Contacts of the strand formed by residues 436 - 439 (chain H) in PDB entry 5LS6
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 ARG 436 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H CYS* 3.4 9.0 - - - -
85H VAL* 3.1 22.4 + - + +
86H ASN* 3.1 20.8 + - + +
126H CYS* 4.3 4.9 - - - +
127H HIS 2.8 34.1 + - - +
128H SER* 4.4 2.8 - - - +
129H GLN* 4.4 4.0 - - - +
130H GLY* 3.1 30.6 - - - +
131H GLU 3.0 13.7 + - - -
132H ILE* 3.7 30.7 - - + +
424H ILE* 3.5 35.7 - - + +
425H LEU 3.7 2.0 - - - -
426H ILE* 3.9 4.0 - - + -
434H ILE* 5.0 0.2 - - - +
435H TRP* 1.3 74.7 - - - +
437H TRP* 1.3 65.0 + - - +
438H ASP* 2.8 34.8 + - - +
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Residues in contact with TRP 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H PHE* 3.9 22.7 - - + -
83H LYS* 3.2 25.8 - - - -
84H CYS* 3.5 32.8 - - + -
386H LEU* 3.5 27.8 - - + +
404H LEU* 3.7 40.8 - - + -
405H THR 3.4 26.7 - - - -
406H HIS* 4.9 2.9 - - + -
409H CYS* 6.2 2.5 - - + -
424H ILE* 3.2 4.2 - - - +
425H LEU* 2.8 56.6 + - + +
427H ALA* 4.9 1.6 - - + -
435H TRP* 3.9 23.8 - + + +
436H ARG* 1.3 77.5 - - - +
438H ASP* 1.3 63.4 + - - +
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Residues in contact with ASP 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H PHE* 3.1 28.5 - - - +
83H LYS* 3.3 16.2 + - + +
85H VAL* 3.2 21.4 - - + +
129H GLN* 4.8 10.0 - - - +
423H SER* 3.2 11.8 - - - +
424H ILE* 4.0 6.0 - - - +
436H ARG* 2.8 43.4 + - - +
437H TRP* 1.3 74.9 - - - +
439H ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 439 (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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80H TYR* 3.2 38.4 - - - +
81H SER 3.8 5.6 - - - +
82H PHE* 3.3 30.7 - - + -
376H MET* 4.2 9.7 - - - +
422H SER* 3.0 44.7 - - - +
423H SER* 2.9 16.0 + - - +
438H ASP* 1.3 78.8 - - - +
440H LEU* 1.3 77.2 + - - +
441H ARG* 3.5 2.9 + - - -
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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
------------------------------------------------------------
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