Contacts of the strand formed by residues 753 - 755 (chain B) in PDB entry 5IA0
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 CYS 753 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ASN* 3.0 28.8 + - - +
700B LEU* 4.2 10.5 - - - -
719B MET* 3.7 41.9 - - - +
722B GLY* 4.4 3.7 - - - -
723B ILE* 3.7 25.7 - - + +
745B ILE* 3.7 7.2 - - + -
746B LEU 3.3 4.3 - - - -
747B VAL* 4.0 20.2 - - - -
751B LEU 3.4 5.5 + - - -
752B VAL* 1.3 74.6 - - - +
754B LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B HIS 5.2 0.4 + - - -
673B HIS* 3.2 38.1 + - - +
674B ASN* 3.2 9.6 - - - +
675B ILE 4.2 5.5 + - - +
676B ILE* 3.9 13.0 - - + +
677B ARG* 4.6 5.7 - - - +
693B GLU* 3.1 40.3 + - - +
695B MET* 3.6 20.2 - - + -
745B ILE* 3.4 5.5 - - - +
746B LEU* 2.8 33.3 + - - +
748B ASN* 4.1 13.8 - - - +
752B VAL* 3.8 15.7 - - + -
753B CYS* 1.3 81.5 - - - +
755B VAL* 1.3 64.5 + - - +
756B SER* 3.6 0.9 + - - -
1005B EDO 4.2 2.0 + - - -
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Residues in contact with VAL 755 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ASN 2.9 15.3 + - - +
675B ILE* 3.9 15.8 - - + -
676B ILE* 3.1 22.7 + - - +
723B ILE* 4.4 26.9 - - + +
726B GLY 4.8 0.9 - - - -
727B MET* 4.1 20.6 - - - -
730B LEU* 4.4 4.7 - - + -
737B HIS* 3.7 22.4 - - + +
740B LEU* 4.6 9.4 - - + -
744B ASN* 4.1 6.1 - - + +
745B ILE* 4.5 4.7 - - + -
754B LYS* 1.3 71.3 - - - +
756B SER* 1.3 73.9 + - - +
758B PHE* 3.5 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
------------------------------------------------------------
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