Contacts of the strand formed by residues 438 - 443 (chain A) in PDB entry 4LG8
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 VAL 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A THR* 2.5 36.9 + - - +
410A ALA* 3.3 28.5 - - + -
411A ALA 4.9 6.8 + - - +
414A SER* 4.7 12.3 - - - -
415A SER 4.7 4.7 - - - +
416A VAL* 4.3 11.4 - - + -
432A LEU* 4.2 12.3 - - + -
436A PHE* 3.9 20.8 + - + -
437A GLU* 1.3 73.0 - - - +
439A LYS* 1.3 58.7 + - - +
440A SER 4.1 9.4 - - - +
441A LEU* 4.1 20.4 - - + -
452A LEU* 4.3 9.0 - - + -
453A GLY 3.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A THR* 3.8 12.5 - - + +
397A SER* 3.8 12.9 + - - -
437A GLU* 3.7 10.0 + - + +
438A VAL* 1.3 77.2 - - - +
440A SER* 1.3 62.3 + - - +
453A GLY 2.8 11.3 + - - +
454A GLY* 4.0 14.6 - - - -
477A LEU* 4.5 17.7 - - + -
478A THR 4.2 8.3 - - - +
479A THR* 5.2 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.6 5.3 - - - -
438A VAL* 3.7 2.2 - - - +
439A LYS* 1.3 80.5 - - - +
441A LEU* 1.3 66.3 + - - +
442A ILE* 5.6 0.2 - - - +
452A LEU* 3.3 7.2 - - - +
453A GLY 3.0 32.2 + - - +
479A THR 4.2 15.9 - - - -
480A GLY* 4.3 4.9 - - - -
481A VAL* 3.7 16.5 + - - +
608A UNX 2.9 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.0 21.2 + - - +
398A ILE 4.4 1.7 - - - +
399A ALA* 3.5 18.1 - - + +
408A ALA* 3.5 39.5 - - + +
409A THR* 3.6 19.1 - - - +
410A ALA* 3.8 10.1 - - + +
416A VAL* 4.0 22.2 - - + -
438A VAL* 4.1 2.9 - - + -
440A SER* 1.3 78.0 + - - +
442A ILE* 1.3 66.7 + - - +
450A LEU* 4.5 9.9 - - + -
451A ALA 3.4 6.7 - - - +
452A LEU* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP* 5.6 4.9 - - - +
399A ALA* 4.0 7.6 - - + -
440A SER* 5.6 0.2 - - - +
441A LEU* 1.3 78.6 - - - +
443A PHE* 1.3 75.1 + - - +
450A LEU* 3.8 6.0 - - - +
451A ALA* 2.8 49.8 + - + -
481A VAL* 3.5 30.5 - - + +
482A ALA* 4.3 12.6 - - + -
483A PHE* 3.6 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ALA* 3.3 28.1 - - + +
400A PHE 3.8 6.7 + - - +
401A SER* 3.6 46.9 - - - +
402A GLU* 5.1 0.9 - - + +
406A TYR* 4.2 11.9 - + + -
408A ALA* 3.8 25.6 - - + -
418A LEU* 4.1 10.1 - - + -
442A ILE* 1.3 90.8 - - - +
444A ASP* 1.3 71.7 + - - +
445A GLN* 5.7 0.2 - - - -
447A GLY* 4.7 4.3 - - - -
449A TYR 3.2 16.6 - - - +
450A LEU* 3.9 13.5 - - + -
462A CYS* 3.8 24.0 - - - -
465A TRP* 4.5 6.5 - + - -
483A PHE* 3.8 2.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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