Contacts of the helix formed by residues 549 - 563 (chain B) in PDB entry 6T8O
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 ASN 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542B MET* 4.5 1.8 - - - -
547B VAL* 3.2 15.6 - - - +
548B ARG* 1.3 90.5 + - + +
550B LEU* 1.3 66.0 + - - +
551B ALA* 4.7 7.5 - - - +
552B GLY* 3.2 18.1 + - - -
621B ALA* 3.4 20.4 - - + +
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Residues in contact with LEU 550 (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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538B ARG* 4.8 5.2 - - - +
542B MET* 4.8 8.1 - - + -
549B ASN* 1.3 75.4 - - - +
551B ALA* 1.3 57.6 + - - +
553B PHE* 3.0 13.8 + - + +
554B ASN* 2.9 40.7 + - - +
587B LEU* 3.9 43.3 - - + +
589B THR* 4.0 23.6 - - + +
621B ALA 3.1 8.5 + - - +
622B ALA* 3.3 30.7 - - - +
623B GLY* 3.9 13.2 - - - +
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Residues in contact with ALA 551 (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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549B ASN* 3.3 7.0 + - - +
550B LEU* 1.3 75.5 - - - +
552B GLY* 1.3 60.8 + - - +
554B ASN* 3.2 13.3 + - + +
555B ARG* 2.9 27.7 + - - +
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Residues in contact with GLY 552 (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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547B VAL* 4.3 6.3 - - - -
549B ASN* 3.2 18.0 + - - -
551B ALA* 1.3 77.9 - - - +
553B PHE* 1.3 56.1 + - - +
555B ARG* 3.2 7.6 + - - +
556B LYS* 2.9 33.0 + - - +
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Residues in contact with PHE 553 (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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541B LEU* 3.6 31.6 - - + -
542B MET* 5.1 1.3 - - + -
545B MET* 3.9 28.3 - - + -
547B VAL* 3.6 29.3 - - + +
550B LEU* 3.0 15.0 + - + +
552B GLY* 1.3 73.5 - - - +
554B ASN* 1.3 61.3 + - - +
556B LYS* 4.1 10.1 - - + -
557B VAL* 2.8 38.3 + - + +
567B LEU* 3.7 30.1 - - + -
586B THR 5.5 0.2 - - - -
587B LEU* 3.7 42.6 - - + -
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Residues in contact with ASN 554 (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 LEU* 2.9 42.8 + - - +
551B ALA* 3.2 13.2 + - + +
553B PHE* 1.3 79.3 - - - +
555B ARG* 1.3 56.3 + - - +
557B VAL* 3.3 6.7 - - - +
558B LYS* 2.9 28.5 + - - +
586B THR* 3.7 21.7 - - + +
587B LEU* 3.7 26.3 + - - +
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Residues in contact with ARG 555 (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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551B ALA 2.9 13.5 + - - +
552B GLY* 3.2 10.1 + - - +
554B ASN* 1.3 73.6 - - - +
556B LYS* 1.3 60.3 + - + +
558B LYS* 3.2 12.4 + - + +
559B ASP* 2.9 42.3 + - - +
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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
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545B MET* 4.9 22.9 + - + +
546B GLY 5.1 4.0 + - - -
547B VAL* 5.0 11.2 - - + +
552B GLY 2.9 22.0 + - - +
553B PHE* 3.7 16.2 - - + +
554B ASN 3.3 0.2 - - - -
555B ARG* 1.3 78.2 - - + +
557B VAL* 1.3 56.4 + - - +
559B ASP* 3.3 13.2 + - + +
560B ALA* 2.9 26.6 + - - +
567B LEU* 6.5 0.2 - - - -
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Residues in contact with VAL 557 (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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553B PHE* 2.8 29.6 + - + +
554B ASN* 3.3 20.6 - - - +
556B LYS* 1.3 74.3 - - - +
558B LYS* 1.3 61.1 + - - +
560B ALA* 3.6 7.4 - - + -
561B GLU* 2.8 33.2 + - + +
567B LEU* 3.8 26.7 - - + -
586B THR* 3.8 40.1 - - + +
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Residues in contact with LYS 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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554B ASN 2.9 19.2 + - - +
555B ARG* 3.4 13.2 - - + +
556B LYS 3.2 0.2 - - - -
557B VAL* 1.3 77.2 - - - +
559B ASP* 1.3 60.9 + - - +
561B GLU* 3.2 6.1 + - + +
562B GLU* 2.9 53.7 + - + +
586B THR* 6.0 2.7 - - + -
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Residues in contact with ASP 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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555B ARG* 2.9 33.5 + - - +
556B LYS* 3.6 15.6 - - + +
558B LYS* 1.3 80.3 - - - +
560B ALA* 1.3 60.2 + - - +
562B GLU* 3.7 19.8 + - - +
563B ALA* 3.3 21.7 + - - +
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Residues in contact with ALA 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 LYS 2.9 17.1 + - - +
557B VAL* 3.6 12.6 - - + +
558B LYS 3.3 0.2 - - - -
559B ASP* 1.3 74.7 - - - +
561B GLU* 1.3 58.5 + - - +
563B ALA* 3.8 0.9 - - - -
564B GLY 2.9 3.3 + - - -
565B THR* 2.5 62.3 + - + +
567B LEU* 4.5 15.3 - - + -
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Residues in contact with GLU 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 VAL* 2.8 20.5 + - + +
558B LYS* 3.2 8.0 + - + +
560B ALA* 1.3 75.5 - - - +
562B GLU* 1.3 64.6 + - + +
563B ALA 3.2 1.1 - - - -
564B GLY* 3.3 11.7 + - - +
586B THR* 6.5 0.4 - - + -
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Residues in contact with GLU 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 LYS* 2.9 41.7 + - + +
559B ASP* 3.9 20.3 - - - +
560B ALA 3.5 0.2 - - - -
561B GLU* 1.3 76.9 - - - +
563B ALA* 1.3 58.9 + - - +
564B GLY 3.4 0.2 - - - -
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Residues in contact with ALA 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 ASP 3.3 15.6 + - - +
560B ALA 3.7 0.9 + - - +
561B GLU 3.2 0.4 - - - -
562B GLU* 1.3 78.1 - - - +
564B GLY* 1.3 61.0 + - - +
565B THR* 3.3 19.6 + - - +
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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