Contacts of the strand formed by residues 267 - 276 (chain A) in PDB entry 2ZT5
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 PHE 267 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.2 14.1 - - + -
254A PHE* 3.7 19.3 - + - -
257A LEU* 4.0 22.2 - - + -
258A LEU* 3.6 39.0 - - + -
261A ASN* 3.1 32.3 - - + +
264A LYS 3.9 14.6 - - - -
265A LEU* 4.4 3.8 - - + -
266A PRO* 1.3 73.7 - - - +
268A ALA* 1.3 70.8 + - - +
269A ALA* 4.7 2.0 - - + -
299A HIS* 3.8 4.4 + - - -
300A PHE* 2.9 61.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 6.0 2.5 - - + +
120A GLN 4.8 1.1 + - - +
121A ILE* 3.1 18.2 - - + +
122A LEU* 3.0 28.4 + - - +
267A PHE* 1.3 80.2 - - - +
269A ALA* 1.3 60.9 + - - +
297A ILE* 4.0 16.6 - - + -
298A GLU 3.2 10.5 - - - +
299A HIS* 3.9 22.9 - - + -
355A PHE* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.5 1.6 - - - +
122A LEU* 3.2 11.7 - - + +
124A ILE* 5.1 2.0 - - + -
250A ILE* 3.5 33.3 - - + +
257A LEU* 3.6 22.9 - - + -
267A PHE* 4.6 3.5 - - + -
268A ALA* 1.3 75.1 - - - +
270A ALA* 1.3 62.4 + - - +
297A ILE* 3.5 1.0 - - - +
298A GLU 2.8 31.5 + - - +
300A PHE* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TRP* 4.4 10.8 - - + -
116A ILE* 4.5 11.7 - - + -
121A ILE* 3.5 16.8 - - + -
122A LEU 2.8 8.1 + - - +
123A GLU* 3.6 5.9 - - - +
124A ILE* 3.2 26.5 + - - +
250A ILE* 3.8 4.7 - - - -
269A ALA* 1.3 77.0 - - - +
271A GLN* 1.3 64.8 + - - +
296A GLU 3.1 13.2 - - - +
297A ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TRP* 5.0 0.2 - - - -
123A GLU* 5.4 1.6 - - - -
124A ILE* 2.9 27.8 - - + +
125A ASP* 3.6 5.2 + - - +
126A CYS* 2.7 44.4 + - - +
243A ARG* 2.8 28.4 + - - +
246A THR* 3.3 40.6 + - + +
250A ILE* 4.1 8.6 - - + +
270A ALA* 1.3 76.2 - - - +
272A ILE* 1.3 65.0 + - - +
273A GLY 3.9 1.1 - - - +
294A MET 3.5 2.0 - - - +
295A ALA* 3.3 3.1 - - - -
296A GLU* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 4.3 22.0 - - + -
111A TRP* 3.4 38.6 - - + -
112A ARG* 3.9 40.8 - - + +
116A ILE* 4.0 6.3 - - + -
123A GLU* 5.4 5.5 + - + +
124A ILE 4.8 1.6 + - - -
125A ASP* 4.5 9.7 + - - +
271A GLN* 1.3 79.7 - - - +
273A GLY* 1.3 57.7 + - - +
293A THR* 4.3 18.2 - - + -
294A MET 3.4 5.4 - - - +
295A ALA* 4.0 4.7 - - + -
527A LEU* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 5.2 3.8 - - - -
243A ARG* 3.6 16.3 - - - +
246A THR* 4.8 2.7 - - - +
271A GLN* 3.9 1.6 - - - +
272A ILE* 1.3 75.9 - - - +
274A ASN* 1.3 66.9 + - - -
293A THR* 4.3 5.6 - - - -
294A MET* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.7 29.8 - - - +
243A ARG* 2.8 35.8 + - - +
273A GLY* 1.3 73.0 - - - -
275A SER* 1.3 59.2 + - - +
276A PHE* 4.4 10.3 - - + -
291A GLU* 5.3 8.4 - - + +
292A PHE* 3.2 13.3 + - - +
293A THR* 3.1 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG 3.4 8.0 + - - -
244A PRO 3.6 18.2 - - - -
245A GLU* 3.4 15.2 - - - -
246A THR* 3.7 2.4 - - - +
273A GLY 4.0 0.2 + - - -
274A ASN* 1.3 75.6 + - - +
276A PHE* 1.3 67.3 + - - +
291A GLU* 3.7 3.3 - - - +
292A PHE* 3.0 40.3 + - - -
294A MET* 3.2 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.7 39.7 - - + -
226A LEU 4.5 2.3 - - - +
227A MET* 5.2 1.6 - - - -
228A PHE* 3.5 23.5 - + + -
242A LEU* 3.5 46.2 - - + +
243A ARG 2.9 11.3 + - - +
244A PRO* 3.3 23.2 - - - +
274A ASN* 4.4 7.2 - - + -
275A SER* 1.3 79.9 - - - +
277A ARG* 1.3 62.8 + - - +
290A ARG 3.5 8.1 - - - +
291A GLU* 3.6 38.6 - - + -
----------------------------------------------------------
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