Contacts of the helix formed by residues 437 - 456 (chain B) in PDB entry 2YEM
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 HIS 437 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ASN* 3.8 10.7 + - + -
434B PRO* 3.1 42.3 + - + +
435B PRO 3.3 0.5 - - - +
436B ASP* 1.3 83.1 + - - +
438B GLU* 1.3 79.0 + - + +
439B VAL* 3.3 21.4 + - + +
440B VAL* 3.1 25.2 + - + +
441B ALA* 3.4 6.2 + - - +
1460B WSH 3.6 60.7 + + - -
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ASP 3.6 2.4 + - - -
437B HIS* 1.3 78.6 + - + +
439B VAL* 1.3 61.2 + - - +
441B ALA* 3.3 9.7 + - + +
442B MET* 3.2 33.2 + - + +
1460B WSH 3.7 25.8 - - + -
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PRO* 4.2 7.0 - - + -
376B PHE* 3.8 10.5 - - + -
429B CYS* 3.7 11.7 - - - -
433B ASN* 3.5 33.4 - - - +
437B HIS* 3.3 18.8 + - + +
438B GLU* 1.3 76.3 - - - +
440B VAL* 1.3 61.6 + - - +
442B MET* 3.5 9.1 + - - +
443B ALA* 3.0 26.9 + - - +
1460B WSH 3.6 51.3 - - + +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A MET* 4.1 22.0 - - + -
429B CYS* 4.2 10.1 - - - +
430B TYR* 3.8 24.2 - - + -
433B ASN* 3.8 22.4 - - + +
434B PRO 3.4 23.6 - - - +
435B PRO* 3.6 18.4 - - + +
437B HIS* 3.1 9.4 + - + +
439B VAL* 1.3 78.1 - - + +
441B ALA* 1.3 65.9 + - - +
443B ALA* 3.2 7.0 + - - +
444B ARG* 3.0 22.9 + - + +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B HIS 3.4 6.2 + - - +
438B GLU* 3.3 13.7 + - + +
440B VAL* 1.3 80.1 - - - +
442B MET* 1.3 62.9 + - + +
444B ARG* 3.5 6.4 + - - +
445B LYS* 3.1 33.1 + - - +
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Residues in contact with MET 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ALA 3.5 15.3 - - - +
372B TYR* 3.6 26.9 - - + +
374B TRP* 3.5 31.9 - - + +
375B PRO* 3.5 24.5 - - + -
376B PHE* 4.1 5.4 - - + -
438B GLU* 3.2 24.8 + - + +
439B VAL* 3.6 8.5 - - - +
440B VAL 3.2 0.4 - - - -
441B ALA* 1.3 75.5 - - + +
443B ALA* 1.3 64.3 + - - +
445B LYS* 3.3 5.5 + - - +
446B LEU* 3.1 23.6 + - - +
1460B WSH 3.7 24.2 - - - -
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 3.5 30.7 - - + -
426B PHE* 3.4 15.0 - - + -
429B CYS* 4.0 8.7 - - + -
430B TYR* 3.6 21.5 - - + +
439B VAL 3.0 14.0 + - - +
440B VAL 3.2 5.4 + - - +
442B MET* 1.3 76.1 - - - +
444B ARG* 1.3 51.2 + - - +
446B LEU 3.2 1.0 + - - -
447B GLN* 2.7 36.4 + - - +
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ARG* 3.0 24.7 + - - +
447A GLN* 3.7 20.3 + - - +
448A ASP* 2.5 44.7 + - - +
451A GLU* 4.2 6.0 - - - +
452A MET* 4.3 15.3 - - + -
430B TYR* 3.1 28.3 - - + +
440B VAL 3.0 18.3 + - - +
441B ALA* 3.8 6.7 - - - +
442B MET 3.3 0.2 - - - -
443B ALA* 1.3 77.4 - - - +
445B LYS* 1.3 56.9 + - - +
447B GLN* 2.9 35.8 + - - +
448B ASP* 2.8 68.4 + - - +
451B GLU* 5.6 0.2 - - - +
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Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 3.9 38.3 - - + -
441B ALA* 3.1 24.0 + - - +
442B MET* 3.3 9.2 + - - +
444B ARG* 1.3 76.0 - - - +
446B LEU* 1.3 61.9 + - - +
448B ASP* 3.4 9.9 + - - +
449B VAL* 3.3 23.6 + - - +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B MET* 3.9 35.8 - - + +
369B HIS* 4.5 4.5 - - + -
372B TYR* 3.9 16.6 - - + +
373B ALA* 3.7 25.6 - - + -
376B PHE* 3.9 23.8 - - + -
400B MET* 4.0 15.7 - - - -
425B MET* 4.7 0.2 - - + -
426B PHE* 3.8 19.5 - - + -
442B MET 3.1 15.6 + - - +
443B ALA* 3.8 3.4 - - - +
445B LYS* 1.3 73.8 - - - +
447B GLN* 1.3 66.2 + - - +
449B VAL* 3.1 9.9 + - + +
450B PHE* 3.0 20.1 + - - +
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN* 4.1 1.2 - - - +
451A GLU* 3.6 24.6 + - - +
423B ARG* 4.5 12.1 - - - +
426B PHE* 3.5 32.9 - - + +
430B TYR* 2.6 35.0 + - - +
443B ALA 2.7 22.0 + - - +
444B ARG* 2.9 22.5 + - - +
446B LEU* 1.3 74.3 - - - +
448B ASP* 1.3 57.3 + - - +
450B PHE* 3.2 1.9 + - + -
451B GLU* 2.8 65.9 + - + +
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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
----------------------------------------------------------
430A TYR* 4.5 4.4 + - - -
444A ARG* 3.4 53.0 + - - +
447A GLN* 4.9 0.9 - - - +
448A ASP* 4.9 2.1 - - - +
444B ARG* 2.8 54.5 + - - +
445B LYS* 3.6 10.0 - - - +
