Contacts of the strand formed by residues 302 - 315 (chain A) in PDB entry 5DST
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 ASP 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 3.7 9.8 - - - +
269A VAL* 3.9 22.7 - - + -
300A ARG* 2.8 44.7 + - - +
301A ASN* 1.3 75.4 - - - +
303A TYR* 1.3 79.0 + - - +
348A VAL* 3.2 20.9 + - - +
319C HIS* 3.0 23.4 - - - -
320C LYS* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 3.0 30.3 + - + +
269A VAL* 4.1 0.5 - - - +
302A ASP* 1.3 85.2 + - - +
304A VAL* 1.3 65.6 + - - +
305A HIS* 3.7 22.0 - + + -
345A TYR* 3.6 26.9 - + + -
346A LEU 3.4 4.5 - - - +
347A THR* 3.7 28.9 - - + -
105C HIS* 2.7 43.8 + - + +
106C ASN* 3.1 14.0 + - - -
319C HIS* 3.5 11.8 - - - +
320C LYS* 3.8 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 3.8 30.7 - - + -
226A ILE 3.4 8.3 - - - +
269A VAL* 3.9 28.3 - - + -
298A ILE* 5.2 0.2 - - + -
303A TYR* 1.3 76.6 - - - +
305A HIS* 1.3 62.3 + - - +
306A ALA 4.0 9.6 - - - +
307A LEU* 5.1 1.3 - - + -
342A LEU* 4.1 15.6 - - + +
345A TYR* 3.3 5.1 - - - -
346A LEU* 2.9 52.6 + - + +
348A VAL* 4.1 13.0 - - + +
354A ILE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE 3.0 4.9 + - - -
227A GLU* 3.9 9.6 - - + +
228A ASP* 3.3 34.2 + - + +
229A ARG* 3.1 40.3 - - + +
232A LYS* 4.2 22.9 - - + +
303A TYR* 3.7 26.2 + + + -
304A VAL* 1.3 73.9 - - - +
306A ALA* 1.3 61.5 + - + +
341A TYR* 3.9 5.1 - - + -
342A LEU* 3.0 31.9 + - - +
345A TYR* 3.6 35.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 3.5 5.0 - - - +
226A ILE* 2.9 39.8 + - + +
304A VAL* 3.7 4.1 - - - +
305A HIS* 1.3 82.9 - - + +
307A LEU* 1.3 65.2 + - - +
339A VAL* 3.8 20.4 - - + -
340A PHE 3.2 21.3 - - - +
341A TYR* 3.9 9.9 - - + -
342A LEU* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 4.6 16.6 - - + -
224A VAL 3.4 3.6 - - - +
225A ALA* 4.0 20.4 - - + -
294A PHE* 4.1 18.2 - - + -
296A LEU* 4.2 14.8 - - + -
304A VAL* 5.1 4.0 - - + -
306A ALA* 1.3 80.0 - - - +
308A VAL* 1.3 64.6 + - - +
340A PHE* 2.7 52.0 + - + +
342A LEU* 4.7 7.6 - - + -
354A ILE* 5.2 2.0 - - + -
358A ILE* 6.3 1.6 - - + -
374A VAL* 3.8 32.8 - - + -
376A LEU* 4.4 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR 3.8 0.2 - - - +
223A VAL* 3.3 3.5 - - - -
224A VAL* 2.8 46.1 + - + +
226A ILE* 3.6 40.2 - - + -
263A VAL* 4.1 7.4 - - + -
307A LEU* 1.3 80.3 - - - +
309A THR* 1.3 69.0 + - - +
310A TYR* 4.2 2.9 + - + -
328A PRO* 4.8 9.2 - - + -
337A GLN* 3.7 31.0 - - + -
338A THR 3.2 9.6 - - - +
339A VAL* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 3.3 21.1 - - - +
221A LEU* 4.2 7.6 - - - -
222A TYR 3.0 15.9 - - - +
