Contacts of the strand formed by residues 366 - 374 (chain A) in PDB entry 1SR5
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 366 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 5.4 5.8 - - - +
211A THR* 6.0 0.4 - - - +
213A LEU 3.7 0.6 + - - +
214A VAL* 3.2 32.4 - - + +
215A LEU 3.3 1.0 + - - +
330A SER* 3.7 17.0 - - - +
332A LYS* 3.8 8.5 - - + -
364A VAL* 3.6 6.5 - - - -
365A SER* 1.3 83.9 - - - +
367A ALA* 1.3 60.4 + - - +
368A PHE* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.7 33.2 - - + -
215A LEU* 3.4 22.2 - - + -
330A SER* 3.3 6.2 - - - -
331A LEU* 2.8 39.0 + - + -
332A LYS* 3.9 9.0 - - - +
344A PHE* 4.9 2.0 - - + -
364A VAL* 4.5 3.1 - - + +
366A ASP* 1.3 74.5 - - - +
368A PHE* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 4.0 28.0 - - + +
202A ILE* 3.2 46.9 - - + -
203A PRO* 4.1 16.6 - - + -
206A ALA* 4.3 15.3 - - + -
207A ILE* 5.6 1.8 - - + -
214A VAL* 5.1 7.4 - - + -
215A LEU 2.6 16.6 + - - +
216A VAL* 4.8 2.5 - - + -
217A ASN* 2.9 34.0 + - - +
329A PHE* 3.5 15.5 - - - +
330A SER* 3.6 24.5 - - - -
331A LEU* 4.1 1.6 - - - -
366A ASP* 3.9 24.5 - - + -
367A ALA* 1.3 77.4 - - - +
369A HIS* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.0 14.9 - - + -
79A SER* 3.0 35.5 + - - -
82A SER* 3.7 29.6 - - - -
83A ILE* 4.1 10.3 - - + +
201A VAL 5.1 0.9 - - - +
217A ASN* 2.7 36.7 + - - +
219A ILE* 4.4 8.7 - - + -
328A GLY* 3.2 1.8 - - - -
329A PHE* 2.9 42.5 + + + +
331A LEU* 3.6 22.8 - - + +
368A PHE* 1.3 73.6 - - - +
370A LYS* 1.3 68.3 + - - +
371A ALA* 4.0 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG 5.4 0.8 + - - -
198A ILE* 3.6 23.0 - - + +
199A THR* 3.0 34.5 + - - +
200A ASP* 3.6 21.2 + - - -
201A VAL* 4.6 10.1 - - + +
217A ASN 3.2 8.1 + - - -
218A THR* 3.2 16.5 - - + -
219A ILE 3.0 26.7 + - - +
326A GLU* 4.0 22.0 + - + +
327A ASP 3.0 13.2 - - - +
328A GLY* 3.1 30.7 - - - +
369A HIS* 1.3 77.4 - - - +
371A ALA* 1.3 60.5 + - - +
372A PHE* 5.6 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.3 41.5 - - + +
78A LEU* 3.8 12.3 - - - -
79A SER 4.4 0.9 - - - +
198A ILE* 4.8 0.2 - - - -
219A ILE* 3.4 17.0 - - + -
325A ILE 3.7 0.2 - - - +
326A GLU* 3.6 1.9 - - - -
327A ASP 2.7 33.6 + - - -
369A HIS* 4.0 5.5 - - + +
370A LYS* 1.3 76.6 - - - +
372A PHE* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.6 5.1 - - - -
197A ARG* 3.1 30.1 - - + -
198A ILE* 3.7 9.9 - - + -
219A ILE 3.0 15.0 + - - +
220A TYR* 3.4 35.5 - + + -
221A PHE 2.9 26.2 + - - +
324A ARG* 4.4 23.8 - - + -
325A ILE 3.1 8.7 - - - -
326A GLU* 3.4 39.7 - - + -
370A LYS* 5.6 1.6 - - - -
371A ALA* 1.3 76.5 - - - +
373A LEU* 1.3 72.7 + - - +
374A GLU* 4.2 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.4 42.6 - - + -
221A PHE* 3.2 29.8 - - + +
223A GLY 5.2 0.7 - - - +
274A PHE* 6.3 0.7 - - + -
281A MET* 4.1 16.6 - - + -
323A PHE* 3.9 15.0 - - + -
324A ARG* 3.1 4.4 - - - +
325A ILE* 2.6 45.9 + - + +
372A PHE* 1.3 76.1 - - - +
374A GLU* 1.3 75.8 + - - +
375A VAL* 3.9 22.4 - - + -
410A VAL* 4.5 4.3 - - + -
412A ILE* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.4 23.5 + - + +
221A PHE 3.3 2.8 + - - +
222A LYS* 3.5 56.5 - - + +
223A GLY 4.2 5.0 + - - +
323A PHE 3.8 2.9 - - - +
324A ARG* 2.8 49.4 + - - +
372A PHE* 4.2 4.3 - - - -
373A LEU* 1.3 83.0 - - - +
375A VAL* 1.3 68.7 + - - +
376A ASN* 4.2 9.8 + - - +
----------------------------------------------------------
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