446B LEU 3.2 0.2 - - - -
447B GLN* 1.3 72.5 - - - +
449B VAL* 1.3 61.5 + - - +
451B GLU* 4.2 4.3 - - - +
452B MET* 3.2 24.3 + - - +
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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
----------------------------------------------------------
444A ARG* 5.7 0.4 - - - +
360B ILE* 6.4 0.4 - - + -
363B GLU* 3.9 14.1 - - + +
364B MET* 4.9 11.9 - - + -
369B HIS* 3.6 46.2 - - + +
372B TYR* 4.2 10.1 - - + +
445B LYS 3.5 13.7 - - - +
446B LEU* 3.1 11.9 + - + +
448B ASP* 1.3 79.2 - - + +
450B PHE* 1.3 63.6 + - - +
452B MET* 3.6 4.1 - - - +
453B ARG* 3.2 32.0 + - + +
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Residues in contact with PHE 450 (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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360B ILE* 3.9 22.4 - - + -
364B MET* 4.1 20.1 - - + +
418B PHE* 3.9 16.8 - + - -
419B GLY* 3.9 15.0 - - - -
422B VAL* 3.6 32.5 - - + -
423B ARG* 3.9 12.3 - - + -
426B PHE* 4.7 0.2 - + - -
446B LEU 3.0 12.8 + - - +
447B GLN* 3.2 12.1 + - + +
449B VAL* 1.3 78.5 - - - +
451B GLU* 1.3 87.9 + - + +
453B ARG* 3.2 2.3 + - - +
454B PHE* 2.8 69.8 + + + +
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Residues in contact with GLU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ARG* 4.8 0.9 - - - +
427A SER* 4.0 9.9 + - - -
430A TYR* 3.8 22.8 - - + -
447A GLN* 4.1 19.5 + - - +
423B ARG* 2.8 44.2 + - - -
444B ARG* 5.6 0.2 - - - +
447B GLN* 2.8 54.6 + - + +
448B ASP* 4.3 4.3 - - - +
450B PHE* 1.3 83.9 - - + +
452B MET* 1.3 57.4 + - - +
454B PHE* 3.9 3.5 - - - +
455B ALA* 2.9 31.5 + - - +
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Residues in contact with MET 452 (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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430A TYR* 3.6 33.0 - - + +
433A ASN 4.7 0.4 - - - +
435A PRO* 4.2 19.1 - - + -
440A VAL* 3.6 22.0 - - + -
444A ARG* 3.2 26.7 - - - +
448B ASP 3.2 16.9 + - - +
449B VAL* 3.6 5.4 - - - +
451B GLU* 1.3 77.9 - - - +
453B ARG* 1.3 81.8 + - - +
455B ALA* 3.4 3.1 + - - +
456B LYS* 3.1 55.4 + - + +
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Residues in contact with ARG 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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435A PRO* 5.3 6.3 - - - +
356B CYS* 5.2 2.1 - - - -
360B ILE* 3.7 34.9 - - + +
363B GLU* 2.6 44.5 + - + +
368B LYS* 4.8 7.7 - - - +
369B HIS* 5.0 2.4 + - - -
449B VAL* 3.2 23.7 + - + +
450B PHE 3.9 1.8 - - - +
452B MET* 1.3 98.4 - - - +
454B PHE* 1.3 65.9 + - - +
456B LYS* 3.3 14.2 + - - +
457B MET* 3.3 11.4 + - - -
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Residues in contact with PHE 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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427A SER* 5.4 2.7 - - - -
360B ILE* 3.6 8.9 - - + +
415B ALA* 3.6 32.5 - - + -
416B GLN* 3.6 31.0 - - - -
418B PHE* 4.4 6.7 - + - -
419B GLY* 3.9 13.0 - - - -
423B ARG* 3.8 29.4 - - - -
450B PHE* 2.8 46.6 + + + +
451B GLU* 3.9 4.5 - - - +
453B ARG* 1.3 78.0 - - - +
455B ALA* 1.3 61.1 + - - +
456B LYS 3.5 0.5 + - - -
457B MET* 3.5 31.7 - - + +
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Residues in contact with ALA 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 3.6 35.6 + - - +
430A TYR* 3.7 15.9 - - + -
431A LYS* 3.5 30.3 - - + +
451B GLU 2.9 20.7 + - - +
452B MET 3.7 2.5 - - - +
453B ARG 3.3 0.2 - - - -
454B PHE* 1.3 79.2 - - - +
456B LYS* 1.3 56.7 + - - +
457B MET 3.3 5.0 + - - +
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Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR 3.3 19.9 + - - +
431A LYS* 3.7 18.2 - - + +
433A ASN 2.6 27.9 + - - -
434A PRO* 3.6 2.2 - - - +
435A PRO* 3.5 26.1 - - + +
452B MET* 3.1 28.5 + - + +
453B ARG* 3.3 9.0 + - - +
455B ALA* 1.3 75.9 - - - +
457B MET* 1.3 63.2 + - - +
458B PRO* 3.6 7.1 - - - +
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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
------------------------------------------------------------
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