Contacts of the helix formed by residues 331 - 340 (chain M) in PDB entry 6KW5
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 GLU 331 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU* 5.8 7.4 - - + -
286M HIS* 3.7 21.0 - - - -
290M SER* 4.1 20.5 + - - +
329M SER* 3.8 9.5 - - - -
330M LYS* 1.3 101.2 + - + +
332M CYS* 1.3 60.1 + - + +
333M SER 3.5 0.4 - - - -
334M LEU* 4.0 5.4 - - - -
335M ILE* 3.3 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 332 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286M HIS* 5.5 1.3 - - + +
289M LEU* 3.7 29.4 - - + +
290M SER* 5.2 8.7 - - - +
293M VAL* 3.7 28.9 - - - +
325M GLU 5.6 0.2 - - - -
326M LEU* 3.4 24.5 - - - +
329M SER* 3.7 20.4 - - - +
331M GLU* 1.3 82.6 - - + +
333M SER* 1.3 58.7 + - - +
334M LEU 3.2 5.0 + - - -
335M ILE* 4.1 0.4 + - - -
336M LEU* 3.8 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326M LEU 4.3 0.8 + - - -
327M PHE* 3.6 51.6 + - - +
328M LYS 4.8 0.3 - - - -
329M SER 2.4 26.7 + - - -
330M LYS* 4.3 2.8 - - - -
332M CYS* 1.3 76.8 - - - +
334M LEU* 1.3 57.6 + - - +
336M LEU* 4.5 3.6 - - - -
337M GLU* 3.4 24.1 + - - +
549M PHE* 4.7 0.7 - - - -
552M ARG* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D GLU* 4.6 9.9 - - + +
455D GLU* 5.6 4.3 - - - +
49I ARG* 3.4 43.2 - - - +
330M LYS* 3.3 29.4 - - + +
331M GLU* 4.0 3.8 + - - -
332M CYS 3.2 0.8 - - - -
333M SER* 1.3 79.6 + - - +
335M ILE* 1.3 66.3 + - - +
336M LEU 3.3 1.3 - - - -
337M GLU* 3.3 31.5 + - - +
338M ALA* 3.9 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 335 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU* 4.4 15.5 - - + -
49I ARG* 4.0 22.9 - - - +
290M SER 5.6 0.9 - - - +
293M VAL* 4.2 22.4 - - + +
294M SER* 4.3 22.0 - - - +
297M LEU* 4.0 26.7 - - + -
331M GLU* 3.3 24.7 + - + +
332M CYS* 4.1 3.1 + - - +
334M LEU* 1.3 76.5 - - + +
336M LEU* 1.3 57.8 + - - +
338M ALA* 3.1 4.9 + - - +
339M THR* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293M VAL* 3.9 13.2 - - + -
296M LEU* 3.7 29.2 - - + -
309M LEU* 5.9 0.4 - - + -
312M LEU* 5.1 4.5 - - + -
326M LEU* 3.7 30.7 - - + -
327M PHE* 4.1 14.1 - - + -
332M CYS 3.8 18.2 + - - +
333M SER 4.8 1.3 - - - +
334M LEU 3.3 0.6 - - - -
335M ILE* 1.3 77.8 - - + +
337M GLU* 1.3 59.2 + - - +
338M ALA 3.2 0.2 - - - -
339M THR* 3.7 7.0 - - - +
340M LEU* 3.6 32.0 + - + +
341M PRO* 3.8 1.6 - - - +
533M PHE* 5.0 12.8 - - + -
549M PHE* 3.3 27.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D GLU* 3.6 18.3 - - - +
53I ASP* 5.8 0.4 - - - -
56I ILE* 5.2 0.3 - - - +
333M SER 3.4 21.0 - - - +
334M LEU* 3.3 24.1 + - - +
335M ILE 3.2 1.2 - - - -
336M LEU* 1.3 77.5 - - - +
338M ALA* 1.3 57.8 + - + +
341M PRO* 3.7 14.3 - - - +
549M PHE* 3.6 19.7 - - + -
552M ARG* 2.4 38.2 + - - +
553M ILE* 3.8 15.1 - - + +
556M LEU* 4.4 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ARG* 4.7 13.5 - - + +
52I LEU* 3.4 25.3 - - + +
53I ASP* 4.0 29.8 - - + +
56I ILE* 4.3 12.2 - - - +
297M LEU* 6.0 0.2 - - + -
334M LEU 3.9 6.5 + - - +
335M ILE 3.1 7.0 + - - +
337M GLU* 1.3 81.1 - - + +
339M THR* 1.3 66.0 + - + +
340M LEU 3.7 0.2 - - - -
341M PRO* 4.2 2.0 - - - +
342M ASN* 3.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I LEU* 4.5 7.4 - - + -
296M LEU* 4.2 28.0 - - + +
297M LEU* 3.7 32.3 - - + -
299M GLU* 5.5 1.7 - - - +
335M ILE* 2.9 25.4 + - + +
336M LEU* 3.7 15.2 - - - +
338M ALA* 1.3 78.7 - - + +
340M LEU* 1.3 61.4 + - - +
342M ASN* 2.9 9.4 + - - +
343M LEU* 2.7 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M LEU* 6.1 0.2 - - + -
309M LEU* 4.7 7.0 - - + -
336M LEU* 3.6 23.5 + - + +
339M THR* 1.3 85.1 + - - +
341M PRO* 1.4 61.6 - - + +
342M ASN 3.5 0.2 + - - -
343M LEU* 3.6 16.5 + - + +
344M LEU* 3.5 18.0 + - - +
530M ALA* 3.9 28.9 - - + +
533M PHE* 3.7 38.1 - - + -
534M LEU* 3.8 27.0 - - + +
537M LEU* 5.0 0.4 - - + -
549M PHE* 4.4 17.9 - - + -
----------------------------------------------------------
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