Contacts of the helix formed by residues 433 - 445 (chain S) in PDB entry 5LN3
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 ASP 433 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430S SER* 4.3 13.2 - - - +
431S PRO* 4.3 12.2 - - - +
432S GLU* 1.4 82.9 + - - +
434S ALA* 1.4 59.2 + - - +
435S GLU 3.7 2.1 + - - -
436S PHE* 3.8 15.7 + - + +
437S ILE* 3.1 26.1 + - + +
240T SER* 3.9 14.4 - - - +
242T ASN* 3.2 25.2 + - - +
243T LYS* 3.0 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423S ALA* 4.8 12.1 - - + +
426S LEU* 4.0 33.4 - - + +
427S GLN* 6.4 0.2 - - - -
430S SER* 4.8 5.6 - - - +
432S GLU* 3.2 12.5 + - - +
433S ASP* 1.4 73.9 - - - +
435S GLU* 1.3 77.4 + - - +
437S ILE* 3.5 6.9 + - - +
438S VAL* 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419S LEU* 4.7 24.7 - - + -
423S ALA* 5.4 4.5 - - - +
432S GLU* 3.9 22.9 - - - +
433S ASP 3.7 0.8 - - - -
434S ALA* 1.3 91.4 + - + +
436S PHE* 1.3 69.6 + - + +
438S VAL* 3.3 8.2 + - - +
439S ALA* 3.0 29.4 + - - +
451S ILE* 5.4 3.6 - - + +
453S HIS* 5.3 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 436 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432S GLU 5.2 2.7 - - - -
433S ASP* 3.9 19.3 - - - +
434S ALA 3.3 0.2 - - - -
435S GLU* 1.3 87.1 - - + +
437S ILE* 1.4 55.3 + - - +
439S ALA* 3.4 7.3 + - - +
440S LYS* 3.1 22.3 + - - +
239T GLY 3.3 24.9 - - - +
240T SER* 4.5 3.8 - - - -
241T TYR* 3.5 36.6 + + + -
242T ASN* 3.3 40.2 - - + -
290T ILE* 6.6 0.4 - - + -
292T PHE* 4.7 20.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403S ILE* 3.7 36.8 - - + +
407S VAL* 5.6 10.5 - - + -
426S LEU* 5.4 9.6 - - + -
430S SER* 4.8 11.7 - - - +
433S ASP* 3.1 22.9 - - + +
434S ALA* 3.7 7.4 - - - +
436S PHE* 1.4 71.3 - - - +
438S VAL* 1.4 64.4 + - + +
440S LYS* 3.1 5.4 + - - +
441S ALA* 3.0 26.2 + - + +
238T GLU* 4.0 30.5 - - + +
240T SER* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 438 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407S VAL* 5.1 14.4 - - + -
419S LEU* 5.7 6.7 - - + -
422S ILE* 4.8 11.0 - - + -
426S LEU* 3.6 23.6 - - + -
434S ALA 3.2 15.3 - - - +
435S GLU* 3.3 10.9 + - - +
437S ILE* 1.4 81.1 - - + +
439S ALA* 1.3 65.3 - - - +
441S ALA* 3.2 8.0 + - - +
442S ILE* 3.1 28.8 + - + +
447S ILE* 5.9 1.1 - - + -
451S ILE* 3.8 22.7 - - + -
458S VAL* 6.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435S GLU 3.0 15.7 + - - +
436S PHE* 3.6 8.7 - - - +
437S ILE 3.2 0.2 - - - -
438S VAL* 1.3 75.5 - - - +
440S LYS* 1.4 66.8 + - - +
442S ILE* 3.1 27.3 - - + +
443S ARG* 3.2 12.5 + - - +
451S ILE* 4.8 5.6 - - + -
241T TYR* 5.0 5.4 - - + +
274T CYS* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 440 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400S HIS* 5.7 2.0 - - + -
404S LYS* 5.4 7.2 - - - +
436S PHE 3.1 13.1 + - - +
437S ILE 3.1 10.1 + - - +
439S ALA* 1.4 78.0 - - - +
441S ALA* 1.3 56.6 - - - +
443S ARG* 3.4 10.0 + - - +
444S ASP* 3.1 31.0 + - + +
236T LEU* 3.8 11.1 + - - +
237T MET* 2.8 34.5 + - - +
238T GLU 3.5 16.2 - - - +
239T GLY* 4.0 2.0 - - - -
241T TYR* 5.1 1.3 + - - +
270T GLU* 3.9 34.9 + - + +
274T CYS* 4.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404S LYS* 4.2 17.0 - - + +
407S VAL* 4.3 32.5 - - + -
437S ILE* 3.0 13.4 + - + +
438S VAL 3.4 9.4 - - - +
439S ALA 3.2 0.2 - - - -
440S LYS* 1.3 77.2 - - - +
442S ILE* 1.4 62.5 + - - +
444S ASP* 3.3 14.4 - - - +
445S GLY 3.6 0.7 + - - -
446S VAL* 3.8 10.3 - - + +
447S ILE* 3.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438S VAL* 3.4 19.5 - - + +
439S ALA* 3.1 22.2 - - + +
441S ALA* 1.4 76.3 - - - +
443S ARG* 1.4 61.2 + - + +
445S GLY* 3.4 3.5 + - - -
447S ILE* 2.9 33.9 - - + +
448S GLU* 3.7 19.2 - - + +
449S ALA* 3.8 48.0 - - + +
451S ILE* 3.9 25.4 - - + -
274T CYS* 4.9 4.0 - - + +
277T LYS* 4.6 6.2 - - + +
278T ALA* 4.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 443 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439S ALA 3.2 17.0 + - - +
440S LYS* 3.6 9.0 - - - +
442S ILE* 1.4 77.1 - - + +
444S ASP* 1.3 68.9 + - - +
445S GLY* 3.4 1.4 + - - -
448S GLU* 5.4 0.3 - - - +
269T ASP 5.5 0.8 + - - -
270T GLU* 3.6 40.8 + - - +
273T GLY* 4.4 4.6 - - - -
274T CYS* 3.4 35.4 - - + +
277T LYS* 3.4 41.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 444 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404S LYS* 3.7 17.1 + - - +
440S LYS* 3.1 18.0 + - + +
441S ALA 3.3 13.5 - - - +
443S ARG* 1.3 81.9 - - - +
445S GLY* 1.3 57.4 + - - +
446S VAL* 3.7 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 445 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441S ALA 3.6 0.6 + - - -
442S ILE 3.4 7.9 + - - -
443S ARG 3.3 4.1 - - - -
444S ASP* 1.3 78.8 - - - +
446S VAL* 1.4 63.6 + - - +
447S ILE* 3.3 10.1 - - - -
448S GLU* 4.6 10.5 - - - +
----------------------------------------------------------
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