Contacts of the helix formed by residues 552 - 566 (chain B) in PDB entry 2AN3
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 GLY 552 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ASP 5.4 4.0 - - - -
549B ASN* 3.0 22.0 + - - +
550B PRO 3.3 1.9 - - - +
551B ASN* 1.3 77.8 - - - +
553B VAL* 1.3 64.9 + - - -
554B GLY 3.4 2.0 - - - -
555B PRO* 3.5 12.0 - - - +
556B TRP* 3.5 15.1 + - - +
756B TYR* 3.1 9.2 + - - -
762B LEU* 3.9 12.6 - - - -
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Residues in contact with VAL 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ASN 6.0 0.7 - - - +
544B ARG* 4.7 19.7 + - + +
552B GLY* 1.3 71.0 - - - -
554B GLY* 1.3 69.0 + - - +
556B TRP* 3.5 2.4 + - + +
557B LYS* 3.0 39.9 + - + +
756B TYR* 3.1 37.9 + - + -
758B MET* 4.3 14.4 - - + -
762B LEU* 3.7 14.0 - - + +
772B VAL* 3.9 21.8 - - + -
3002B CTL 4.5 11.9 - - + -
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Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG 4.6 6.5 + - - -
547B LEU* 4.1 14.4 - - - -
553B VAL* 1.3 84.4 - - - +
555B PRO* 1.3 68.8 - - - +
557B LYS* 3.2 15.1 + - - +
558B LEU* 3.0 29.3 + - - +
585B TYR* 6.1 0.2 - - - -
626B TYR* 4.6 8.5 - - - -
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Residues in contact with PRO 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG 5.6 0.2 - - - +
546B ASP 4.8 1.8 - - - +
547B LEU* 3.6 31.9 - - + +
549B ASN 3.4 22.0 - - - +
550B PRO* 4.2 8.1 - - + +
552B GLY* 3.5 17.7 - - - +
554B GLY* 1.3 91.8 - - - +
556B TRP* 1.3 55.6 + - - +
558B LEU* 3.5 1.6 + - + +
559B ARG* 2.8 44.0 + - - +
629B HIS* 3.7 26.5 - - + +
633B ILE* 4.7 1.4 - - - +
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Residues in contact with TRP 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B GLY 3.5 16.3 + - - +
553B VAL* 3.5 4.7 + - + +
554B GLY 3.2 0.8 - - - -
555B PRO* 1.3 76.5 - - - +
557B LYS* 1.3 80.6 + - + +
559B ARG* 3.3 26.2 + - + +
560B CYS* 2.9 42.8 + - - -
714B ILE* 5.5 1.3 - - + -
754B ARG* 3.7 31.5 - - + +
755B THR 3.8 3.3 + - - -
756B TYR* 3.5 49.6 - + + +
772B VAL* 3.7 37.9 - - + -
773B PHE 4.4 0.2 - - - -
774B PHE* 3.7 25.1 - - + -
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Residues in contact with LYS 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ASN 5.3 0.8 + - - -
540B TYR* 3.6 34.7 + - - -
553B VAL* 3.0 36.2 + - + +
554B GLY* 3.2 13.2 + - - +
556B TRP* 1.3 93.4 - - + +
558B LEU* 1.3 61.5 + - - +
560B CYS* 3.2 5.2 + - - +
561B LEU* 3.1 29.2 + - - +
585B TYR* 3.7 20.1 + - + +
626B TYR* 5.8 1.1 - - - -
682B PHE* 3.7 32.1 - - + -
714B ILE* 4.2 21.0 - - + +
772B VAL* 4.6 0.9 - - + -
3002B CTL 4.0 11.9 - - - -
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Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B LEU* 4.4 3.1 - - + -
554B GLY 3.0 21.3 + - - +
555B PRO 3.8 2.7 - - - +
557B LYS* 1.3 76.8 - - - +
559B ARG* 1.3 57.4 + - - +
561B LEU* 3.3 7.8 + - + +
562B ALA* 2.8 32.6 + - - +
585B TYR* 4.0 38.4 - - + +
588B LEU* 4.8 7.0 - - + -
589B SER* 4.5 2.4 + - - +
626B TYR* 3.9 29.4 - - + +
629B HIS* 3.6 35.7 - - + -
630B ALA* 4.3 8.1 - - + +
633B ILE* 3.6 13.2 - - + +
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Residues in contact with ARG 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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550B PRO* 3.5 22.8 + - - +
555B PRO* 2.8 47.5 + - - +
556B TRP* 3.6 32.9 - - - +
558B LEU* 1.3 77.1 - - - +
560B CYS* 1.3 56.9 + - - +
