Contacts of the strand formed by residues 422 - 426 (chain A) in PDB entry 1L5G
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 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.8 10.8 - - + -
25A PHE* 4.5 0.4 - - - -
345A ALA* 5.8 0.2 - - + -
347A LEU* 3.2 34.8 - - + -
350A LEU* 5.6 0.2 - - + -
359A ALA* 4.3 15.9 - - + -
373A VAL* 5.1 4.3 - - + -
375A ILE* 5.2 5.8 - - + -
391A LEU* 5.4 3.8 - - + -
408A MET* 3.9 15.7 - - + -
409A LYS 3.4 9.9 - - - +
421A ASP* 1.3 80.4 - - - +
423A ILE* 1.3 86.1 + - - +
424A VAL* 3.4 28.9 - - + -
433A ILE 3.3 1.6 - - - +
434A LEU* 3.3 3.8 - - - +
435A TYR* 2.7 45.3 + - + +
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Residues in contact with ILE 423 (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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23A VAL* 3.4 26.9 - - + +
24A ASP* 3.5 25.4 - - - +
25A PHE* 3.3 36.1 - - + -
36A LEU* 3.5 35.0 - - + -
38A VAL* 5.5 0.9 - - + -
408A MET* 3.0 25.6 - - - +
409A LYS* 2.8 14.0 + - + +
422A LEU* 1.3 77.3 - - - +
424A VAL* 1.3 64.2 + - - +
432A ALA* 4.2 8.1 - - + -
433A ILE 3.1 8.1 - - - +
434A LEU* 3.8 10.3 - - + -
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 3.7 24.7 - - + -
391A LEU* 5.3 1.3 - - + -
404A PHE* 3.9 17.7 - - + -
405A GLY* 3.3 36.6 - - - +
407A SER 3.6 3.6 - - - +
408A MET* 3.9 4.3 - - + -
422A LEU* 3.4 22.7 - - + -
423A ILE* 1.3 74.1 - - - +
425A GLY* 1.3 59.2 + - - +
426A ALA 4.3 0.3 + - - -
432A ALA* 3.3 2.1 - - - +
433A ILE* 2.7 35.2 + - + +
435A TYR* 3.8 24.7 - - + -
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Residues in contact with GLY 425 (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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20A GLY 3.7 11.9 - - - +
23A VAL* 4.3 6.7 - - - +
403A SER 3.4 5.4 - - - +
404A PHE* 5.5 0.2 - - - -
405A GLY 3.3 17.1 + - - -
406A TYR* 3.5 7.4 + - - +
407A SER* 2.8 29.0 + - - -
424A VAL* 1.3 75.7 - - - +
426A ALA* 1.3 60.8 + - - -
427A PHE 4.1 0.5 + - - -
431A ARG 3.7 6.5 - - - -
432A ALA* 4.2 2.9 - - - -
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Residues in contact with ALA 426 (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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19A PHE 4.2 0.4 - - - -
20A GLY 4.1 0.2 + - - -
395A TRP* 5.4 3.6 - - + -
402A PRO* 3.2 18.8 - - + +
403A SER 3.8 1.6 - - - -
404A PHE* 3.5 27.4 - - + +
424A VAL 4.3 0.4 + - - -
425A GLY* 1.3 71.0 - - - -
427A PHE* 1.3 63.8 + - - +
428A GLY 3.2 0.5 + - - -
429A VAL* 3.3 17.6 + - + +
430A ASP 3.1 15.6 + - - -
431A ARG* 2.9 22.8 + - + +
433A ILE* 6.5 0.4 - - + -
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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