Contacts of the strand formed by residues 215 - 224 (chain A) in PDB entry 2ZB5
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 ASN 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A NAG 1.5 73.7 + - - +
213A GLY 4.0 0.8 + - - -
214A TYR* 1.3 71.5 - - - +
216A VAL* 1.3 64.2 + - - +
217A SER* 4.0 2.4 + - - -
233A LEU 3.9 0.9 - - - +
234A VAL* 3.7 2.0 - - - -
235A GLU* 3.2 54.9 + - + +
251A MET* 5.8 0.5 - - - +
593A HIS* 4.3 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.1 3.6 - - + -
209A TYR* 3.7 26.7 - - + -
210A LEU* 3.5 27.4 - - + +
214A TYR* 2.8 14.6 + - + +
215A ASN* 1.3 76.6 + - - +
217A SER* 1.3 65.0 + - - +
219A ILE* 3.7 29.9 - - + +
232A TYR* 3.9 16.2 - - + -
233A LEU 3.3 10.8 - - - +
234A VAL* 3.8 10.5 - - + -
584A VAL* 6.0 0.2 - - - +
595A THR* 3.8 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A NAG 3.8 30.2 + - - -
215A ASN* 4.8 4.0 + - - -
216A VAL* 1.3 76.7 - - - +
218A SER* 1.3 68.5 + - - +
219A ILE* 3.3 5.3 + - - -
232A TYR* 3.7 0.7 - - - +
233A LEU* 2.8 55.4 + - - +
251A MET* 4.6 0.9 - - - +
584A VAL* 6.5 1.3 - - - -
593A HIS* 6.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 1.3 79.9 + - - +
219A ILE* 1.3 63.8 + - - +
220A VAL* 3.8 8.6 - - - +
231A THR 3.4 10.4 - - - +
232A TYR* 3.6 4.7 - - - -
233A LEU* 3.8 23.8 - - - +
253A ARG* 4.3 11.8 + - - -
285A SER 4.2 7.6 + - - -
286A ASN* 5.2 10.3 + - - +
565A GLU* 5.0 10.2 + - - -
584A VAL* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.3 18.8 - - + -
210A LEU* 4.4 7.4 - - + -
216A VAL* 3.7 34.1 - - + +
217A SER* 4.4 3.8 - - - -
218A SER* 1.3 76.9 - - - +
220A VAL* 1.3 65.8 + - - +
221A THR* 3.4 17.5 - - + +
231A THR 3.6 6.3 - - - +
232A TYR* 4.0 6.3 - - + -
355A ARG* 5.2 0.2 + - - -
565A GLU* 3.9 12.3 + - - +
567A GLN* 2.8 33.9 + - - +
582A PHE* 3.8 30.5 - - + -
584A VAL* 6.0 3.8 - - + -
595A THR* 4.6 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER 3.8 10.8 - - - +
219A ILE* 1.3 82.2 - - - +
221A THR* 1.3 59.9 + - - +
230A GLY* 3.0 5.9 - - - -
231A THR* 3.0 36.2 + - + +
286A ASN* 4.3 11.9 - - - +
287A CYS 4.1 17.7 - - - +
289A VAL* 3.8 25.3 - - + +
353A SER* 4.7 11.4 - - - +
354A HIS 4.4 12.8 - - - +
355A ARG* 4.4 17.9 - - + +
567A GLN* 3.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.6 15.5 - - + -
219A ILE* 3.4 19.3 - - + +
220A VAL* 1.3 74.8 - - - +
222A MET* 1.3 68.6 + - - +
228A TYR* 4.9 9.0 - - + -
229A GLY* 3.2 26.7 - - - +
230A GLY* 4.2 2.9 - - - -
232A TYR* 6.4 0.9 - - + -
355A ARG* 3.2 18.9 + - - -
567A GLN* 2.6 14.5 + - - +
568A VAL 5.0 1.0 - - - +
569A GLU* 3.1 26.9 - - - +
582A PHE* 3.7 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A THR* 1.3 82.6 - - - +
223A THR* 1.3 72.7 + - - +
224A SER* 4.3 4.3 - - - -
228A TYR* 3.4 1.9 - - - -
229A GLY 3.0 33.3 + - - +
289A VAL* 3.9 25.6 - - + +
290A ALA* 3.9 2.2 - - - -
291A LEU* 3.2 48.9 - - + +
355A ARG* 4.1 24.2 - - + -
356A GLY 3.8 12.3 - - - +
444A TYR* 5.6 11.7 - - + +
569A GLU* 3.4 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A MET* 1.3 88.5 - - - +
224A SER* 1.3 67.7 + - - +
227A MET 3.3 11.0 - - - -
228A TYR* 4.4 2.2 - - + -
260A ILE* 4.2 10.8 - - + -
270A PHE* 4.2 11.4 - - + -
291A LEU* 3.8 1.3 - - - -
444A TYR* 5.6 4.7 - - - -
569A GLU* 3.7 27.6 - - + +
570A CYS 2.9 23.6 + - - +
571A PHE* 3.8 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A MET* 4.3 4.5 - - - -
223A THR* 1.3 80.8 + - - +
225A GLN* 1.3 89.9 + - - +
226A GLY 3.2 2.4 - - - +
227A MET* 2.8 28.0 + - - +
291A LEU* 3.7 31.2 + - - +
292A GLY* 4.5 0.7 + - - -
----------------------------------------------------------
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