Contacts of the helix formed by residues 25 - 35 (chain B) in PDB entry 1NBI
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 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 2.5 32.2 + - + +
24B GLY* 1.3 71.9 - - - +
26B ALA* 1.3 67.8 + - - +
28B ARG* 3.1 42.1 + - - +
29B VAL* 3.3 10.7 + - - +
236B SER* 2.7 34.5 + - - -
237B LYS 4.1 18.5 + - - +
238B PHE* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN 5.4 2.9 - - - +
21B TYR* 4.2 16.4 - - + -
23B ASP* 4.2 4.2 + - - +
24B GLY 3.4 0.2 - - - -
25B GLU* 1.3 78.4 - - - +
27B ALA* 1.3 56.7 + - - +
29B VAL* 2.9 9.2 + - - +
30B TRP* 2.8 44.1 + - + -
238B PHE* 3.7 41.5 - - + +
240B LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 4.6 2.2 - - + -
24B GLY* 3.8 16.0 + - - +
25B GLU 3.3 0.2 - - - -
26B ALA* 1.3 79.1 - - - +
28B ARG* 1.3 55.5 + - - +
29B VAL 3.4 0.2 - - - -
30B TRP* 3.8 4.7 + - - +
31B GLN* 2.9 19.6 + - - +
67B THR* 4.7 1.2 - - - +
89B LYS* 4.0 19.1 - - + +
90B MET* 3.3 41.2 - - + -
93B TYR* 3.6 18.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.1 16.2 + - - +
25B GLU* 3.1 41.1 + - - +
26B ALA 3.0 0.2 - - - -
27B ALA* 1.3 73.9 - - - +
29B VAL* 1.3 57.7 + - - +
31B GLN* 2.7 26.9 + - - +
32B LEU* 5.8 0.2 - - - +
93B TYR* 3.9 14.5 + - - +
224B VAL* 3.4 35.2 - - - +
236B SER* 3.7 15.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU 3.6 6.1 - - - +
26B ALA 3.3 10.3 - - - +
28B ARG* 1.3 83.8 - - - +
30B TRP* 1.3 50.0 + - - +
31B GLN* 2.9 7.4 - - - -
32B LEU* 2.5 34.1 + - + -
33B TYR* 2.6 15.4 + - + -
222B VAL* 3.6 24.2 - - + -
224B VAL* 3.6 31.6 - - + -
236B SER* 3.7 16.4 - - - +
238B PHE* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.2 31.4 - + - -
26B ALA* 2.8 33.0 + - + +
27B ALA* 3.9 8.7 - - - +
29B VAL* 1.3 72.8 - - - +
31B GLN* 1.3 65.8 + - - +
33B TYR* 3.3 47.8 - + + -
34B ILE* 2.6 64.7 + - + +
67B THR* 3.8 22.0 - - + -
90B MET* 4.1 12.8 - - + +
194B TYR* 3.7 5.8 - + - -
238B PHE* 4.6 2.2 - + - -
240B LEU* 4.0 13.5 - - + -
242B TYR* 5.6 1.1 - - - -
1293B SAM 3.2 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 2.9 15.6 + - - +
28B ARG 2.7 23.9 + - - +
29B VAL 4.0 0.2 - - - -
30B TRP* 1.3 95.9 - - - +
32B LEU* 1.3 76.8 + - + +
34B ILE* 4.1 6.8 - - - +
35B GLY 3.4 21.5 + - - +
37B THR* 5.8 1.8 - - - +
67B THR* 5.1 4.5 - - - +
93B TYR* 4.0 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 2.5 21.3 + - + +
31B GLN* 1.3 88.8 - - + +
33B TYR* 1.3 63.4 + - - +
34B ILE 3.2 0.2 - - - -
35B GLY* 2.9 10.9 + - - -
196B SER* 2.7 23.4 + - - -
198B LEU* 3.4 21.5 - - + +
222B VAL* 4.3 6.1 - - + -
223B GLN 4.1 2.7 - - - +
224B VAL* 3.9 22.2 - - + -
225B PRO* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 2.6 18.7 + - + +
30B TRP* 3.3 59.5 - + + +
32B LEU* 1.3 74.2 - - - +
34B ILE* 1.3 61.7 + - - +
35B GLY 3.3 0.5 + - - -
194B TYR* 3.6 38.9 - + + +
195B LYS 4.0 7.1 + - - -
196B SER* 3.7 11.0 - - - -
199B THR* 4.4 16.1 + - + -
202B ILE* 6.0 0.4 - - + -
220B TYR* 3.3 45.0 + + - -
222B VAL* 4.5 21.3 - - + +
238B PHE* 4.5 5.2 - + - -
240B LEU* 5.1 1.1 - - + -
242B TYR* 4.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 2.6 47.1 + - + +
31B GLN* 4.1 6.3 - - - +
33B TYR* 1.3 72.4 - - - +
35B GLY* 1.3 66.4 + - - +
36B ASP 4.0 2.3 + - - +
37B THR* 4.2 17.7 - - + -
40B ARG* 3.8 29.3 - - + +
67B THR* 4.4 4.7 - - - +
69B VAL* 4.3 16.6 - - + -
193B TYR 3.8 1.5 - - - +
194B TYR* 3.7 17.1 - - + -
195B LYS* 3.0 22.7 + - - +
1293B SAM 3.2 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN 3.4 12.8 - - - +
32B LEU 2.9 17.3 + - - -
34B ILE* 1.3 81.8 - - - +
36B ASP* 1.3 63.6 + - - -
37B THR* 3.5 4.3 + - - +
195B LYS* 2.9 16.6 - - - -
196B SER* 3.9 4.5 - - - -
----------------------------------------------------------
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