Contacts of the helix formed by residues 535 - 540 (chain M) in PDB entry 5D4C
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 SER 535 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9M ILE* 5.0 1.8 - - - -
11M GLU* 2.6 42.7 + - - -
458M TYR* 4.3 6.1 - - - -
499M ALA* 3.9 7.0 - - - -
533M ASP* 3.5 2.9 - - - -
534M VAL* 1.3 86.6 - - - +
536M PRO* 1.3 78.3 - - - +
537M LYS* 3.1 16.1 + - - +
538M GLN* 3.1 24.9 + - - +
539M VAL* 5.0 0.2 - - - +
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Residues in contact with PRO 536 (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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9M ILE* 4.1 23.1 - - + -
11M GLU* 4.8 0.4 - - - +
499M ALA* 3.9 15.2 - - + -
500M ASN* 5.9 1.8 - - + +
535M SER* 1.3 89.6 - - - +
537M LYS* 1.3 62.3 + - + +
538M GLN 2.9 1.9 + - - -
539M VAL* 2.9 24.6 + - + +
540M PHE* 3.9 7.3 - - - -
905M ILE* 3.6 27.1 - - + +
906M PHE* 3.9 23.6 - - + -
907M ASP* 4.9 0.9 - - + +
1067N VAL* 4.0 19.3 - - + -
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Residues in contact with LYS 537 (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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11M GLU* 4.2 20.9 - - - +
15M LEU* 5.3 3.4 - - + -
457M ALA* 3.4 8.9 - - + +
458M TYR* 4.2 17.3 - - + +
535M SER* 3.0 15.0 - - - +
536M PRO* 1.3 77.4 - - + +
538M GLN* 1.3 60.1 + - - +
539M VAL 3.2 0.8 + - - -
540M PHE 3.2 18.6 + - - +
545M ASN* 3.2 25.4 + - - +
581M THR* 3.4 38.1 + - - +
582M GLY 5.7 1.8 - - - -
583M LEU* 4.0 27.7 - - + +
904M PRO* 4.5 15.1 - - + +
905M ILE* 4.1 10.3 - - + +
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Residues in contact with GLN 538 (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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435M TYR* 4.4 5.5 - - - -
436M GLY* 3.3 10.4 - - - +
456M ALA* 3.2 26.5 - - - +
458M TYR* 3.8 31.7 - - + +
469M THR* 2.8 27.3 + - - +
470M PRO* 3.1 25.0 + - - +
471M TYR* 4.3 5.5 - - - -
533M ASP* 3.6 33.8 - - - +
534M VAL* 3.6 8.6 + - - +
535M SER 3.1 18.8 + - - +
536M PRO 2.9 1.6 + - - -
537M LYS* 1.3 77.0 - - - +
539M VAL* 1.3 68.9 + - + +
540M PHE 3.3 0.2 - - - -
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Residues in contact with VAL 539 (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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434M HIS 5.3 0.2 - - - +
435M TYR* 3.6 42.0 - - + +
436M GLY 4.3 9.0 + - - +
438M ILE 4.3 2.4 - - - +
439M CYS* 4.1 3.6 - - - -
440M PRO* 3.3 19.3 - - + +
456M ALA* 4.7 3.3 - - - +
536M PRO* 2.9 16.2 + - + +
538M GLN* 1.3 84.1 - - + +
540M PHE* 1.3 82.3 - - + +
1067N VAL* 3.8 13.9 - - + -
1071N PHE* 4.4 24.7 - - + -
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Residues in contact with PHE 540 (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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439M CYS* 3.7 5.8 - - - -
440M PRO* 4.2 10.5 - - + -
441M VAL* 3.5 34.5 - - + -
456M ALA* 4.3 3.1 - - - -
457M ALA 3.2 17.4 + - - -
536M PRO 3.9 10.5 - - - -
537M LYS 3.2 2.6 + - - +
539M VAL* 1.3 105.4 - - + +
541M SER* 1.3 58.2 + - - +
544M THR* 3.6 22.7 - - + -
545M ASN* 2.7 25.8 + - - +
550M LEU* 4.2 3.1 - - + -
905M ILE* 3.9 12.1 - - + -
906M PHE* 3.5 33.9 - + - -
1067N VAL* 4.8 4.9 - - + -
1070N TYR* 3.7 25.6 - + + -
1071N PHE 5.7 0.9 - - - -
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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