Contacts of the strand formed by residues 310 - 316 (chain B) in PDB entry 1JEY
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 ILE 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LYS* 3.6 28.3 - - + -
288A LEU 3.0 15.9 - - - +
296A VAL* 4.5 7.9 - - + -
295B TYR* 3.3 52.7 - - + -
305B VAL* 4.0 17.7 - - + +
306B LEU 4.3 4.5 - - - +
307B LYS* 3.7 14.6 + - - +
308B GLU 3.8 0.6 - - - -
309B ASP* 1.3 82.9 - - - +
311B ILE* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LYS* 3.7 3.3 - - - +
288A LEU* 3.0 44.5 + - + +
290A ARG* 4.0 44.9 - - + +
293A ASN* 3.4 26.0 - - - +
310B ILE* 1.3 83.1 - - - +
312B GLN* 1.3 62.9 + - - +
322B PRO* 3.7 22.4 - - + -
324B SER* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 3.3 29.5 - - + +
286A ILE 4.0 3.4 - - - -
287A LYS* 5.3 0.7 - - - +
288A LEU* 4.5 0.4 - - - -
311B ILE* 1.3 81.0 - - - +
313B GLY* 1.3 64.0 + - - +
314B PHE* 3.6 10.7 - - + -
322B PRO* 3.4 8.1 - - - +
323B PHE 3.0 39.7 + - - +
324B SER* 3.9 9.9 + - - +
325B LYS* 3.0 49.9 - - + +
328B GLU* 3.3 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 3.6 2.8 - - - +
286A ILE* 3.0 37.8 + - - -
288A LEU* 3.9 14.8 - - - -
312B GLN* 1.3 79.4 - - - +
314B PHE* 1.3 70.1 + - - -
320B ILE* 5.8 0.4 - - - -
321B VAL 3.3 11.4 - - - -
323B PHE 3.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LYS* 4.7 2.9 - - - -
283A PRO* 3.7 23.8 - - + -
284A PRO 4.0 3.6 - - - -
285A PRO* 3.5 30.3 - - + -
286A ILE* 5.1 3.1 - - - +
288A LEU* 5.2 0.4 - - - +
486A HIS* 3.9 17.9 - + - +
490A LEU* 4.0 23.8 - - + -
312B GLN* 3.6 24.5 - - - -
313B GLY* 1.3 78.1 - - - -
315B ARG* 1.3 65.0 + - - +
320B ILE* 3.5 4.6 - - - +
321B VAL* 2.7 34.7 + - - +
323B PHE* 3.6 36.3 - + + -
328B GLU* 3.1 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 5.5 7.7 - - + +
284A PRO 5.8 0.4 + - - -
286A ILE* 3.5 36.4 - - + +
295A PRO* 4.5 18.0 - - - +
487A PHE* 4.4 8.0 - - - -
490A LEU* 3.9 11.9 - - - +
314B PHE* 1.3 76.9 - - - +
316B TYR* 1.3 60.8 + - - +
317B GLY 3.8 15.9 + - - +
318B SER* 5.3 5.3 + - - +
319B ASP 3.3 7.8 + - - +
320B ILE* 4.1 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.8 3.9 - - + +
75A ILE* 3.4 28.4 - - + +
76A ILE* 6.0 0.2 - - + -
112A GLY* 4.0 1.7 - - - -
113A ALA* 3.6 39.3 - - + -
116A ILE* 3.6 17.5 - - + +
487A PHE* 3.7 34.5 - + + -
490A LEU* 3.8 18.6 - - + -
491A GLU* 2.5 43.8 + - + +
494A ALA* 5.3 1.3 - - + -
314B PHE 4.0 0.2 + - - -
315B ARG* 1.3 73.1 - - - +
317B GLY* 1.3 58.4 + - - +
318B SER 3.1 0.7 + - - -
319B ASP* 2.9 39.2 + - + +
321B VAL* 4.3 13.0 - - + -
----------------------------------------------------------
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