Contacts of the helix formed by residues 498 - 508 (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 GLU 498 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494F VAL* 4.5 6.9 - - + +
495F PRO* 2.7 37.2 + - + +
497F SER* 1.3 87.6 + - - +
499F PHE* 1.3 59.7 + - - +
500F ALA 3.3 2.9 - - - -
501F CYS* 3.4 4.8 + - - +
502F ALA* 2.8 32.3 + - - +
529F GLU 4.0 3.7 - - - +
530F HIS* 2.6 63.5 + - - +
531F ALA* 5.3 1.3 - - + -
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Residues in contact with PHE 499 (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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411F LEU* 4.5 16.2 - - + -
413F VAL* 4.4 23.1 - - + -
431F LEU* 3.9 27.4 - - + -
433F THR* 3.4 29.8 - - + -
494F VAL* 4.4 1.6 - - - -
495F PRO 3.4 3.9 + - - -
496F TYR* 3.4 37.3 + + + +
497F SER 3.5 0.4 - - - -
498F GLU* 1.3 77.0 - - - +
500F ALA* 1.3 56.1 + - - +
502F ALA* 4.4 3.1 - - - -
503F LEU* 2.7 60.4 + - + +
554F PRO 5.6 4.7 - - - +
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Residues in contact with ALA 500 (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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497F SER 5.4 1.0 + - - +
498F GLU 3.3 0.6 - - - -
499F PHE* 1.3 82.5 - - - +
501F CYS* 1.3 57.5 + - - +
503F LEU* 3.6 5.8 - - - +
504F LEU* 3.0 29.8 + - - +
553F THR* 3.0 32.8 - - - +
554F PRO 3.7 11.7 + - - +
555F THR* 3.7 23.3 - - - +
556F GLU* 4.0 7.3 - - - +
559F VAL* 5.0 3.1 - - + -
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Residues in contact with CYS 501 (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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497F SER 6.1 0.2 - - - -
498F GLU* 3.4 5.3 + - - +
500F ALA* 1.3 77.3 - - - +
502F ALA* 1.3 64.8 + - - +
504F LEU* 3.9 7.0 - - - +
505F TYR* 3.2 22.9 + - - +
527F LEU* 4.5 6.2 - - + +
528F SER 3.6 17.3 - - - +
529F GLU* 3.6 6.7 - - - +
530F HIS 3.8 14.8 - - - +
531F ALA* 3.3 31.0 - - - -
532F LEU 3.8 2.7 - - - -
553F THR* 3.5 25.4 - - - -
559F VAL* 4.4 11.0 - - - -
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Residues in contact with ALA 502 (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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431F LEU* 3.8 9.2 - - + -
492F ILE* 5.0 2.4 - - + +
494F VAL* 3.7 35.0 - - + -
498F GLU 2.8 22.2 + - - +
499F PHE 3.7 1.6 - - - +
501F CYS* 1.3 70.0 - - - +
503F LEU* 1.3 61.0 + - - +
505F TYR* 3.2 5.2 + - + +
506F PHE* 2.8 31.5 + - - +
529F GLU* 3.3 20.1 + - + +
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Residues in contact with LEU 503 (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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413F VAL* 4.3 14.1 - - + -
415F CYS* 3.8 23.6 - - - -
419F ARG* 3.1 42.8 - - - +
431F LEU* 3.5 14.0 - - + +
499F PHE* 2.7 46.1 + - + +
500F ALA* 3.6 5.4 - - - +
502F ALA* 1.3 74.1 - - - +
504F LEU* 1.3 60.0 + - - +
506F PHE* 3.1 1.2 + - - +
507F THR* 2.7 31.4 + - - -
556F GLU* 3.3 13.0 - - + +
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Residues in contact with LEU 504 (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 3.0 14.1 + - - +
501F CYS* 3.9 4.9 - - - +
503F LEU* 1.3 80.2 - - - +
505F TYR* 1.3 62.7 - - - +
507F THR* 3.5 3.9 + - - -
508F GLY* 3.4 15.2 + - - +
512F PHE* 4.1 15.5 - - + -
513F ASN* 3.6 9.3 - - - +
516F MET* 4.2 13.0 - - - -
527F LEU* 4.2 14.8 - - + -
556F GLU* 3.3 15.6 + - + +
559F VAL* 3.6 37.0 - - + -
560F PHE* 3.9 21.5 - - + -
573F ARG* 3.7 21.8 - - - +
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Residues in contact with TYR 505 (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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492F ILE* 5.8 7.4 - - + -
501F CYS 3.2 16.6 + - - +
502F ALA* 3.4 6.3 - - + +
503F LEU 3.1 0.4 - - - -
504F LEU* 1.3 80.8 - - - +
506F PHE* 1.3 89.7 + + + +
508F GLY 3.2 3.1 + - - -
513F ASN* 3.0 29.8 + - - -
517F ARG* 3.3 26.0 - - - +
528F SER 5.2 0.4 - - - -
529F GLU* 3.5 35.4 + - + +
702F D3T 3.2 36.5 - + - +
7G A 4.9 3.6 - + - -
6H T 2.8 37.8 + - - +
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Residues in contact with PHE 506 (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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415F CYS* 3.6 27.4 - - + -
416F GLY* 2.8 23.6 + - - -
429F ASP* 3.6 29.2 - - + -
430F VAL 3.5 15.0 - - - -
431F LEU* 4.1 8.7 - - + -
490F ASP* 3.3 30.3 - - - -
492F ILE* 3.5 32.5 - - + -
502F ALA 2.8 19.0 + - - +
505F TYR* 1.3 92.0 - + + +
507F THR* 1.3 61.5 + - - +
702F D3T 3.4 27.2 - - - +
6H T 4.6 5.6 - - - -
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Residues in contact with THR 507 (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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415F CYS* 4.1 1.3 - - - +
416F GLY* 3.8 8.1 - - - +
419F ARG* 2.6 46.8 + - + +
420F ARG* 2.8 36.5 + - + +
503F LEU* 2.7 20.3 + - - +
504F LEU 3.7 5.8 - - - -
506F PHE* 1.3 78.3 - - - +
508F GLY* 1.3 63.6 + - - +
570F PRO* 4.0 13.9 - - + -
573F ARG* 3.6 22.0 - - - +
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Residues in contact with GLY 508 (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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420F ARG* 4.0 0.9 - - - -
504F LEU 3.4 4.6 + - - +
505F TYR 3.2 6.9 + - - -
506F PHE 3.3 0.4 - - - -
507F THR* 1.3 83.1 - - - +
509F SER* 1.3 71.0 + - - -
512F PHE* 3.7 12.9 - - - -
513F ASN* 3.5 6.3 - - - -
573F ARG* 3.5 25.3 - - - +
702F D3T 3.4 13.7 - - - -
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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