Contacts of the strand formed by residues 302 - 314 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I GLU* 3.6 13.7 - - - +
269I VAL* 3.9 23.6 - - + -
300I ARG* 2.6 46.7 + - - +
301I ASN* 1.3 76.0 - - - +
303I TYR* 1.3 71.9 + - - +
348I VAL* 3.0 21.1 + - - +
319K HIS* 3.0 22.4 + - - -
320K LYS* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I GLU* 3.2 28.9 + - + +
269I VAL* 4.1 2.1 - - - +
302I ASP* 1.3 83.0 + - - +
304I VAL* 1.3 65.7 + - - +
305I HIS* 3.9 21.1 - + + -
345I TYR* 3.7 25.8 - + + -
346I LEU 3.3 5.2 - - - +
347I THR* 3.7 30.1 - - + -
105K HIS* 2.5 46.8 + - + +
106K ASN* 3.0 14.7 + - - -
319K HIS* 3.6 11.4 - - - +
320K LYS* 4.0 36.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I ALA* 3.9 17.0 - - + -
226I ILE 3.4 9.6 - - - +
269I VAL* 4.0 30.3 - - + -
298I ILE* 5.2 0.4 - - + -
303I TYR* 1.3 78.1 - - - +
305I HIS* 1.3 61.7 + - - +
306I ALA 3.8 16.8 - - - +
307I LEU* 5.1 1.3 - - + -
342I LEU* 4.1 15.6 - - + +
345I TYR* 3.2 5.0 - - - -
346I LEU* 2.8 54.9 + - + +
348I VAL* 4.1 12.6 - - + -
354I ILE* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ILE 2.9 5.3 + - - -
227I GLU* 3.9 7.7 - - + -
228I ASP* 3.2 36.1 + - + +
229I ARG* 3.1 41.5 - - + +
232I LYS* 4.2 22.7 - - + +
303I TYR* 3.9 25.7 + + + -
304I VAL* 1.3 74.9 - - - +
306I ALA* 1.3 62.9 + - + +
341I TYR* 3.9 5.2 - - + -
342I LEU* 3.0 32.7 + - - +
345I TYR* 3.6 34.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I ALA* 3.5 3.8 - - - -
226I ILE* 2.9 37.9 + - + +
304I VAL* 3.7 6.4 - - - +
305I HIS* 1.3 82.7 - - + +
307I LEU* 1.3 65.4 + - - +
339I VAL* 3.7 20.6 - - + -
340I PHE 3.1 22.2 - - - +
341I TYR* 3.8 10.5 - - + -
342I LEU* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I VAL* 4.6 15.7 - - + -
224I VAL 3.4 4.3 - - - +
225I ALA* 3.9 18.6 - - + -
294I PHE* 4.0 18.6 - - + -
296I LEU* 4.2 13.7 - - + -
304I VAL* 5.1 4.0 - - + -
306I ALA* 1.3 80.9 - - - +
308I VAL* 1.3 62.4 + - - +
339I VAL* 3.6 0.2 - - - -
340I PHE* 2.7 46.3 + - + +
342I LEU* 4.7 9.8 - - + +
354I ILE* 5.2 3.1 - - + -
358I ILE* 6.4 0.9 - - + -
374I VAL* 3.8 33.0 - - + -
376I LEU* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I VAL* 3.2 5.4 - - - +
224I VAL* 2.8 40.1 + - + +
226I ILE* 3.6 42.8 - - + -
263I VAL* 4.3 6.7 - - + -
307I LEU* 1.3 79.5 - - - +
309I THR* 1.3 67.6 + - - +
310I TYR* 5.1 2.3 - - + -
328I PRO* 4.8 8.7 - - + -
337I GLN* 3.6 32.5 - - + -
338I THR 3.2 9.9 - - - +
339I VAL* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I CYS* 3.4 18.0 - - - +
221I LEU* 4.2 11.7 - - - -
222I TYR 3.0 15.0 - - - +
223I VAL* 3.7 17.5 - - + -
275I ILE* 4.6 9.6 - - + -
308I VAL* 1.3 79.3 - - - +
310I TYR* 1.3 62.5 + - - +
337I GLN* 3.9 4.3 - - - -
338I THR* 2.9 47.2 + - - -
340I PHE* 3.8 19.0 - - + -
358I ILE* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 310 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I CYS* 6.4 0.4 - - - +
221I LEU* 3.6 4.9 - - - +
222I TYR* 2.9 61.6 + + + +
224I VAL* 4.2 25.4 - - + -
272I ALA* 3.3 21.1 - - - +
308I VAL* 5.1 2.2 - - + -
309I THR* 1.3 77.0 - - - +
311I PHE* 1.3 67.3 + - - +
312I ASN* 3.9 17.7 - - - -
326I THR* 3.6 15.7 - - - +
327I ALA* 3.5 36.8 - - + -
328I PRO* 3.9 18.8 - - + -
329I ASP* 5.6 2.5 + - - -
336I LYS 5.4 0.4 - - - -
337I GLN* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I MET* 4.1 9.2 - - + -
188I GLY 3.7 6.7 - - - -
190I CYS* 4.4 5.4 - - - -
191I LEU* 3.5 47.8 - - + -
220I ALA 3.0 19.3 - - - +
221I LEU* 4.1 8.1 - - + -
310I TYR* 1.3 77.7 - - - +
312I ASN* 1.3 64.1 + - - +
313I ILE* 3.7 32.3 - - + -
324I PHE* 4.6 2.0 - + - -
326I THR* 2.9 52.4 + - + +
335I TRP* 3.6 44.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I ARG* 6.1 4.0 - - - +
219I ALA* 3.3 4.7 - - - -
220I ALA* 2.9 35.3 + - + +
222I TYR* 3.4 26.0 + - + -
310I TYR* 3.9 11.1 - - - -
311I PHE* 1.3 76.6 + - - +
313I ILE* 1.3 70.2 + - - +
324I PHE 3.4 8.3 - - - +
325I SER* 2.7 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I TRP* 4.9 1.6 - - + -
187I MET* 3.8 25.6 - - + -
191I LEU* 4.3 0.2 - - + -
216I PRO* 3.5 32.1 - - + -
218I ARG* 3.6 3.4 - - - +
219I ALA* 3.7 20.4 - - + -
311I PHE* 3.7 26.7 - - + -
312I ASN* 1.3 84.9 - - - +
314I GLU* 1.3 65.9 + - - +
315I PHE* 4.1 12.6 - - + -
321I LYS* 4.7 2.6 + - - -
323I GLY* 3.0 21.9 - - - -
324I PHE* 2.9 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216I PRO* 3.3 3.5 - - - +
217I ASP* 3.3 7.8 + - - +
218I ARG* 2.9 65.9 + - + +
313I ILE* 1.3 76.3 - - - +
315I PHE* 1.3 73.4 + - - +
316I THR* 3.8 18.7 - - + +
321I LYS* 3.8 29.4 + - + +
322I MET 3.5 13.0 - - - +
323I GLY* 4.2 0.2 - - - -
----------------------------------------------------------
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