Contacts of the helix formed by residues 535 - 546 (chain H) in PDB entry 5G04
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 GLY 535 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503H CYS* 3.9 24.8 - - - -
507H ARG* 4.8 12.6 - - - -
522H PHE* 4.3 5.7 - - - -
532H ARG* 4.6 1.0 - - - +
533H VAL 3.4 0.2 - - - -
534H GLU* 1.3 77.1 - - - +
536H MET* 1.3 68.8 + - - +
537H GLU* 3.3 7.4 - - - -
538H ILE* 3.2 24.7 + - - +
539H TYR 3.5 3.3 + - - -
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Residues in contact with MET 536 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503H CYS* 4.9 2.0 - - - -
522H PHE* 4.8 6.5 - - + -
525H VAL* 4.4 15.7 - - + -
526H ARG* 3.6 39.9 - - + +
529H GLU 5.2 0.9 - - - +
532H ARG* 3.7 36.6 - - + +
533H VAL* 3.5 19.7 + - - +
535H GLY* 1.3 78.6 - - - +
537H GLU* 1.3 55.8 + - - +
538H ILE 3.3 0.2 - - - -
539H TYR* 3.5 16.9 - - + +
540H SER* 2.7 36.6 + - - -
555H LEU* 4.5 6.6 - - + +
559H LEU* 3.8 30.3 - - + -
568H GLU 5.1 2.7 - - - +
572H ALA* 5.1 1.6 - - + -
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Residues in contact with GLU 537 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507H ARG* 5.5 1.2 + - - -
534H GLU 4.1 0.7 - - - +
535H GLY* 3.8 10.9 - - - +
536H MET* 1.3 75.1 - - - +
538H ILE* 1.3 55.5 + - + +
540H SER* 2.9 18.2 + - - -
541H THR* 2.8 28.3 + - - -
568H GLU* 2.7 49.8 + - - +
571H CYS* 3.6 34.1 - - + -
572H ALA 5.1 0.4 - - - +
575H ASN* 4.1 0.3 + - - -
600H TYR* 2.6 39.4 + - + +
602H TYR* 4.1 18.2 - - + -
606H LEU* 4.9 0.2 - - - +
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Residues in contact with ILE 538 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507H ARG* 4.1 27.1 - - + +
510H PHE* 3.9 39.3 - - + -
511H GLU* 5.4 6.7 - - + +
522H PHE* 3.6 24.5 - - + -
535H GLY 3.2 10.6 + - - +
537H GLU* 1.3 81.5 - - + +
539H TYR* 1.3 56.7 + - - +
541H THR* 3.4 7.4 - - - -
542H THR* 2.7 34.0 + - - -
600H TYR* 6.1 0.9 - - - +
602H TYR* 3.7 31.6 - - + -
636H ASN* 5.6 0.4 - - - +
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Residues in contact with TYR 539 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519H GLU* 4.2 9.0 + - + +
522H PHE* 3.0 49.8 - + + -
523H SER* 4.0 24.2 - - - -
526H ARG* 4.1 13.3 - - + +
535H GLY 3.5 1.8 + - - -
536H MET* 3.3 24.2 + - - +
538H ILE* 1.3 78.2 - - - +
540H SER* 1.3 58.7 + - - +
542H THR* 3.0 11.8 - - - -
543H LEU* 3.0 57.0 + - + +
551H ALA* 5.5 3.1 + - - +
555H LEU* 4.0 37.8 - - + +
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Residues in contact with SER 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536H MET 2.7 19.6 + - - -
537H GLU* 2.9 12.3 + - - -
539H TYR* 1.3 68.1 - - - +
541H THR* 1.3 56.1 + - - +
543H LEU* 3.3 5.8 + - - +
544H TRP* 2.8 32.9 + - - +
552H LEU* 3.6 19.4 - - - +
555H LEU* 3.7 18.4 - - - -
571H CYS 4.4 0.7 + - - -
572H ALA* 3.8 16.1 - - - -
575H ASN* 2.5 33.3 + - - +
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Residues in contact with THR 541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 3.6 18.6 - - + -
537H GLU 2.8 16.8 + - - -
538H ILE 3.4 9.4 - - - -
540H SER* 1.3 79.7 + - - +
542H THR* 1.3 53.5 + - - +
544H TRP* 2.9 7.7 + - + +
545H HIS* 2.7 42.0 + - + -
575H ASN* 3.4 14.1 + - - +
602H TYR* 3.4 21.0 + - - +
606H LEU* 4.0 1.9 - - - +
184L ARG* 3.4 38.1 - - + -
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Residues in contact with THR 542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 3.4 16.6 - - - +
515H TYR* 3.7 16.8 - - + +
518H ALA* 3.9 7.5 - - + +
519H GLU* 3.5 38.6 - - + +
522H PHE* 4.1 7.3 - - + -
538H ILE 2.7 22.1 + - - -
539H TYR* 3.0 18.6 + - + -
541H THR* 1.3 73.6 - - - +
543H LEU* 1.3 60.6 + - - +
545H HIS* 3.0 13.7 + - - +
546H LEU* 2.9 20.8 + - - +
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Residues in contact with LEU 543 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519H GLU* 3.8 21.8 - - + +
539H TYR* 3.0 47.2 + - + +
540H SER 3.4 4.7 - - - +
542H THR* 1.3 74.9 - - - +
544H TRP* 1.3 58.5 + - - +
546H LEU* 2.9 7.3 + - - +
547H GLN 2.8 25.5 + - - -
548H LYS* 3.0 18.2 + - + -
551H ALA* 4.1 17.9 - - + +
552H LEU* 3.5 49.8 - - + +
555H LEU* 3.9 15.7 - - + -
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Residues in contact with TRP 544 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540H SER 2.8 18.6 + - - +
541H THR* 2.9 16.7 + - - +
543H LEU* 1.3 69.9 - - - +
545H HIS* 1.3 97.5 + + - +
547H GLN* 3.3 23.5 + - - -
552H LEU* 4.5 4.7 - - + +
575H ASN* 4.1 13.7 - - - -
578H SER* 3.7 8.4 + - - -
579H LEU* 3.5 49.8 - - + +
613H LEU* 5.2 10.0 - - + +
178L MET 5.9 2.0 - - - -
181L ARG* 4.7 26.7 - - + -
182L SER* 4.8 9.0 - - - -
184L ARG* 3.1 51.7 - - + +
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Residues in contact with HIS 545 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 3.8 1.9 - + - -
515H TYR* 3.2 50.0 + + + -
541H THR* 2.7 37.0 + - + +
542H THR 3.3 7.0 - - - +
544H TRP* 1.3 96.1 - + - +
546H LEU* 1.3 58.4 + - + +
547H GLN* 3.0 20.0 + - - +
175L ILE* 5.4 1.0 - - - +
178L MET 5.4 0.8 + - - -
179L MET* 3.5 33.1 + - - +
182L SER 3.2 27.5 + - - -
184L ARG* 3.4 24.2 + - + +
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Residues in contact with LEU 546 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515H TYR* 3.7 29.2 - - + +
516H MET* 3.5 39.0 - - + +
519H GLU* 3.4 36.3 - - + +
542H THR 2.9 13.7 + - - +
543H LEU* 2.9 11.1 + - - +
545H HIS* 1.3 74.9 - - - +
547H GLN* 1.3 61.4 + - - +
548H LYS* 3.0 28.7 + - + +
175L ILE* 5.3 6.3 - - - +
179L MET* 4.5 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