Contacts of the helix formed by residues 555 - 564 (chain K) in PDB entry 3HX0
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 THR 555 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500K ALA* 3.6 14.2 - - - +
553K THR 4.3 0.2 - - - -
554K PRO* 1.3 86.1 - - + +
556K GLU* 1.3 66.1 + - - +
557K LYS* 3.5 18.4 + - - +
558K ASP* 2.6 42.5 + - - +
559K VAL* 3.5 5.4 + - - +
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Residues in contact with GLU 556 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K ARG* 3.0 39.7 + - - -
500K ALA* 4.0 19.5 - - - +
503K LEU* 3.4 18.8 - - + +
504K LEU* 3.5 13.4 - - + +
555K THR* 1.3 74.8 - - - +
557K LYS* 1.3 64.2 + - - +
559K VAL* 2.9 20.8 + - - +
560K PHE* 3.1 23.2 + - + -
567K TYR* 3.4 14.5 + - + -
573K ARG* 2.6 36.9 + - - -
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Residues in contact with LYS 557 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555K THR* 3.2 11.2 + - - +
556K GLU* 1.3 76.9 - - - +
558K ASP* 1.3 52.9 + - - +
560K PHE* 3.2 4.3 + - - +
561K ARG* 2.8 37.3 + - - +
567K TYR* 3.2 45.1 - - + -
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Residues in contact with ASP 558 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552K PRO 4.7 0.7 - - - +
553K THR* 3.9 10.1 - - + -
554K PRO* 3.2 30.2 - - + +
555K THR* 2.6 43.0 + - - +
557K LYS* 1.3 78.9 - - - +
559K VAL* 1.3 54.5 + - - +
561K ARG* 2.9 34.9 + - - +
562K LEU* 3.0 36.6 + - + +
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Residues in contact with VAL 559 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501K CYS* 4.3 15.3 - - - +
504K LEU* 3.7 30.1 - - + -
516K MET* 4.4 1.8 - - + -
527K LEU* 4.1 16.2 - - + -
532K LEU* 4.3 7.4 - - + +
553K THR* 3.8 30.7 - - + +
555K THR 3.9 5.6 - - - +
556K GLU* 2.9 13.5 + - - +
558K ASP* 1.3 74.7 - - - +
560K PHE* 1.3 66.0 + - - +
562K LEU* 3.3 2.3 + - - +
563K LEU* 3.0 42.4 + - + +
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Residues in contact with PHE 560 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K LEU* 3.8 20.9 - - + -
512K PHE* 3.7 32.5 - + - -
516K MET* 4.2 12.6 - - + -
556K GLU* 3.1 29.0 + - + -
557K LYS* 3.6 6.7 - - - +
559K VAL* 1.3 80.1 - - + +
561K ARG* 1.3 57.7 + - - +
563K LEU* 3.3 6.6 + - - +
564K GLY 2.8 24.6 + - - -
565K LEU* 3.0 33.2 + - + +
566K PRO 4.0 6.1 - - - -
567K TYR* 3.6 25.8 - + + +
568K ARG* 3.5 27.4 - - + -
573K ARG* 4.0 20.9 - - - -
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Residues in contact with ARG 561 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552K PRO 5.2 4.2 + - - -
554K PRO* 5.6 0.6 - - - +
557K LYS 2.8 19.7 + - - +
558K ASP* 2.9 36.5 + - - +
560K PHE* 1.3 73.1 - - - +
562K LEU* 1.3 85.4 + - - +
564K GLY* 2.9 20.8 + - - -
565K LEU 4.7 3.1 - - - +
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Residues in contact with LEU 562 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523K LYS* 6.0 0.5 - - - +
525K MET* 4.3 16.0 - - + +
532K LEU* 3.7 21.1 - - + -
551K LEU* 3.8 33.7 - - + -
552K PRO* 4.3 9.6 - - + +
553K THR* 4.0 10.8 - - + -
558K ASP 3.0 20.2 + - - +
561K ARG* 1.3 102.3 - - - +
563K LEU* 1.3 60.2 + - - +
564K GLY 3.6 0.2 + - - -
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Residues in contact with LEU 563 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516K MET* 3.6 41.5 - - + +
519K LEU* 3.6 17.8 - - + +
520K ALA* 3.5 35.4 - - + -
523K LYS* 3.7 17.6 + - + +
525K MET* 4.2 17.3 - - - -
527K LEU* 4.5 9.0 - - + -
532K LEU* 4.3 10.1 - - + -
559K VAL* 3.0 27.7 + - + +
560K PHE* 3.7 2.0 - - - +
562K LEU* 1.3 77.4 - - - +
564K GLY* 1.3 60.3 + - - +
565K LEU* 3.3 20.6 - - + +
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Residues in contact with GLY 564 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523K LYS* 5.6 3.1 + - - -
560K PHE 2.8 6.7 + - - -
561K ARG 2.9 12.5 + - - -
562K LEU 3.3 0.4 - - - -
563K LEU* 1.3 76.2 - - - +
565K LEU* 1.3 66.4 + - - +
566K PRO* 4.7 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