Contacts of the helix formed by residues 555 - 564 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496P TYR* 6.0 1.8 - - - +
500P ALA* 4.2 7.1 - - - +
554P PRO* 1.3 84.0 - - + +
556P GLU* 1.3 66.2 + - - +
557P LYS* 3.5 24.7 + - - +
558P ASP* 2.6 38.2 + - - +
559P VAL* 3.5 6.1 + - - +
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Residues in contact with GLU 556 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419P ARG* 3.0 25.3 + - - -
500P ALA* 4.1 11.4 - - - +
503P LEU* 3.0 35.4 - - + +
504P LEU* 3.5 22.9 + - + -
555P THR* 1.3 73.5 - - - +
557P LYS* 1.3 62.9 + - + +
559P VAL* 3.0 21.7 + - - +
560P PHE* 3.1 22.9 + - + -
567P TYR* 3.5 12.9 + - + +
573P ARG* 2.8 34.6 + - - +
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Residues in contact with LYS 557 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555P THR* 3.0 15.2 - - + +
556P GLU* 1.3 77.9 - - + +
558P ASP* 1.3 58.2 + - - +
560P PHE* 3.2 5.8 + - - +
561P ARG* 2.9 29.9 + - - +
567P TYR* 3.4 38.1 - - + -
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Residues in contact with ASP 558 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552P PRO 5.1 0.2 - - - +
553P THR* 4.1 11.0 - - + -
554P PRO* 3.1 29.5 - - + +
555P THR* 2.6 41.8 + - - +
557P LYS* 1.3 78.4 - - - +
559P VAL* 1.3 62.4 + - - +
561P ARG* 2.7 34.8 + - - +
562P LEU* 3.0 30.1 + - + +
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Residues in contact with VAL 559 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500P ALA 5.0 0.2 - - - -
501P CYS* 4.2 20.2 - - - +
504P LEU* 3.5 31.2 - - + -
516P MET* 5.6 0.4 - - + -
527P LEU* 4.0 12.3 - - + -
532P LEU* 4.2 15.2 - - + +
553P THR* 4.1 18.8 - - + +
555P THR 4.0 9.0 - - - +
556P GLU* 3.0 14.3 + - - +
558P ASP* 1.3 77.0 - - - +
560P PHE* 1.3 58.4 + - + +
562P LEU 4.0 0.5 - - - -
563P LEU* 2.9 46.9 + - + +
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Residues in contact with PHE 560 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504P LEU* 4.3 15.3 - - + -
512P PHE* 3.8 24.2 - + - -
516P MET* 4.1 18.6 - - + -
556P GLU* 3.1 26.8 + - + -
557P LYS* 3.2 9.9 + - - +
559P VAL* 1.3 78.9 - - + +
561P ARG* 1.3 59.3 + - - +
563P LEU* 3.0 7.0 + - - +
564P GLY 2.8 25.3 + - - -
565P LEU* 2.9 33.7 + - + +
566P PRO 3.8 15.7 - - - -
567P TYR* 4.0 13.5 - + + +
568P ARG* 3.9 26.5 - - + -
573P ARG* 3.8 26.9 - - - -
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Residues in contact with ARG 561 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552P PRO 5.6 0.6 + - - -
554P PRO* 5.4 1.4 - - - +
557P LYS 2.9 16.2 + - - +
558P ASP* 2.7 39.7 + - - +
560P PHE* 1.3 70.1 - - - +
562P LEU* 1.3 91.1 + - + +
563P LEU 2.9 3.6 - - - -
564P GLY* 2.7 26.7 + - - -
565P LEU 4.2 4.0 + - - +
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Residues in contact with LEU 562 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523P LYS* 5.1 1.9 - - - +
525P MET* 4.0 17.4 - - - +
532P LEU* 4.3 11.4 - - + -
551P LEU* 4.4 24.2 - - + -
552P PRO* 4.0 21.1 - - + +
553P THR* 4.1 12.1 - - + -
558P ASP* 3.0 16.4 + - + +
559P VAL 4.0 0.2 - - - -
561P ARG* 1.3 105.4 - - - +
563P LEU* 1.3 58.9 + - - +
564P GLY 3.4 0.2 - - - -
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Residues in contact with LEU 563 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516P MET* 3.4 34.5 - - + +
519P LEU* 3.5 27.4 - - + +
520P ALA* 3.6 27.1 - - + +
523P LYS* 2.9 31.7 - - + +
525P MET* 4.9 4.7 - - - -
527P LEU* 4.6 5.6 - - + -
532P LEU* 4.4 13.5 - - + -
559P VAL* 2.9 38.3 + - + +
560P PHE* 3.0 6.7 + - - +
561P ARG 2.8 1.4 + - - -
562P LEU* 1.3 77.8 - - - +
564P GLY* 1.3 58.7 + - - +
565P LEU* 3.1 13.6 - - + +
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Residues in contact with GLY 564 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523P LYS* 4.3 10.3 - - - -
560P PHE 2.8 2.6 + - - -
561P ARG 2.7 14.3 + - - -
562P LEU 3.4 0.4 - - - -
563P LEU* 1.3 79.4 - - - +
565P LEU* 1.3 62.2 + - - +
566P PRO* 4.7 1.0 - - - +
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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