Contacts of the strand formed by residues 476 - 485 (chain A) in PDB entry 5LZ6
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 LEU 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A TYR* 4.8 19.5 - - + -
433A PHE 3.3 3.1 - - - +
434A GLU* 3.6 32.8 - - + +
435A TRP* 5.0 0.2 - - - -
474A PRO* 3.8 12.0 + - + +
475A LEU* 1.3 92.5 - - - +
477A ASP* 1.3 68.3 + - - +
478A GLU 4.4 0.2 + - - -
505A LEU* 3.9 22.7 - - + -
507A LYS* 6.3 1.3 - - - -
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Residues in contact with ASP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 3.5 26.8 - - + +
432A TYR* 3.3 8.7 - - - -
433A PHE* 2.9 38.6 + - + +
435A TRP* 2.6 32.5 + - - -
475A LEU* 6.0 1.3 - - - +
476A LEU* 1.3 76.3 - - - +
478A GLU* 1.3 62.6 + - - +
479A ILE* 3.4 15.5 + - + +
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 5.5 1.7 - - - +
432A TYR* 3.6 37.8 + - + -
476A LEU 4.3 0.4 + - - -
477A ASP* 1.3 70.5 + - - +
479A ILE* 1.3 66.1 + - - +
480A VAL 4.5 0.9 - - - -
481A PRO* 3.5 42.2 - - + +
482A VAL 4.6 0.9 + - - -
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Residues in contact with ILE 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 3.6 20.6 - - + -
370A ALA 5.1 0.2 - - - +
372A PRO* 3.4 36.7 - - + +
418A TRP* 5.4 0.4 - - + -
431A VAL* 3.0 23.6 + - + +
432A TYR 4.2 2.9 - - - -
433A PHE* 4.1 17.0 - - + +
477A ASP* 3.8 20.0 - - + +
478A GLU* 1.3 79.7 - - - +
480A VAL* 1.3 64.2 + - + +
481A PRO* 3.8 7.4 - - - +
496A HIS* 3.5 50.7 - - + +
504A TYR* 4.6 0.7 - - + -
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PRO* 3.7 22.4 - - + -
374A MET* 3.4 29.8 - - + -
418A TRP* 4.0 14.8 - - + -
429A PHE* 4.3 5.2 - - + -
430A GLY* 3.1 9.7 - - - -
431A VAL* 2.9 42.3 + - + +
432A TYR* 4.9 0.9 - - - -
478A GLU* 4.5 3.1 - - - +
479A ILE* 1.3 81.6 - - + +
481A PRO* 1.3 67.0 - - - +
482A VAL* 3.5 1.9 + - - +
485A ARG* 3.3 29.2 - - - +
32B THR 3.8 3.4 - - - +
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Residues in contact with PRO 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PHE 3.4 0.9 - - - +
432A TYR* 5.4 0.2 - - - +
478A GLU* 3.5 30.7 - - + +
479A ILE 3.8 8.3 - - - +
480A VAL* 1.3 83.7 - - - +
482A VAL* 1.3 62.7 + - - +
483A TYR 3.3 0.2 + - - -
485A ARG* 3.2 24.8 + - - -
32B THR* 3.7 14.8 - - - +
33B HIS* 4.1 23.1 - - + +
34B LEU* 4.2 10.9 - - + +
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 4.4 2.5 - - - -
429A PHE 3.3 16.4 - - - +
430A GLY* 3.9 15.7 - - - +
432A TYR* 4.0 28.2 + - + +
478A GLU* 4.6 2.0 + - - -
481A PRO* 1.3 71.4 - - - +
483A TYR* 1.3 64.4 + - - +
507A LYS* 4.5 10.3 - - + -
509A ASP* 4.1 30.1 - - + +
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Residues in contact with TYR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A GLY* 3.9 3.1 - - - -
429A PHE 2.9 26.3 + - - -
481A PRO 3.3 1.4 + - - -
482A VAL* 1.3 76.7 - - - +
484A ARG* 1.3 68.2 + - - +
485A ARG* 3.2 13.7 + - - +
34B LEU* 3.4 37.7 - - + -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 2.9 26.5 + - - +
427A ILE 3.4 5.8 - - - +
428A GLY* 3.9 4.9 - - - +
483A TYR* 1.3 76.4 - - - +
485A ARG* 1.3 63.5 + - - +
486A ASP* 4.4 0.7 + - - +
512A TYR* 3.3 61.4 - - + +
601A BGC 3.4 29.1 + - - -
34B LEU* 5.9 0.9 - - - +
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A MET* 3.5 17.1 - - - -
420A PHE* 4.4 5.6 - - + -
426A ASP* 3.3 16.0 - - - +
427A ILE 2.9 9.1 + - - +
429A PHE* 3.7 24.1 + - + +
480A VAL* 3.3 18.8 - - - +
481A PRO 3.2 26.5 + - - -
483A TYR* 3.2 19.3 + - - +
484A ARG* 1.3 77.4 - - - +
486A ASP* 1.3 60.0 + - - +
487A CYS* 2.8 24.3 + - + +
492A TYR* 3.8 31.9 - - + -
31B PRO 3.0 27.3 + - - -
32B THR 3.4 8.3 + - - -
34B LEU* 3.9 18.3 - - - +
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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