Contacts of the helix formed by residues 333 - 341 (chain L) in PDB entry 3SWD
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 MET 333 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K GLY* 4.3 7.7 - - - -
115K QPA 3.7 35.9 - - - +
116K THR* 4.2 10.8 - - + -
116L THR* 3.5 45.8 - - + +
117L ILE* 5.6 3.4 - - + -
330L ASN 5.2 4.5 - - - +
331L ARG 3.9 1.4 - - - -
332L PHE* 1.3 76.4 - - - +
334L HIS* 1.3 57.8 + - - +
336L PRO* 2.9 22.0 - - - +
337L GLU* 3.7 15.3 - - + +
368L THR* 3.9 36.3 - - + +
369L ASP* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 334 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307L GLN* 3.0 29.8 + - - -
308L ALA* 3.5 33.9 - - + +
311L THR* 3.6 14.3 + - + -
331L ARG* 3.2 23.1 + - + +
332L PHE* 3.8 7.4 - + - -
333L MET* 1.3 71.5 + - - +
335L VAL* 1.3 78.1 + - + +
337L GLU* 3.1 10.7 + - - +
338L LEU* 2.8 37.1 + - + +
372L ALA* 4.1 15.3 - - + +
373L SER* 5.8 1.6 - - - +
375L SER* 4.0 16.2 - - - +
376L LEU* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L THR* 4.3 7.4 - - + -
315L LEU* 5.6 2.3 - - + +
332L PHE* 2.9 17.3 + - + +
334L HIS* 1.3 92.7 - - + +
336L PRO* 1.3 71.3 - - + +
338L LEU* 3.0 10.3 + - - +
339L SER* 2.9 25.0 + - - +
343L ALA* 5.5 0.2 - - - +
345L ALA* 4.2 26.7 - - + +
347L ILE* 4.0 25.6 - - + -
352L VAL* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 336 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K ARG* 6.0 0.4 - - - +
111K LEU* 4.7 0.3 - - - +
112K PRO 4.5 5.4 - - - +
113K GLY* 3.7 8.3 - - - +
114K GLY* 3.6 28.3 - - - +
119K ALA* 5.6 4.3 - - - -
120K ARG 5.5 10.3 - - - +
332L PHE 3.2 10.3 - - - +
333L MET* 2.9 22.4 - - - +
335L VAL* 1.3 88.4 - - + +
337L GLU* 1.3 61.0 + - - +
339L SER* 3.0 19.3 + - - +
340L ARG* 3.2 16.4 + - - +
347L ILE* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K TYR* 4.5 1.9 + - - -
113K GLY* 3.5 5.9 - - - -
114K GLY* 2.9 25.6 + - - +
333L MET* 3.7 14.8 - - + +
334L HIS* 3.1 8.4 + - - +
336L PRO* 1.3 75.5 - - - +
338L LEU* 1.3 64.2 + - - +
340L ARG* 2.9 28.4 + - - +
341L MET* 3.6 3.1 + - - +
365L VAL* 3.4 21.4 - - + +
366L MET* 2.9 49.5 + - - +
376L LEU* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L THR* 4.8 0.7 - - + -
312L LEU* 4.3 26.2 - - + +
315L LEU* 3.6 24.0 - - + -
334L HIS* 2.8 33.0 + - + +
335L VAL* 3.6 7.0 - - - +
337L GLU* 1.3 74.6 - - - +
339L SER* 1.3 57.4 + - - +
341L MET* 2.9 27.0 + - - +
343L ALA* 3.2 29.0 + - + +
360L LEU* 4.8 3.7 - - + +
375L SER* 4.5 7.9 - - - +
376L LEU* 3.9 17.3 - - + -
379L ALA* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K LEU* 4.1 14.1 - - - +
138K LEU* 3.2 14.9 - - - +
335L VAL* 2.9 20.6 + - - +
336L PRO* 3.0 15.9 + - - +
338L LEU* 1.3 73.1 - - - +
340L ARG* 1.3 59.2 + - - +
341L MET 2.9 5.4 - - - -
342L GLY* 3.1 11.3 + - - -
343L ALA* 3.7 21.8 + - - +
345L ALA* 4.8 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K TYR* 3.1 21.1 - - - -
110K SER* 2.8 25.7 + - - -
111K LEU* 2.9 34.4 + - + +
112K PRO 4.4 2.2 - - - +
113K GLY* 4.1 10.1 - - - +
138K LEU* 4.0 6.7 - - - +
140K GLU 4.4 0.4 + - - -
141K GLY* 2.8 47.3 + - - -
142K TYR* 4.4 3.8 - - - -
336L PRO 3.2 14.5 + - - +
337L GLU* 2.9 25.2 + - - +
339L SER* 1.3 76.9 - - - +
341L MET* 1.3 59.4 + - - +
342L GLY 3.3 1.0 + - - -
361L SER* 4.5 1.2 - - - +
363L ALA* 3.7 9.6 - - + +
364L GLN* 2.4 48.4 + - - +
365L VAL* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 341 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K LEU* 5.8 0.2 - - - -
337L GLU 4.0 6.3 - - - +
338L LEU* 2.9 19.0 + - - +
340L ARG* 1.3 80.6 - - - +
342L GLY* 1.3 55.4 + - - +
343L ALA 3.5 1.8 - - - -
360L LEU* 3.5 15.9 - - + +
361L SER* 2.7 47.5 + - - +
363L ALA* 4.2 6.7 - - + +
365L VAL* 4.1 25.4 - - + -
376L LEU* 4.9 2.2 - - - +
379L ALA* 3.6 35.0 - - + -
380L GLY* 3.9 1.6 - - - +
383L ALA* 3.5 23.3 - - + -
387L THR* 3.5 28.7 - - + +
----------------------------------------------------------
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