Contacts of the strand formed by residues 302 - 312 (chain B) in PDB entry 2NNT
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 ALA 302 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 3.1 13.7 + - - -
202A ALA* 3.0 26.7 - - - +
203A THR 3.3 2.1 + - - +
228A SER* 3.3 1.1 + - - -
229A THR* 4.7 1.8 - - - +
300B MET* 3.4 7.0 - - - +
301B GLY* 1.3 76.3 - - - +
303B THR* 1.3 69.1 + - - +
328B SER* 3.3 31.6 - - - +
401C GLY* 4.4 2.2 - - - -
402C ALA 3.2 21.8 - - - +
403C THR* 4.0 0.4 - - + -
430C TRP* 4.8 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.5 3.1 - - - +
226A LEU* 3.5 35.7 - - + +
228A SER* 2.6 19.3 + - - +
300B MET* 4.3 2.7 - - - +
302B ALA* 1.3 79.7 - - - +
304B ALA* 1.4 60.0 + - - +
326B LEU* 3.5 20.3 - - + +
327B GLU 2.5 30.8 + - - +
402C ALA 3.3 5.2 + - - +
403C THR* 3.3 35.0 - - - +
404C ALA 3.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR 3.2 6.5 + - - -
204A ALA* 3.3 16.3 - - + -
205A VAL 3.1 23.1 + - - +
226A LEU* 3.5 3.8 - - - +
300B MET* 4.1 19.3 - - + -
303B THR* 1.4 75.0 - - - +
305B VAL* 1.3 60.3 + - - +
326B LEU* 3.6 4.7 - - - -
400C MET* 6.1 0.7 - - - -
404C ALA* 4.1 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.2 13.9 - - + +
224A ARG 5.9 0.4 - - - +
226A LEU* 4.0 17.0 - - + -
304B ALA* 1.3 74.4 - - - +
306B SER* 1.3 70.6 + - - +
324B ARG* 3.4 42.2 - - + +
326B LEU* 3.4 32.6 - - + +
404C ALA 3.5 3.6 + - - +
405C VAL* 3.7 20.4 - - + -
406C SER* 3.3 25.0 + - - +
407C GLU* 6.4 1.1 - - + -
424C ARG* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL 2.9 6.1 + - - -
206A SER* 3.3 16.9 - - - -
207A GLU 3.3 0.8 + - - -
305B VAL* 1.3 80.6 + - - +
307B GLU* 1.3 58.7 + - - +
308B TRP* 3.6 34.8 - - - -
324B ARG* 2.8 24.2 + - - -
406C SER* 3.3 19.1 - - - -
407C GLU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.6 13.7 - - + +
209A THR* 3.9 12.5 + - - +
222A ASN* 4.7 4.6 + - - -
306B SER* 1.3 71.5 - - - +
308B TRP* 1.4 71.6 + - - +
309B THR* 3.4 17.3 + - - -
320B TYR* 4.0 9.8 + - - -
322B ASN* 3.6 28.7 + - - +
324B ARG* 3.1 40.8 + - - +
406C SER 3.1 8.9 + - - +
407C GLU* 3.9 27.7 - - + +
408C TRP* 3.1 26.0 + - - +
409C THR* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.8 31.2 - - - -
207A GLU 3.0 28.4 + - - +
208A TRP* 3.5 52.7 + + + -
209A THR 2.9 23.4 + - - +
306B SER* 3.6 23.7 - - - -
307B GLU* 1.4 76.0 + - - +
309B THR* 1.3 59.3 + - - +
310B GLU 4.0 0.2 + - - -
406C SER 5.4 0.8 + - - -
408C TRP* 4.0 17.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR* 3.5 18.0 - - + +
307B GLU* 3.4 22.9 + - - -
308B TRP* 1.3 70.1 + - - +
310B GLU* 1.3 61.0 + - - +
311B TYR* 4.0 28.5 - - + +
320B TYR* 4.6 10.8 + - + +
408C TRP* 3.0 11.2 + - - +
409C THR* 3.4 35.4 + - + -
410C GLU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TRP* 5.7 4.7 - - + +
209A THR 2.8 16.1 + - - +
210A GLU* 4.7 14.5 - - + +
211A TYR 2.9 31.5 + - - +
212A LYS* 5.9 1.4 - - - +
308B TRP 5.3 0.4 - - - +
309B THR* 1.3 73.6 - - - +
311B TYR* 1.4 54.6 + - - +
312B LYS* 3.0 47.9 + - + +
410C GLU* 3.4 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR* 3.7 8.5 - - + -
211A TYR* 3.3 49.5 - + + -
218A THR* 4.7 4.7 + - - -
220A TYR* 3.2 30.9 - + - +
309B THR* 4.0 19.0 - - + -
310B GLU* 1.4 71.1 - - - +
312B LYS* 1.3 62.3 + - - +
313B THR* 3.8 6.3 - - - -
318B THR* 3.7 29.2 - - + -
319B PHE 4.7 1.3 + - - -
320B TYR* 3.4 29.1 - + + +
410C GLU 3.1 6.2 + - - +
411C TYR* 3.5 38.2 - + + -
412C LYS 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR 2.8 13.9 + - - +
212A LYS* 3.4 31.4 - - + +
213A THR 4.1 1.6 + - - +
310B GLU* 3.0 52.5 + - + +
311B TYR* 1.3 76.6 - - - +
313B THR* 1.3 60.7 + - - +
314B ALA 4.0 2.1 + - - -
410C GLU* 3.5 35.3 + - - +
411C TYR 5.0 0.4 - - - -
412C LYS* 3.6 30.1 - - + -
----------------------------------------------------------
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