Contacts of the strand formed by residues 348 - 354 (chain A) in PDB entry 2ZXI
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 TYR 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.9 4.9 + - - -
164A ILE* 3.6 24.0 - - + -
165A TYR 3.4 6.3 - - - +
166A ILE* 3.4 22.4 - - + -
175A ARG* 3.9 5.8 - - - +
176A LEU* 3.1 51.1 + - + +
201A GLY* 3.3 1.4 - - - -
202A THR* 2.9 46.7 + - + +
205A ARG* 5.9 1.3 - - - -
321A THR 3.2 9.9 + - - +
322A SER* 4.4 1.3 - - - +
346A PRO 3.6 13.7 - - - -
347A ALA* 1.3 77.1 - - - +
349A ALA* 1.3 67.7 + - - +
350A ILE* 4.5 3.8 - - + -
618A FAD 3.5 36.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL 3.8 0.2 - - - +
164A ILE* 3.5 2.8 - - - -
165A TYR* 2.7 38.8 + - + +
199A LYS* 4.1 20.9 - - + -
200A THR 3.3 11.9 - - - +
201A GLY* 3.8 5.8 - - - -
322A SER* 3.6 22.2 - - - +
348A TYR* 1.3 80.4 - - - +
350A ILE* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 3.9 20.4 - - + +
163A VAL 3.5 15.9 - - - +
164A ILE* 3.6 19.5 - - + -
173A GLY 3.4 25.1 - - - +
174A GLY 3.7 19.1 - - - +
175A ARG* 4.4 1.8 - - - +
198A PHE 3.6 0.9 - - - +
199A LYS* 3.0 6.6 - - - -
200A THR* 2.7 39.7 + - - +
348A TYR* 4.5 1.1 - - + -
349A ALA* 1.3 74.1 - - - +
351A GLU* 1.3 62.6 + - - +
352A TYR* 3.9 10.6 - - + -
618A FAD 3.4 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY* 3.1 5.0 - - - -
163A VAL 2.9 31.2 + - - +
165A TYR* 3.6 29.2 + - + -
197A ARG* 2.6 48.6 + - + +
198A PHE 3.1 15.5 - - - +
199A LYS* 3.1 31.8 + - + +
350A ILE* 1.3 73.7 - - - +
352A TYR* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY 3.4 17.7 - - - +
158A THR* 3.5 43.5 - - + +
160A LEU 3.6 8.5 - - - +
162A GLY* 4.5 0.4 - - - -
197A ARG* 3.1 36.3 - - - +
198A PHE* 3.1 35.8 + - + +
199A LYS 4.6 0.2 - - - -
200A THR* 4.4 10.8 + - - +
350A ILE* 3.9 14.6 - - + -
351A GLU* 1.3 81.1 - - - +
353A ASP* 1.3 71.5 + - - +
354A VAL* 3.4 20.4 - - + -
377A ASN* 3.2 31.1 + - + -
381A THR 4.3 4.9 + - - -
382A THR* 5.1 0.2 - - - -
432A PRO* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY 4.6 0.9 - - - +
160A LEU* 2.9 35.5 + - + +
161A ASN* 2.6 32.5 + - - +
185A SER* 3.7 11.3 - - - -
189A ARG* 4.3 6.1 + - - -
195A LEU* 4.5 16.9 - - + +
196A ILE 3.6 3.1 - - - +
197A ARG* 2.9 30.5 + - - +
352A TYR* 1.3 80.6 - - - +
354A VAL* 1.3 64.8 + - - +
378A PHE* 3.4 16.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.5 4.8 - - - -
196A ILE* 2.7 62.3 + - + +
198A PHE* 4.1 14.6 - - + -
352A TYR* 3.4 20.2 - - + +
353A ASP* 1.3 80.4 - - - +
355A VAL* 1.3 73.0 + - - +
356A PRO* 3.6 1.5 - - + +
357A PRO* 5.3 0.4 - - + -
377A ASN 3.3 20.9 - - - +
378A PHE* 3.5 13.0 - - - +
380A GLY* 3.7 19.5 - - - +
----------------------------------------------------------
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