562B ALA* 4.5 1.1 - - - -
563B GLN* 2.9 67.8 + - + +
629B HIS* 5.0 4.2 + - - -
633B ILE* 3.6 19.9 - - + +
754B ARG* 5.0 3.5 - - - +
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Residues in contact with CYS 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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556B TRP* 2.9 58.0 + - - +
557B LYS* 3.2 6.7 + - - +
559B ARG* 1.3 76.5 - - - +
561B LEU* 1.3 57.7 + - - +
563B GLN* 4.3 0.9 - - - +
564B THR* 2.7 32.7 + - - -
754B ARG* 3.8 29.5 + - - +
774B PHE* 3.6 31.9 - - + -
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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
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557B LYS 3.1 20.7 + - - +
558B LEU* 3.7 7.4 - - + +
560B CYS* 1.3 75.5 - - - +
562B ALA* 1.3 64.0 + - - +
564B THR* 3.2 4.2 + - - -
565B PHE* 3.0 39.2 + - + -
585B TYR* 4.5 9.4 - - + +
586B GLN* 4.0 34.1 - - + +
589B SER* 4.2 8.5 - - - +
679B VAL* 5.1 5.6 - - + -
712B LEU* 3.9 29.4 - - + -
714B ILE* 3.9 22.0 - - + -
774B PHE* 4.1 12.3 - - + -
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Residues in contact with ALA 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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558B LEU 2.8 21.3 + - - +
559B ARG* 3.9 2.7 - - - +
561B LEU* 1.3 73.5 - - - +
563B GLN* 1.3 59.2 + - + +
565B PHE* 3.2 3.3 + - - +
566B ALA* 2.9 30.4 + - - +
589B SER* 3.5 22.8 + - - +
633B ILE* 4.0 23.3 - - + +
634B GLU* 4.3 14.5 - - + +
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Residues in contact with GLN 563 (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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559B ARG* 2.9 54.1 + - + +
562B ALA* 1.3 76.2 - - + +
564B THR* 1.3 62.5 + - - +
566B ALA* 3.4 16.7 + - - +
567B THR* 3.5 15.2 - - - +
754B ARG* 2.7 42.2 + - - +
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Residues in contact with THR 564 (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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560B CYS 2.7 21.6 + - - -
561B LEU 3.2 5.6 + - - -
563B GLN* 1.3 78.9 - - - +
565B PHE* 1.3 58.4 + - - +
567B THR* 2.9 29.6 + - - -
568B GLY 4.4 0.2 + - - -
570B VAL* 4.0 14.2 - - + +
712B LEU* 3.6 31.2 - - + -
752B ASP* 5.0 0.5 + - - -
754B ARG* 4.7 4.4 + - - +
774B PHE* 3.3 19.1 - - - -
776B TRP* 3.7 26.8 - - + -
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Residues in contact with PHE 565 (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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561B LEU* 3.0 39.8 + - + +
562B ALA 3.9 3.1 - - - +
564B THR* 1.3 77.6 - - - +
566B ALA* 1.3 62.1 + - - +
567B THR 3.2 0.2 - - - -
568B GLY* 3.2 11.5 + - - +
570B VAL* 3.8 33.9 - - + +
575B LEU* 4.8 1.1 - - + -
586B GLN 5.4 1.1 - - - -
589B SER* 3.8 18.4 - - - +
590B ALA* 3.1 33.4 - - + -
593B HIS* 3.4 43.1 - + + +
594B PHE* 3.8 19.7 - + - -
679B VAL* 4.7 7.6 - - + -
712B LEU* 3.3 29.2 - - + -
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Residues in contact with ALA 566 (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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562B ALA 2.9 17.2 + - - +
563B GLN* 3.6 11.7 - - - +
564B THR 3.1 0.8 - - - -
565B PHE* 1.3 74.6 - - - +
567B THR* 1.3 59.3 + - - +
568B GLY* 3.0 6.2 + - - -
593B HIS* 5.5 0.7 - - - -
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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