Contacts of the helix formed by residues 313 - 325 (chain A) in PDB entry 1YI1
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 SER 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLY 4.6 0.7 + - - -
310A CYS* 2.8 13.6 + - - -
312A ASN* 1.3 81.1 + - - +
314A SER* 1.3 55.9 + - - +
315A ASP 3.4 2.5 - - - -
316A GLU* 3.3 11.7 - - - -
317A LEU* 2.7 36.4 + - - +
414A ASP* 4.7 0.2 + - - -
415A VAL* 3.5 12.0 - - - +
416A LYS* 3.1 34.3 + - - +
419A LEU* 3.7 22.2 - - - -
701A FAD 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A CYS 3.7 4.0 + - - -
311A LEU 5.1 1.6 - - - -
312A ASN 3.5 2.6 + - - -
313A SER* 1.3 76.5 - - - +
315A ASP* 1.3 64.6 + - - +
316A GLU* 4.0 0.4 + - - -
317A LEU* 3.7 3.0 - - - +
318A GLY* 2.9 25.1 + - - -
336A GLY 4.5 0.5 + - - -
337A SER 3.2 24.1 + - - +
338A TYR* 5.9 0.2 - - - -
339A PRO* 6.0 0.5 - - - +
499A LYS 5.3 0.7 + - - -
500A LYS* 4.6 11.6 + - - +
501A PRO* 3.7 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER 3.4 0.2 - - - -
314A SER* 1.3 78.9 + - - +
316A GLU* 1.3 78.9 + - - +
318A GLY* 2.9 4.1 + - - -
319A ARG* 2.9 25.2 + - - +
500A LYS* 4.9 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASN 4.0 0.5 - - - +
313A SER* 3.3 20.9 - - - +
314A SER 4.0 0.2 + - - -
315A ASP* 1.3 81.0 + - - +
317A LEU* 1.3 62.8 + - - +
319A ARG* 3.4 2.6 + - - -
320A PHE* 3.0 20.8 + - - +
416A LYS* 3.2 41.3 - - + +
419A LEU* 3.6 24.2 - - + -
420A GLN* 3.2 29.5 + - + +
423A ASN* 3.3 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.4 12.8 - - + -
306A VAL* 3.9 44.0 - - + -
310A CYS* 4.5 7.4 - - + -
313A SER* 2.7 23.7 + - - +
314A SER 3.7 2.9 - - - +
316A GLU* 1.3 69.3 - - - +
318A GLY* 1.3 68.3 + - - +
320A PHE* 3.1 6.8 + - + +
321A VAL* 3.0 38.5 + - + +
328A VAL* 5.1 0.7 - - + -
337A SER* 4.0 24.0 - - - +
338A TYR* 4.0 13.5 - - + -
370A PHE* 5.1 3.4 - - + -
419A LEU* 3.5 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER 2.9 16.6 + - - -
315A ASP* 2.9 3.6 + - - -
317A LEU* 1.3 76.4 - - - +
319A ARG* 1.3 61.9 + - - +
321A VAL* 2.9 19.6 + - - +
322A GLU* 3.2 13.6 + - - +
338A TYR* 4.4 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP 2.9 14.4 + - - +
316A GLU* 3.7 9.6 - - - +
318A GLY* 1.3 69.9 - - - -
320A PHE* 1.3 63.8 - - - +
322A GLU* 2.8 39.2 + - - +
323A LEU* 3.1 64.7 + - + +
423A ASN* 3.8 14.4 - - + +
427A GLU* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 5.9 0.2 - - + -
296A ILE* 3.7 25.8 - - + -
304A LEU* 3.9 36.1 - - + -
316A GLU 3.0 12.5 + - - +
317A LEU* 3.1 11.2 + - + +
319A ARG* 1.3 77.2 - - - +
321A VAL* 1.3 55.3 + - - +
323A LEU* 3.4 2.5 + - - +
324A THR* 2.7 45.7 + - + +
326A ILE* 4.4 0.9 - - + -
368A LEU* 4.0 9.9 - - + -
370A PHE* 4.2 2.5 - + - -
419A LEU* 3.7 23.1 - - + -
422A MET* 3.7 33.4 - - + -
423A ASN* 2.9 24.4 + - - +
426A LEU* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.9 23.1 - - + -
317A LEU* 3.0 20.6 - - + +
318A GLY 2.9 7.7 + - - +
320A PHE* 1.3 74.7 - - - +
322A GLU* 1.3 56.8 + - - +
323A LEU 3.1 1.8 - - - -
324A THR* 3.9 4.5 - - - -
325A GLY* 2.5 35.5 + - - -
326A ILE 3.8 14.1 - - - +
328A VAL* 3.9 6.7 - - + -
338A TYR* 3.6 40.2 - - + +
344A LEU* 3.6 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLY 3.2 6.5 + - - +
319A ARG* 2.8 58.2 + - - +
321A VAL* 1.3 75.9 - - - +
323A LEU* 1.3 62.1 + - + +
324A THR 3.3 0.2 - - - -
325A GLY* 4.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 3.1 59.1 + - + +
320A PHE 3.8 4.7 - - - +
322A GLU* 1.3 80.9 - - + +
324A THR* 1.3 63.5 + - - +
423A ASN* 3.6 46.7 - - + +
426A LEU* 4.0 18.6 - - + +
427A GLU* 3.9 12.3 - - + +
435A LEU* 3.6 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 4.5 3.8 - - + -
320A PHE* 2.7 29.1 + - + +
321A VAL* 3.7 2.8 + - - -
323A LEU* 1.3 81.1 - - - +
325A GLY* 1.3 64.5 + - - +
326A ILE* 3.3 34.0 + - + +
426A LEU* 3.3 33.9 - - + -
435A LEU* 3.8 25.2 - - + +
437A PHE* 3.0 26.0 - - - -
441A ARG* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL 2.5 23.1 + - - -
322A GLU* 4.3 2.9 + - - -
323A LEU 3.9 0.2 - - - -
324A THR* 1.3 74.6 - - - +
326A ILE* 1.3 58.1 + - - +
327A PRO* 4.0 0.9 - - - +
344A LEU* 4.0 14.6 - - - -
437A PHE* 3.9 8.7 - - - +
441A ARG* 3.0 37.3 + - - -
----------------------------------------------------------
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