Contacts of the helix formed by residues 535 - 542 (chain B) in PDB entry 3II5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 831 6.4 2.0 - - - -
534B SER* 1.3 79.8 - - - +
536B LEU* 1.3 64.3 + - - +
537B TYR* 3.4 10.1 + - - +
538B HIS* 3.1 24.1 + - - +
539B HIS* 3.2 21.2 + - - -
578B SER 4.1 0.2 - - - -
579B ASN* 3.7 25.4 + - - +
581B ILE 3.5 7.2 - - - -
582B PHE* 4.0 12.6 - - - -
594B PHE* 6.1 0.2 - - - -
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B SER 3.9 0.2 + - - -
535B SER* 1.3 69.8 - - - +
537B TYR* 1.3 69.3 + - - +
539B HIS* 3.3 3.0 + - + -
540B LEU* 3.0 45.4 + - + +
547B PHE* 4.7 4.7 - - + -
555B ILE* 4.3 12.3 - - + -
578B SER* 3.4 13.0 + - - +
581B ILE* 2.7 41.0 + - + +
583B LEU* 4.0 24.4 - - + +
644B VAL* 4.1 21.3 - - + -
647B GLU* 6.1 0.2 - - - -
648B LEU* 4.0 23.6 - - + -
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Residues in contact with TYR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 3.5 7.9 - - - +
536B LEU* 1.3 78.1 - - - +
538B HIS* 1.3 69.5 + - - +
540B LEU* 3.6 0.2 - - - -
541B HIS* 2.8 48.7 + + + +
542B ILE* 4.3 23.1 - - + +
578B SER* 3.2 31.4 + - - +
579B ASN* 3.1 36.8 - - - +
618B TRP* 4.5 4.5 - + - -
647B GLU* 4.3 0.4 - - - -
653B LEU* 3.7 30.3 - - + +
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Residues in contact with HIS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 831 6.5 1.6 - - - -
534B SER* 3.3 26.1 + - - +
535B SER* 3.1 21.6 + - - +
537B TYR* 1.3 79.7 - - + +
539B HIS* 1.3 57.6 + - - +
542B ILE* 2.9 52.1 + - + +
543B ILE* 3.0 50.0 + - + +
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Residues in contact with HIS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B SER* 3.1 32.3 + - - -
535B SER 3.2 21.5 + - - +
536B LEU* 3.6 9.0 - - - +
537B TYR 3.0 1.2 + - - -
538B HIS* 1.3 79.2 - - - +
540B LEU* 1.3 61.6 + - - +
543B ILE* 3.9 11.9 - - + -
544B GLU 3.3 5.7 + - - -
545B THR* 2.8 55.6 + - + +
547B PHE* 3.8 26.4 - + + -
583B LEU* 3.9 12.9 - - + +
586B ASP* 3.5 36.9 + - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 3.0 41.1 + - + +
537B TYR 2.9 1.6 + - - +
539B HIS* 1.3 78.5 - - - +
541B HIS* 1.3 76.2 + - + +
544B GLU* 4.0 16.9 - - - +
545B THR 4.7 7.3 - - - +
547B PHE* 3.9 31.2 - - + -
552B LEU* 4.9 4.5 - - + -
647B GLU* 4.0 32.8 - - + +
648B LEU* 3.9 17.5 - - + +
651B GLY* 3.6 20.9 - - - +
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Residues in contact with HIS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B TYR* 2.8 56.4 + + + +
540B LEU* 1.3 87.2 - - + +
542B ILE* 1.3 69.4 + - + +
544B GLU* 3.6 14.3 - - - +
647B GLU* 2.6 35.2 + - + +
651B GLY 3.3 19.3 + - - -
652B GLN* 3.5 33.1 - - - -
653B LEU* 3.8 15.7 - - + +
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Residues in contact with ILE 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B TYR* 4.3 22.0 - - + +
538B HIS* 2.9 48.3 + - + +
540B LEU 3.7 0.4 - - - -
541B HIS* 1.3 91.3 - - + +
543B ILE* 1.3 64.4 + - + +
544B GLU* 3.2 13.6 + - - +
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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