223A VAL* 3.5 22.0 - - + -
275A ILE* 4.7 9.9 - - + -
308A VAL* 1.3 76.5 - - - +
310A TYR* 1.3 60.6 + - - +
337A GLN* 3.9 4.2 - - - -
338A THR* 3.0 46.5 + - - -
340A PHE* 3.7 18.0 - - + -
358A ILE* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 6.4 0.4 - - - +
221A LEU* 3.6 5.6 - - - +
222A TYR* 2.8 63.1 + + + -
224A VAL* 4.2 22.2 - - + -
272A ALA* 3.3 21.7 - - - +
308A VAL* 4.8 6.1 - - + -
309A THR* 1.3 75.0 - - - +
311A PHE* 1.3 66.4 + - - +
312A ASN* 3.9 17.5 - - - -
325A SER* 4.5 0.2 - - - -
326A THR* 3.6 15.5 - - - +
327A ALA* 3.5 35.7 - - + -
328A PRO* 3.8 19.3 - - + -
329A ASP* 5.7 1.6 - - - -
336A LYS 5.4 0.7 - - - -
337A GLN* 4.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MET* 4.2 9.6 - - + -
188A GLY 3.8 4.9 - - - -
190A CYS* 4.4 6.5 - - - -
191A LEU* 3.5 48.0 - - + -
220A ALA 3.0 19.3 - - - +
221A LEU* 4.1 8.1 - - + -
222A TYR* 4.8 0.2 - - - -
310A TYR* 1.3 78.0 - - - +
312A ASN* 1.3 64.0 + - - +
313A ILE* 3.7 31.8 - - + +
324A PHE* 4.5 2.7 - + - -
326A THR* 2.8 53.4 + - + +
335A TRP* 3.6 41.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 6.1 3.4 - - - +
219A ALA* 3.4 4.3 - - - -
220A ALA* 2.8 34.3 + - + +
222A TYR* 3.1 29.4 + - + -
310A TYR* 3.9 11.9 - - - -
311A PHE* 1.3 78.5 + - - +
313A ILE* 1.3 67.9 + - - +
324A PHE 3.4 7.6 - - - +
325A SER* 2.8 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 5.0 0.7 - - + -
187A MET* 3.8 26.0 - - + -
191A LEU* 4.3 0.2 - - + -
216A PRO* 3.5 30.7 - - + -
218A ARG* 3.7 2.7 - - - +
219A ALA* 3.7 20.6 - - + -
311A PHE* 3.7 26.9 - - + -
312A ASN* 1.3 84.8 - - - +
314A GLU* 1.3 66.0 + - - +
315A PHE* 4.1 12.3 - - + -
321A LYS* 4.7 3.1 + - - -
323A GLY* 3.1 21.5 - - - -
324A PHE* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 3.3 3.2 - - - +
217A ASP* 3.2 25.3 + - - +
218A ARG* 2.8 48.8 + - + +
313A ILE* 1.3 76.2 - - - +
315A PHE* 1.3 74.9 + - - +
316A THR* 3.7 18.5 - - + +
321A LYS* 3.8 29.8 + - - +
322A MET 3.5 13.6 + - - +
323A GLY* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 3.5 28.7 - - + -
99A TYR* 3.9 37.0 - + - -
102A SER* 3.7 15.7 - - - -
214A MET 5.5 0.7 - - - +
215A PHE* 3.6 26.7 - + + -
216A PRO* 3.4 40.6 - - + -
217A ASP* 3.9 4.0 - - - -
313A ILE* 4.1 10.8 - - + -
314A GLU* 1.3 76.2 - - - +
316A THR* 1.3 63.3 + - - +
317A LYS* 3.4 2.6 + - + -
318A CYS* 3.6 30.5 + - - +
320A LYS 4.8 0.3 - - - +
321A LYS* 5.5 0.3 - - - -
322A MET* 2.9 30.2 + - + +
323A GLY* 4.4 1.6 - - - -
324A PHE* 4.7 1.8 - + - -
----------------------------------------------------------
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