Contacts of the helix formed by residues 555 - 562 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500F ALA* 3.7 13.9 - - - +
553F THR 3.9 1.7 - - - +
554F PRO* 1.3 85.9 - - + +
556F GLU* 1.3 65.0 + - - +
557F LYS* 3.7 14.0 + - - +
558F ASP* 2.9 34.9 + - - +
559F VAL* 3.9 2.9 + - - +
365P SER 4.8 6.0 + - - +
366P GLN* 4.5 28.5 - - + +
367P ALA 5.3 2.9 - - - +
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Residues in contact with GLU 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F ARG* 2.6 42.4 + - - -
500F ALA* 4.0 17.9 - - - +
503F LEU* 3.3 17.2 - - + +
504F LEU* 3.3 17.7 + - + -
555F THR* 1.3 70.1 - - - +
557F LYS* 1.3 66.1 + - - +
558F ASP 2.8 6.6 + - - -
559F VAL* 2.9 20.1 + - - +
560F PHE* 3.4 16.6 + - + -
567F TYR* 3.6 13.5 + - + +
573F ARG* 2.9 31.1 + - - +
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Residues in contact with LYS 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555F THR* 3.4 10.2 + - - +
556F GLU* 1.3 78.7 - - - +
558F ASP* 1.3 56.4 + - - +
560F PHE* 3.5 5.7 + - - +
561F ARG* 3.0 28.8 + - - +
567F TYR* 3.8 54.4 - - + +
363P ILE 5.7 0.2 + - - -
364P ARG* 4.3 20.1 + - - +
365P SER 4.9 11.8 + - - +
367P ALA 5.8 3.7 + - - +
369P LEU* 4.3 21.3 - - - +
374P ALA* 5.9 2.8 - - - +
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Residues in contact with ASP 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552F PRO 4.5 2.7 - - - +
553F THR* 4.1 13.5 - - + -
554F PRO* 3.2 19.6 - - + +
555F THR* 2.9 39.2 + - - +
556F GLU 2.8 1.8 + - - -
557F LYS* 1.3 76.4 - - - +
559F VAL* 1.3 67.2 + - - +
561F ARG* 2.8 37.0 + - - +
562F LEU* 2.7 30.6 + - + +
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Residues in contact with VAL 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F ALA* 5.0 5.2 - - + +
501F CYS* 4.4 12.6 - - - -
504F LEU* 3.6 32.3 - - + -
516F MET* 5.0 1.8 - - - -
527F LEU* 4.0 17.9 - - + -
532F LEU* 4.3 7.6 - - + +
553F THR* 3.8 30.3 - - + -
555F THR 4.2 4.7 - - - +
556F GLU* 2.9 17.2 + - - +
558F ASP* 1.3 72.6 - - - +
560F PHE* 1.3 66.9 + - + +
562F LEU* 3.6 2.3 + - - +
563F LEU* 3.3 33.2 + - + +
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Residues in contact with PHE 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F LEU* 3.9 14.1 - - + -
512F PHE* 3.8 18.4 - + - -
516F MET* 3.3 30.3 - - + -
556F GLU* 3.5 15.0 - - + -
557F LYS 3.6 6.3 - - - +
558F ASP 3.1 0.6 - - - -
559F VAL* 1.3 80.7 - - + +
561F ARG* 1.3 55.1 + - - +
563F LEU* 2.8 26.9 + - - +
565F LEU* 3.0 37.5 + - + +
566F PRO 2.9 27.8 - - - +
567F TYR* 3.9 17.0 - + + +
568F ARG* 3.7 20.9 - - + -
573F ARG* 3.8 25.8 - - - -
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Residues in contact with ARG 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552F PRO 5.3 2.2 + - - -
557F LYS 3.0 11.1 + - - +
558F ASP* 2.8 38.0 + - - +
560F PHE* 1.3 78.3 - - - +
562F LEU* 1.3 86.9 + - - +
563F LEU 2.8 6.2 + - - -
564F GLY* 2.8 15.5 + - - +
565F LEU 3.7 6.5 + - - +
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Residues in contact with LEU 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A PRO* 5.1 6.6 - - + +
483A GLY* 4.5 21.1 - - - +
525F MET* 3.6 24.9 - - - +
532F LEU* 3.9 12.6 - - + -
551F LEU* 4.0 25.4 - - + -
552F PRO* 3.8 24.5 - - + +
553F THR* 4.0 18.6 - - + -
558F ASP* 2.7 21.7 + - + +
559F VAL 3.8 0.9 - - - +
561F ARG* 1.3 98.6 - - - +
563F LEU* 1.3 57.3 + - - +
564F GLY 3.6 0.2 - - - -
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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