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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318B LEU* 5.7 8.5 - - + -
321B PHE* 5.5 7.4 - - + -
451B LEU* 3.4 23.1 - - + +
452B LEU* 3.9 7.6 - - + +
453B TYR 3.0 1.2 - - - -
454B TYR* 1.3 82.2 - - + +
456B LEU* 1.3 62.5 + - - +
575B VAL* 3.4 50.6 - - + +
578B ALA* 4.4 17.7 - - + -
579B SER* 4.8 8.1 - - - +
582B LEU* 3.7 30.7 - - + -
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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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452B LEU* 2.9 20.3 + - + +
455B ILE* 1.3 79.8 - - - +
457B GLY* 1.3 61.1 + - - +
458B VAL 3.8 1.6 + - - -
459B SER* 4.0 19.2 + - - +
460B ALA* 3.9 24.5 - - + +
558B THR* 6.5 0.9 - - - -
562B HIS* 4.3 14.6 + - - -
567B LYS* 4.7 3.5 - - - -
575B VAL* 5.3 1.8 - - - -
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Residues in contact with GLY 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B TYR* 2.9 30.2 + - - -
454B TYR 4.8 0.9 - - - -
455B ILE 3.7 0.6 - - - -
456B LEU* 1.3 74.4 - - - +
458B VAL* 1.3 61.5 + - - -
459B SER 3.1 4.6 + - - -
460B ALA* 3.4 17.0 + - - +
567B LYS* 4.9 4.9 - - - -
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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
------------------------------------------------------------
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