Contacts of the helix formed by residues 551 - 563 (chain B) in PDB entry 4D1Q
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 TYR 551 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B GLU* 2.8 51.1 - - + +
526B PHE* 3.3 19.7 + + - -
527B TYR* 3.5 20.8 - + + -
530B GLU* 2.5 29.5 + - - -
543B TRP* 4.3 10.1 - + - -
544B TRP* 4.3 11.2 - + + -
547B ASN* 2.8 33.6 + - + +
548B SER 2.9 11.1 - - - +
550B LYS* 1.3 100.3 - - + +
552B PRO* 1.3 63.2 - - - +
554B LEU* 3.9 9.6 - - + -
555B SER* 3.1 28.5 + - - +
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Residues in contact with PRO 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PRO* 5.0 5.8 - - + -
523B GLU* 2.8 13.6 - - + +
548B SER 3.4 7.9 - - - +
549B LYS* 3.3 15.3 - - - +
550B LYS 3.2 12.3 - - - +
551B TYR* 1.3 87.6 - - - +
553B LYS* 1.3 65.6 + - + +
555B SER* 3.8 3.1 + - - -
556B LYS* 3.6 23.0 - - - +
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Residues in contact with LYS 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B MET* 3.3 33.3 - - + +
461B LEU* 5.6 1.6 - - - +
462B GLU* 2.7 41.8 + - + +
518B VAL 4.2 14.4 - - - +
519B CYS* 4.9 0.9 - - - +
520B PRO* 4.1 22.0 - - + -
523B GLU* 3.0 17.1 + - - +
552B PRO* 1.3 82.6 - - + +
554B LEU* 1.3 60.5 + - - +
556B LYS* 4.1 13.9 + - - +
557B LEU 3.8 8.8 + - - -
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Residues in contact with LEU 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE* 4.4 20.6 - - + -
454B CYS* 4.8 4.3 - - + -
458B MET* 3.3 29.8 - - + -
523B GLU* 2.7 32.4 + - + +
524B PHE* 4.4 15.9 - - + +
527B TYR* 4.0 24.5 - - + -
544B TRP* 3.9 23.8 - - + -
551B TYR* 3.9 7.2 - - + -
553B LYS* 1.3 71.5 - - - +
555B SER* 1.3 66.9 + - - +
556B LYS 2.9 3.4 + - - -
557B LEU* 3.0 11.0 + - + +
558B ALA* 2.9 19.4 + - - +
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Residues in contact with SER 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B TRP* 3.7 31.6 - - - -
547B ASN 4.3 1.1 - - - -
548B SER* 3.4 28.3 + - - -
551B TYR* 3.1 23.9 + - - +
552B PRO 3.8 3.6 + - - -
554B LEU* 1.3 77.1 - - - +
556B LYS* 1.3 72.1 + - - +
559B LEU* 2.9 33.0 + - - +
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Residues in contact with LYS 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B LEU* 3.7 32.7 + - + +
464B ILE* 3.7 27.3 - - - +
552B PRO 3.6 17.5 + - - +
553B LYS* 4.1 13.9 - - - +
554B LEU 2.9 1.4 + - - -
555B SER* 1.3 85.0 + - - +
557B LEU* 1.3 64.1 + - - +
558B ALA 3.0 0.2 + - - -
559B LEU* 3.1 5.3 + - - +
560B SER* 3.0 21.6 + - - -
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Residues in contact with LEU 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B TRP* 5.9 0.2 - - + -
431B THR* 5.2 1.3 - - + -
435B PHE* 3.7 14.1 - - + -
453B PHE* 5.3 2.2 - - + -
454B CYS* 3.4 46.9 - - + +
457B LYS* 3.9 30.3 - - + +
458B MET* 4.5 9.9 - - + -
461B LEU* 5.0 6.3 - - + +
553B LYS 3.8 9.2 + - - +
554B LEU* 3.0 14.4 + - + +
556B LYS* 1.3 77.7 - - - +
558B ALA* 1.3 62.0 + - - +
560B SER* 3.2 11.3 - - - +
561B LEU* 3.1 35.0 + - + +
