Contacts of the helix formed by residues 543 - 553 (chain M) in PDB entry 3HOU
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 LEU 543 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542M GLU* 1.3 71.0 - - - +
544M ASP* 1.3 67.2 + - - +
545M GLN 2.9 0.3 + - - -
546M VAL* 3.0 2.3 + - + -
547M LEU* 2.9 62.5 + - + +
560M ILE* 5.0 1.3 - - + -
570M PRO* 4.3 7.9 + - + +
572M TRP* 3.3 36.2 - - + -
79T TRP* 3.9 28.0 - - + -
81T PRO* 4.6 16.8 - - + -
82T PRO* 5.8 1.3 - - + -
51W LEU* 5.6 6.3 - - + -
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Residues in contact with ASP 544 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542M GLU* 3.0 32.7 - - - +
543M LEU* 1.3 76.5 - - - +
545M GLN* 1.3 78.0 + - - +
547M LEU* 3.7 12.6 - - - +
548M ASN* 3.7 3.1 + - - -
1079N LYS* 5.3 5.5 + - - +
47W ARG* 3.2 29.6 + - - +
51W LEU* 4.0 25.1 - - + -
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Residues in contact with GLN 545 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541M ILE* 3.8 11.2 - - + +
542M GLU* 3.7 7.9 - - + +
544M ASP* 1.3 88.6 + - - +
546M VAL* 1.3 71.2 + - - +
547M LEU 2.8 1.8 - - - -
548M ASN* 2.6 24.1 + - - +
549M MET* 2.9 36.8 + - + +
655M PHE* 4.5 13.5 - - + -
656M TRP* 4.1 9.6 + - - -
659M HIS* 4.1 30.6 - - + +
1079N LYS* 4.8 16.6 - - - +
47W ARG* 4.9 0.2 - - - +
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Residues in contact with VAL 546 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541M ILE* 3.2 42.5 - - + +
542M GLU 3.0 10.8 + - - +
543M LEU* 3.6 7.0 - - + +
545M GLN* 1.3 74.6 - - - +
547M LEU* 1.3 59.9 + - + +
549M MET* 3.4 7.6 + - - +
550M LEU* 2.8 42.1 + - + +
560M ILE* 5.2 1.1 - - + -
561M PRO* 5.5 0.7 - - + -
572M TRP* 3.6 40.4 - - + +
577M ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 547 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543M LEU* 2.9 40.6 + - + +
544M ASP 3.7 6.5 - - - +
545M GLN 2.7 4.4 + - - -
546M VAL* 1.3 74.3 - - + +
548M ASN* 1.3 63.6 + - - +
550M LEU* 3.4 3.9 + - + +
551M TYR 3.0 17.5 + - - -
560M ILE* 3.3 38.4 - - + -
51W LEU* 4.2 16.4 - - + -
57W LEU 5.2 1.3 - - - +
58W PHE* 3.3 21.2 - - + -
59W ALA 3.6 39.7 - - - +
60W ALA* 3.5 9.5 - - - +
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Residues in contact with ASN 548 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544M ASP 3.7 4.2 + - - -
545M GLN* 2.6 17.5 + - - +
547M LEU* 1.3 71.0 - - - +
549M MET* 1.3 66.8 + - - +
551M TYR* 3.0 4.4 + - - +
552M TRP* 2.9 29.8 + - + +
655M PHE* 3.7 26.0 - - + -
659M HIS* 6.2 0.2 - - - -
47W ARG* 2.8 33.4 + - - +
60W ALA* 3.2 8.7 - - - +
61W TYR* 3.1 43.0 + - - +
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Residues in contact with MET 549 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534M LEU* 4.9 0.7 - - - -
541M ILE* 3.1 40.4 - - + -
545M GLN* 2.9 27.7 + - - +
546M VAL 3.6 7.9 - - - +
548M ASN* 1.3 78.3 - - - +
550M LEU* 1.3 66.6 + - - +
552M TRP* 3.2 14.4 + - - +
553M VAL* 3.6 10.9 + - - +
577M ILE* 3.1 27.8 - - + -
652M VAL* 4.1 20.0 - - + +
655M PHE* 3.7 22.7 - - + -
656M TRP* 3.1 34.3 - - + -
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Residues in contact with LEU 550 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546M VAL* 2.8 33.5 + - + +
547M LEU* 3.6 10.1 - - + +
548M ASN 3.1 0.2 - - - -
549M MET* 1.3 75.9 - - - +
551M TYR* 1.3 64.6 + - - +
553M VAL* 2.9 25.8 + - - +
556M TRP* 3.5 54.9 - - + +
560M ILE* 3.9 16.4 - - + -
561M PRO* 3.8 25.6 - - + -
577M ILE* 4.8 5.4 - - + -
580M VAL* 3.9 29.4 - - + -
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Residues in contact with TYR 551 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547M LEU 3.0 13.0 + - - +
548M ASN* 3.0 7.9 + - - +
550M LEU* 1.3 76.3 - - - +
552M TRP* 1.3 63.1 + - - +
553M VAL 3.2 7.3 + - - +
554M PRO* 4.8 0.2 - - - +
556M TRP* 4.2 10.9 - + - -
24W ASP* 5.6 1.1 - - - -
32W VAL* 3.3 31.5 - - + +
58W PHE* 4.3 3.4 - - + -
60W ALA* 3.9 9.0 - - + -
61W TYR* 4.3 16.8 - - - +
62W LYS* 3.2 49.3 + - + -
72W LYS* 3.7 25.6 - - + +
74W ARG* 3.6 45.5 - - + -
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Residues in contact with TRP 552 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358M ASN* 3.9 13.9 - - - -
548M ASN* 2.9 21.7 + - + +
549M MET* 3.5 11.9 - - - +
550M LEU 3.0 0.6 + - - -
551M TYR* 1.3 76.8 - - + +
553M VAL* 1.3 57.5 + - + +
554M PRO* 3.0 14.7 - - - +
651M LYS* 3.8 54.7 - - + +
652M VAL* 5.2 1.6 - - - +
655M PHE* 3.7 39.8 - + + -
61W TYR 4.9 1.7 + - - -
62W LYS* 3.6 39.4 + - + +
63W VAL* 3.7 31.9 - - + -
64W GLU* 3.8 17.7 - - - -
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Residues in contact with VAL 553 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M MET 3.9 8.5 - - - +
550M LEU* 2.9 8.1 + - - +
551M TYR* 3.4 7.6 - - - +
552M TRP* 1.3 74.1 - - - +
554M PRO* 1.3 64.4 - - + +
555M ASP* 3.1 10.5 + - + +
556M TRP* 3.2 33.2 + - + +
577M ILE 5.8 0.2 - - - +
580M VAL* 4.6 25.6 - - + +
581M ALA* 4.7 3.8 - - + -
648M ASN* 3.9 28.0 - - + +
651M LYS* 5.7 0.4 - - - -
652M VAL* 3.2 34.3 - - + -
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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