Contacts of the strand formed by residues 234 - 240 (chain K) in PDB entry 3Q2K
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 234 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K TYR 3.0 7.8 + - - +
155K MET* 3.2 8.9 - - - +
156K VAL* 3.0 21.1 + - - +
227K LEU 3.5 8.3 - - - +
228K ARG* 4.3 12.8 - - + -
229K TRP* 3.8 6.6 - - - -
232K GLY 3.6 4.2 + - - +
233K ALA* 1.3 77.7 - - - +
235K GLY* 1.3 59.7 + - - +
209L TYR* 3.7 42.8 - - + +
210L THR* 3.7 10.8 - - - +
211L ALA* 3.9 13.0 - - + -
213L LEU* 3.8 16.8 - - + -
222L THR* 3.6 41.7 - - + +
223L GLY* 4.1 1.8 - - - -
224L VAL* 4.0 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K MET* 4.3 1.3 - - - -
156K VAL 3.0 13.2 - - - -
226K ALA* 3.4 5.0 - - - -
227K LEU* 2.8 41.7 + - - +
229K TRP* 3.8 5.7 - - - -
234K MET* 1.3 78.6 - - - +
236K SER* 1.3 58.9 + - - -
224L VAL* 3.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K VAL 3.1 6.2 + - - +
157K THR* 3.5 4.0 - - - +
158K VAL* 3.0 26.9 + - - +
196K LEU* 5.3 0.5 - - - +
224K VAL* 4.7 0.7 - - - -
225K ALA 3.2 14.1 - - - -
226K ALA* 4.5 0.4 - - - -
227K LEU* 3.8 7.3 - - - +
235K GLY* 1.3 75.4 - - - -
237K ILE* 1.3 61.3 + - - +
238K ASN* 3.3 19.4 + - - -
224L VAL* 3.9 8.7 - - - -
236L SER* 3.5 10.5 + - - -
238L ASN* 2.7 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158K VAL* 3.3 33.0 - - + +
160K VAL* 5.2 0.7 - - + -
185K PHE* 3.9 13.0 - - + -
189K ALA 5.0 0.7 - - - +
192K TYR* 3.9 16.4 - - + +
193K VAL* 3.9 27.6 - - + +
196K LEU* 4.0 22.0 - - + -
224K VAL* 3.4 3.3 - - - -
225K ALA* 2.9 50.9 + - + +
227K LEU* 4.0 4.3 - - + -
236K SER* 1.3 74.4 - - - +
238K ASN* 1.3 63.0 + - - +
239K VAL* 4.0 17.7 - - + -
335K ILE* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157K THR* 4.0 5.3 - - - +
158K VAL 3.1 7.5 + - - -
159K ASN* 2.9 24.9 + - - +
160K VAL 3.0 24.8 + - - +
161K PHE* 3.9 11.3 - - + -
223K GLY 3.6 4.9 - - - -
224K VAL* 3.2 16.9 - - - +
236K SER* 3.3 19.8 + - - -
237K ILE* 1.3 70.3 - - - +
239K VAL* 1.3 62.3 + - - +
155L MET* 4.1 7.5 - - - +
157L THR* 3.1 20.3 - - + +
235L GLY 4.5 0.5 - - - -
236L SER* 2.5 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K VAL* 3.2 14.4 - - + +
161K PHE* 5.0 0.2 - - - -
184K ALA* 4.0 27.4 - - + +
185K PHE* 3.8 31.6 - - + -
189K ALA* 4.0 16.4 - - + -
222K THR* 3.3 2.4 - - - -
223K GLY 2.8 39.0 + - - +
237K ILE* 4.0 14.8 - - + -
238K ASN* 1.3 82.2 - - - +
240K THR* 1.3 64.9 + - - +
241K MET* 3.9 18.6 - - + -
155L MET* 3.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 240 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K VAL 2.9 8.5 + - - +
161K PHE* 4.3 4.7 - - + -
162K TRP 2.8 31.7 + - - +
221K ASP 3.3 5.4 - - - -
222K THR* 3.1 29.5 + - - +
239K VAL* 1.3 75.9 - - - +
241K MET* 1.3 62.1 + - - +
242K LEU* 3.2 18.9 + - + +
243K THR* 3.6 19.5 - - - +
154L TYR* 4.6 2.5 - - + +
155L MET* 4.0 11.0 - - + -
255L LEU* 3.9 23.1 - - + -
----------------------------------------------------------
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