Contacts of the strand formed by residues 331 - 337 (chain D) in PDB entry 6CET
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 GLN 331 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D MET* 3.6 12.5 - - - -
317D PHE* 3.2 43.7 - - + +
320D HIS* 3.8 33.9 + - - +
324D ARG* 4.7 8.7 - - - +
329D THR 3.9 10.3 + - - +
330D GLY* 1.3 77.7 - - - +
332D MET* 1.3 62.8 + - - +
360D ASN* 5.4 6.2 + - - +
361D GLY 4.5 3.1 - - - +
362D ILE* 3.6 30.3 - - + +
750D PRO* 5.0 5.9 - - - +
751D ALA 5.5 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ALA* 5.8 0.7 - - + -
170D MET 2.9 11.2 + - - +
171D VAL* 3.3 21.5 - - + +
172D TYR* 2.9 26.2 + - - +
203D LEU* 6.2 1.8 - - + -
207D TRP* 5.6 4.3 - - + -
214D HIS* 5.7 0.7 - - - -
317D PHE* 4.1 2.7 - - - -
331D GLN* 1.3 76.4 - - - +
333D SER* 1.3 63.8 + - - +
334D VAL* 3.6 26.2 - - + -
362D ILE* 3.6 6.8 - - - +
364D VAL* 5.5 8.3 - - + -
746D SER 4.1 5.4 - - - +
747D LEU* 3.3 46.2 - - + +
750D PRO* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR* 3.5 8.5 - - - +
174D PHE* 6.4 1.1 - - - -
310D ILE* 6.0 2.9 - - - -
313D SER* 3.8 22.7 + - - -
314D PHE* 6.4 0.7 - - - -
317D PHE* 3.2 27.9 - - - -
332D MET* 1.3 70.4 - - - +
334D VAL* 1.3 62.7 + - - +
335D VAL* 3.8 8.6 + - - +
362D ILE* 2.9 20.9 + - - +
363D GLY* 3.7 7.1 - - - -
364D VAL* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D VAL* 4.6 2.0 - - + -
172D TYR 2.9 7.3 + - - +
173D ILE* 3.1 27.1 - - + -
174D PHE* 2.9 24.3 + - - +
199D PHE* 5.0 5.2 - - + -
203D LEU* 6.1 4.5 - - + -
332D MET* 3.6 33.3 - - + -
333D SER* 1.3 73.8 - - - +
335D VAL* 1.3 64.9 + - - +
336D ILE* 4.2 12.1 - - + -
364D VAL* 3.4 10.3 - - + +
366D LEU* 3.7 27.1 - - + -
747D LEU* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D PHE* 3.9 28.9 - - + +
176D GLN* 5.6 0.4 - - + -
221D PHE* 4.9 8.7 - - + -
306D TYR* 3.5 33.4 - - + +
309D ALA* 6.1 0.4 - - + -
310D ILE* 3.7 28.7 - - + -
333D SER* 4.6 9.9 - - - +
334D VAL* 1.3 77.9 - - - +
336D ILE* 1.3 71.5 + - - +
337D THR* 4.9 1.1 - - - +
364D VAL 3.0 10.9 + - - +
365D ASP* 2.9 23.7 - - - +
366D LEU 3.0 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ILE* 5.1 5.6 - - + -
174D PHE 2.9 14.4 + - - +
175D ILE* 4.5 23.3 - - + -
176D GLN* 3.1 28.1 + - - +
195D ALA* 4.8 9.9 - - + +
199D PHE* 3.6 29.2 - - + -
200D LEU* 4.3 15.5 - - + -
334D VAL* 4.2 8.3 - - + -
335D VAL* 1.3 74.0 - - - +
337D THR* 1.3 67.9 + - - +
338D PRO* 4.2 2.2 - - + +
366D LEU* 3.6 24.0 - - + -
368D CYS* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D GLN* 3.6 14.1 + - - -
300D THR* 4.2 0.7 - - - +
306D TYR* 5.3 4.5 - - + -
335D VAL* 3.8 0.6 + - - -
336D ILE* 1.3 79.0 - - - +
338D PRO* 1.3 64.9 - - - +
339D GLY* 2.7 27.4 + - - +
340D VAL 5.3 0.4 - - - +
341D GLY 5.5 1.1 - - - +
343D PHE* 4.2 23.5 - - + -
365D ASP* 3.8 13.5 - - - +
366D LEU 3.0 14.8 + - - +
367D VAL* 3.2 25.9 - - + -
368D CYS* 2.9 24.9 + - - +
----------------------------------------------------------
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