Contacts of the helix formed by residues 549 - 563 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542C MET* 3.5 15.3 - - - +
547C VAL* 4.0 2.1 - - - +
548C ARG* 1.3 84.9 + - + +
550C LEU* 1.3 63.5 + - - +
551C ALA* 4.2 9.0 - - - +
552C GLY* 2.9 29.4 + - - +
553C PHE* 3.3 14.2 + - - +
621C ALA* 4.0 19.5 - - + +
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Residues in contact with LEU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C ARG* 4.4 10.5 - - + +
542C MET* 4.3 8.1 - - + -
549C ASN* 1.3 74.3 - - - +
551C ALA* 1.3 61.4 + - - +
553C PHE* 3.0 11.2 + - + +
554C ASN* 2.9 46.5 + - - +
587C LEU* 4.3 32.3 - - + +
588C PRO 4.7 1.3 - - - +
589C THR* 4.1 18.4 - - + +
621C ALA 3.1 20.1 + - - +
622C ALA 3.8 10.5 - - - +
623C GLY* 3.7 24.9 - - - +
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Residues in contact with ALA 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C ASN* 3.5 10.6 + - - +
550C LEU* 1.3 78.2 - - - +
552C GLY* 1.3 57.1 + - - +
554C ASN* 3.8 9.2 - - - +
555C ARG* 2.9 43.2 + - - +
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Residues in contact with GLY 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C VAL* 4.3 11.7 - - - +
548C ARG 5.7 0.2 - - - -
549C ASN* 2.9 23.2 + - - -
551C ALA* 1.3 78.5 - - - +
553C PHE* 1.3 55.4 + - - +
555C ARG* 3.4 6.6 + - - +
556C LYS* 2.9 28.8 + - - +
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Residues in contact with PHE 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C LEU* 3.6 29.8 - - + -
542C MET* 4.6 9.2 - - + -
545C MET* 4.0 13.7 - - + -
547C VAL* 3.8 26.8 - - + +
549C ASN 3.3 7.9 + - - +
550C LEU* 3.0 15.2 + - + +
552C GLY* 1.3 73.5 - - - +
554C ASN* 1.3 68.6 + - - +
556C LYS* 3.2 9.2 + - + +
557C VAL* 2.9 34.7 + - + +
584C LEU* 3.7 28.9 - - + -
585C SER 3.8 19.5 - - - -
587C LEU* 3.7 31.0 - - + -
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Residues in contact with ASN 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C LEU* 2.9 41.2 + - - +
551C ALA* 3.9 7.8 - - - +
552C GLY 3.4 0.2 - - - -
553C PHE* 1.3 79.5 - - - +
555C ARG* 1.3 58.9 + - + +
557C VAL* 3.3 7.0 - - - +
558C LYS* 2.9 28.5 + - - +
586C THR* 3.7 15.2 - - + +
587C LEU* 3.2 40.6 + - - +
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Residues in contact with ARG 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C LYS* 3.7 26.2 - - - +
551C ALA* 2.9 26.4 + - + +
552C GLY* 4.0 6.3 - - - +
554C ASN* 1.3 75.3 - - + +
556C LYS* 1.3 59.9 + - - +
558C LYS* 3.6 15.9 - - + +
559C ASP* 2.8 40.0 + - - +
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Residues in contact with LYS 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C MET* 3.9 32.3 + - + +
546C GLY 5.0 2.2 + - - -
547C VAL* 3.4 26.2 - - + +
552C GLY 2.9 17.4 + - - +
553C PHE* 3.2 13.9 + - + +
555C ARG* 1.3 77.0 - - - +
557C VAL* 1.3 58.1 + - - +
559C ASP* 3.1 13.4 + - + +
560C ALA* 2.9 24.9 + - - +
567C LEU* 4.5 13.1 - - + +
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Residues in contact with VAL 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C PHE* 2.9 25.6 + - + +
554C ASN* 3.3 19.3 - - - +
556C LYS* 1.3 75.3 - - - +
558C LYS* 1.3 59.4 + - - +
560C ALA* 3.3 11.4 + - + +
561C GLU* 2.9 33.5 + - + +
567C LEU* 5.6 4.0 - - + +
584C LEU* 4.3 22.0 - - + +
585C SER* 4.3 18.8 - - - +
586C THR* 3.7 30.3 - - + +
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Residues in contact with LYS 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C LYS* 6.1 1.6 - - - +
554C ASN 2.9 19.6 + - - +
555C ARG* 3.6 17.7 - - + +
557C VAL* 1.3 78.7 - - + +
559C ASP* 1.3 58.4 + - - +
561C GLU* 3.0 19.2 + - + +
562C GLU* 2.9 53.0 + - + +
586C THR* 5.8 1.6 - - + -
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Residues in contact with ASP 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C ARG* 2.8 26.5 + - - +
556C LYS* 3.5 13.1 - - + +
558C LYS* 1.3 72.9 - - - +
560C ALA* 1.3 64.7 + - - +
562C GLU* 3.0 25.8 - - - +
563C ALA* 3.3 24.1 + - - +
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Residues in contact with ALA 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C LYS 2.9 8.6 + - - +
557C VAL* 3.4 17.3 - - + +
559C ASP* 1.3 79.1 - - - +
561C GLU* 1.3 59.4 + - + +
564C GLY 3.4 2.3 + - - -
565C THR* 3.0 50.1 + - - +
567C LEU* 3.7 33.6 - - + +
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Residues in contact with GLU 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C VAL* 2.9 23.5 + - + +
558C LYS* 3.0 22.0 + - + +
560C ALA* 1.3 76.8 - - + +
562C GLU* 1.3 63.8 + - + +
564C GLY* 3.5 10.2 + - - +
585C SER* 6.2 0.2 - - - -
586C THR* 3.8 23.3 - - - +
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Residues in contact with GLU 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C LYS* 2.9 39.8 + - + +
559C ASP* 3.0 29.2 - - - +
560C ALA 3.3 0.6 - - - -
561C GLU* 1.3 79.3 - - + +
563C ALA* 1.3 60.2 + - - +
564C GLY 3.2 1.9 + - - -
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Residues in contact with ALA 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C ASP 3.3 13.9 + - - +
562C GLU* 1.3 76.6 - - - +
564C GLY* 1.3 60.7 + - - +
565C THR* 3.3 20.1 + - - +
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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
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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