Contacts of the helix formed by residues 536 - 544 (chain B) in PDB entry 3C5R
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 ASP 536 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505B GLY* 6.3 2.5 - - - -
507B VAL* 4.6 6.6 - - - +
534B THR* 3.1 12.2 + - - +
535B ASP* 1.3 77.6 - - - +
537B GLU* 1.3 59.8 + - - +
538B SER* 3.1 15.7 + - - -
539B MET* 2.9 29.7 + - + +
540B LYS* 2.9 31.2 + - - +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B ASP 3.6 7.8 + - - +
536B ASP* 1.3 72.7 + - - +
538B SER* 1.3 60.4 + - - +
540B LYS* 3.1 38.7 + - - +
541B SER* 3.0 29.8 + - - -
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Residues in contact with SER 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B VAL* 4.6 13.1 - - - +
536B ASP* 3.1 16.0 + - - -
537B GLU* 1.3 78.2 - - - +
539B MET* 1.3 58.6 + - - +
541B SER* 2.7 21.2 + - - -
542B LEU* 3.5 18.5 + - - +
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Residues in contact with MET 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B ALA* 3.8 18.2 - - + +
505B GLY* 3.6 31.0 - - - -
506B HIS 3.7 3.8 - - - +
507B VAL* 3.5 26.4 - - + +
510B VAL* 3.6 33.4 - - + -
534B THR* 3.5 36.3 - - + +
536B ASP* 2.9 15.6 + - + +
537B GLU 3.3 0.2 - - - -
538B SER* 1.3 76.8 - - - +
540B LYS* 1.3 61.7 + - - +
542B LEU* 3.1 17.5 + - - +
543B LEU* 3.2 21.7 + - + +
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Residues in contact with LYS 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B VAL* 4.0 19.5 - - + +
534B THR* 3.9 20.4 - - + +
535B ASP* 4.4 16.9 + - - +
536B ASP 2.9 19.2 + - - +
537B GLU* 3.1 40.6 + - - +
539B MET* 1.3 72.6 - - - +
541B SER* 1.3 59.8 + - - +
543B LEU 3.0 0.7 + - - -
544B LEU* 2.8 50.9 + - + +
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Residues in contact with SER 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B GLU 3.0 13.8 + - - -
538B SER* 2.7 25.8 + - - -
540B LYS* 1.3 75.6 - - - +
542B LEU* 1.3 67.8 + - - +
544B LEU* 3.4 14.9 - - - +
545B LEU 5.5 0.3 - - - -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B VAL* 4.0 24.2 - - + +
510B VAL* 4.3 17.9 - - + -
511B LYS* 3.8 46.4 - - + -
514B LEU* 3.8 20.1 - - + +
520B ARG* 4.1 7.3 - - - -
538B SER* 3.5 18.1 + - - +
539B MET* 3.1 13.4 + - - +
540B LYS 3.1 0.8 - - - -
541B SER* 1.3 89.8 + - - +
543B LEU* 1.3 59.4 + - - +
544B LEU 3.6 1.8 - - - +
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU* 4.0 28.7 - - + -
502B ALA* 4.0 9.4 - - + -
510B VAL* 4.3 17.7 - - + -
514B LEU* 4.7 2.7 - - + -
520B ARG* 2.9 42.4 + - + +
521B ASN* 4.6 4.2 + - - -
530B PRO* 4.0 10.1 - - + -
531B VAL* 3.8 44.8 - - + +
539B MET* 3.2 31.8 + - + +
540B LYS 3.0 2.6 + - - +
542B LEU* 1.3 79.7 - - - +
544B LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ARG* 4.1 5.0 - - - +
521B ASN* 5.8 3.4 - - - +
529B ARG* 6.1 1.8 - - - +
531B VAL* 3.4 36.8 - - + -
540B LYS* 2.8 35.5 + - + +
541B SER* 3.4 16.5 - - - +
542B LEU 4.5 1.9 - - - +
543B LEU* 1.3 82.6 + - - +
545B LEU* 1.3 71.3 + - - +
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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