Contacts of the strand formed by residues 236 - 242 (chain A) 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 SER 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.8 30.0 + - - -
28A ARG* 3.8 13.2 - - - -
29A VAL* 3.6 31.0 - - - +
221A THR* 3.4 1.2 - - - -
222A VAL* 2.5 48.0 + - - +
224A VAL* 4.1 3.0 - - - +
235A PHE* 1.3 72.7 - - - +
237A LYS* 1.3 60.6 + - - +
238A PHE* 4.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 5.2 1.2 - - - +
25A GLU* 4.1 15.7 + - - +
220A TYR 3.3 8.1 - - - +
221A THR* 2.4 53.8 + - - +
235A PHE* 4.1 15.8 - - - +
236A SER* 1.3 78.1 + - - +
238A PHE* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 4.9 9.6 - - - +
25A GLU* 4.6 4.7 - - + -
26A ALA* 3.7 39.0 - - + +
29A VAL* 3.4 29.6 - - + -
30A TRP* 4.7 2.5 - + - -
33A TYR* 4.5 12.1 - + - -
219A ASP* 3.6 1.2 - - - +
220A TYR* 2.7 73.2 + + + +
222A VAL* 3.5 19.7 - - + -
236A SER* 4.3 6.5 - - - -
237A LYS* 1.3 79.7 - - - +
239A ARG* 1.3 60.0 + - - +
240A LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 4.2 10.0 - - - +
205A SER* 6.0 0.6 - - - -
217A THR* 3.4 29.4 + - + +
218A LEU 3.2 11.7 - - - +
219A ASP* 2.6 37.9 + - + -
238A PHE* 1.3 82.6 - - - +
240A LEU* 1.3 73.2 + - - +
241A SER* 4.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 3.3 28.5 - - + +
21A TYR* 3.6 33.7 - - + +
26A ALA* 4.9 2.9 - - + -
30A TRP* 4.0 12.6 - - + -
33A TYR* 5.2 0.9 - - - +
142A HIS* 3.7 8.7 - - + -
218A LEU* 2.7 39.3 + - - +
220A TYR* 4.0 7.1 - - + -
238A PHE* 3.8 30.1 - - + -
239A ARG* 1.3 84.2 - - - +
241A SER* 1.3 60.1 + - - +
242A TYR* 3.5 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 2.7 38.5 + - - -
142A HIS* 4.1 7.4 + - - +
215A MET* 4.0 20.0 - - - -
216A VAL 3.3 4.3 - - - -
217A THR* 2.9 26.9 + - - +
239A ARG* 4.6 7.8 + - - +
240A LEU* 1.3 74.1 - - - +
242A TYR* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 5.5 1.4 - - - -
33A TYR* 4.2 5.2 + - - -
138A ASN* 3.3 30.7 - - + -
141A ALA* 3.4 14.4 - - + +
142A HIS* 3.6 25.7 + + - -
144A PRO* 6.3 1.1 - - - -
177A TYR* 3.1 21.8 - - + +
215A MET* 3.5 7.1 - - - +
216A VAL* 2.7 47.3 + - + +
218A LEU* 4.0 11.9 - - + -
220A TYR* 3.1 25.0 + - - -
240A LEU* 3.5 43.6 - - + +
241A SER* 1.3 77.3 - - - +
243A TYR* 1.3 61.3 + - - +
293A SAM 5.6 2.3 - - + +
----------------------------------------------------------
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