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Residues in contact with ALA 558 (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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435B PHE* 3.9 22.4 - - + -
544B TRP* 3.7 42.6 - - + +
554B LEU 2.9 11.7 + - - +
555B SER 3.6 7.2 - - - +
556B LYS 3.0 0.8 + - - -
557B LEU* 1.3 72.2 - - - +
559B LEU* 1.3 51.5 + - - +
560B SER 2.9 4.0 - - - -
561B LEU* 2.7 24.8 + - - +
562B LEU* 2.7 22.1 + - + +
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Residues in contact with LEU 559 (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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199B HIS* 3.4 51.0 - - + +
541B MET* 4.2 20.4 - - + +
544B TRP* 4.0 26.5 - - + +
545B ASN* 3.9 16.6 - - - +
548B SER* 5.9 1.3 - - - -
555B SER* 2.9 33.6 + - - +
556B LYS* 3.9 4.5 - - + +
558B ALA* 1.3 72.8 - - - +
560B SER* 1.3 60.4 + - - +
562B LEU* 3.9 9.1 - - + +
563B SER* 3.2 24.9 + - - -
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Residues in contact with SER 560 (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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172B LYS 5.7 0.4 - - - -
173B ASP 3.3 24.6 + - - -
174B GLY* 4.0 13.5 - - - -
199B HIS* 6.1 0.2 - - - -
244B LYS* 3.3 21.0 + - - -
428B TRP* 5.5 0.3 - - - -
461B LEU* 6.5 0.9 - - - -
556B LYS 3.0 12.8 + - - -
557B LEU* 3.2 20.8 + - - +
559B LEU* 1.3 74.2 - - - +
561B LEU* 1.3 72.2 + - - +
563B SER* 3.3 16.6 + - - -
564B ILE* 3.7 2.6 - - - +
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LYS* 4.8 0.2 - - + -
382B LEU* 4.8 2.6 - - - +
428B TRP* 3.3 51.6 - - + +
431B THR* 3.7 36.3 - - + -
432B ALA* 3.9 16.2 - - + +
435B PHE* 4.1 11.2 - - + -
453B PHE* 4.4 4.5 - - + -
557B LEU* 3.1 23.2 + - + +
558B ALA 2.7 11.1 + - - +
560B SER* 1.3 78.0 - - - +
562B LEU* 1.3 53.9 + - - +
563B SER 2.7 16.4 + - - -
564B ILE* 2.7 30.3 + - + +
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Residues in contact with LEU 562 (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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204B LEU* 4.2 2.0 - - - +
380B PRO* 3.0 41.6 - - + +
381B SER 4.4 0.2 + - - -
382B LEU* 5.8 2.0 - - - +
383B CYS* 4.2 19.1 - - + +
432B ALA* 4.0 25.6 - - + +
435B PHE* 4.3 10.3 - - + +
540B VAL* 3.4 44.4 - - + +
541B MET* 4.7 3.4 - - + +
544B TRP* 3.9 17.7 - - + +
558B ALA 2.7 24.5 + - - +
559B LEU* 3.9 11.4 - - + +
561B LEU* 1.3 73.5 - - + +
563B SER* 1.3 58.6 + - - +
564B ILE 3.4 4.2 - - - +
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Residues in contact with SER 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLY 3.8 7.4 + - - -
176B SER* 3.7 7.4 + - - -
197B HIS* 3.8 7.8 - - - +
198B TYR* 3.5 29.3 - - - -
199B HIS* 4.0 1.7 + - - -
204B LEU* 3.4 32.0 - - - +
559B LEU 3.2 14.0 + - - -
560B SER 3.3 12.5 + - - -
561B LEU 2.7 6.5 + - - -
562B LEU* 1.3 73.1 - - - +
564B ILE* 1.3 61.8 + - - +
565B PRO* 3.2 13.3 - - - +
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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