Contacts of the strand formed by residues 357 - 366 (chain B) in PDB entry 1JEQ
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 MET 357 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.9 24.9 - - + -
278A GLN* 4.1 3.6 - - - +
279A LYS* 3.3 46.0 - - + +
361A TYR* 2.9 20.1 + - - -
364A PRO* 4.6 7.6 - - + -
355B PHE 3.2 9.2 - - - +
356B PHE* 1.3 79.7 - - - +
358B GLY* 1.3 64.1 + - - +
360B GLN 4.8 1.4 - - - +
422B VAL* 4.1 0.5 - - - +
423B GLN* 2.8 43.7 + - + +
424B LEU 4.5 1.3 - - - +
425B PRO* 3.6 29.8 - - - -
429B ASP* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 6.4 2.2 - - - -
361A TYR* 2.4 26.7 + - - -
363A ARG* 4.0 0.5 - - - -
364A PRO* 3.7 5.1 - - - +
357B MET* 1.3 81.8 - - - +
359B ASN* 1.3 76.0 + - - +
360B GLN* 3.6 3.6 - - - -
423B GLN* 3.6 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 6.2 2.2 - - - +
362A LEU 4.0 13.6 - - - +
363A ARG* 4.0 18.5 + - - +
364A PRO* 4.2 4.8 - - - +
268B LEU* 3.8 22.0 - - + +
269B GLN* 4.4 5.7 + - + +
271B ARG* 4.5 20.1 + - - +
358B GLY* 1.3 83.1 - - - +
360B GLN* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TYR* 4.0 12.4 - - - -
362A LEU* 6.4 0.2 - - - +
265B LYS* 3.4 32.8 - - + +
267B ILE* 3.1 14.1 - - - +
268B LEU* 4.5 8.3 - - + +
357B MET 4.8 2.1 - - - +
358B GLY* 3.6 1.6 - - - -
359B ASN* 1.3 83.9 - - - +
361B VAL* 1.3 70.6 + - - +
362B LEU* 3.8 28.0 + - + +
395B TYR* 4.3 16.6 + - - -
404B GLN* 5.2 7.9 + - - +
421B TYR* 4.6 6.4 - - + +
422B VAL* 4.5 8.1 - - - +
423B GLN 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A HIS* 3.9 13.0 - - + +
361A TYR* 3.3 42.8 - - + +
265B LYS* 3.5 3.3 - - - -
266B SER* 2.6 45.6 + - - +
267B ILE* 2.8 23.3 + - + -
360B GLN* 1.3 80.8 - - - +
362B LEU* 1.3 55.4 + - - +
420B VAL* 3.3 33.9 - - + -
421B TYR 3.8 4.5 - - - +
422B VAL* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 5.6 0.4 - - + -
263B ALA* 4.4 20.2 - - + -
264B TYR* 3.3 5.4 - - - +
265B LYS* 3.7 36.3 - - + +
340B PHE* 5.8 0.7 - - + -
360B GLN* 3.8 21.5 - - + +
361B VAL* 1.3 76.1 - - - +
363B LYS* 1.3 61.6 + - - +
364B VAL* 4.0 1.6 - - + -
395B TYR* 3.5 39.7 - - + +
419B LEU 3.7 0.2 - - - +
420B VAL* 3.4 5.5 - - - +
421B TYR* 2.7 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A HIS* 5.3 10.0 - - - -
446A MET* 3.1 28.5 - - + +
263B ALA* 3.3 1.9 - - - -
264B TYR 2.7 36.3 + - - +
266B SER* 3.4 26.9 + - - -
362B LEU* 1.3 73.3 - - - +
364B VAL* 1.3 60.6 + - - +
365B PHE* 3.6 20.9 - - + -
411B HIS* 3.7 19.3 + - - -
416B TYR* 2.9 26.4 + - - +
418B CYS* 4.0 17.7 - - - -
419B LEU 3.5 3.6 - - - +
420B VAL* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ILE* 3.4 44.9 - - + -
262B ALA 3.5 5.4 - - - +
263B ALA* 4.2 13.2 - - + -
340B PHE* 3.9 30.1 - - + -
362B LEU* 4.7 1.3 - - + +
363B LYS* 1.3 75.9 - - - +
365B PHE* 1.3 62.6 + - - +
377B LEU* 3.9 8.0 - - + +
418B CYS* 2.9 24.6 - - - +
419B LEU* 2.8 32.5 + - + +
421B TYR* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A MET* 3.8 24.9 - - + -
447A PRO 5.6 4.5 - - - -
448A PHE* 6.1 2.7 - - + -
261B ILE* 3.0 7.1 - - - +
262B ALA 2.6 35.4 + - - +
264B TYR* 3.5 35.0 - + + -
363B LYS* 3.6 21.3 - - + -
364B VAL* 1.3 75.2 - - - +
366B ALA* 1.3 64.3 + - - +
377B LEU* 3.7 10.8 - - - -
416B TYR* 3.6 38.1 - + + -
417B GLU 3.6 14.1 - - - -
418B CYS* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG 3.4 6.5 - - - -
261B ILE* 4.1 0.9 - - - +
262B ALA* 4.2 2.5 - - - +
365B PHE* 1.3 82.4 - - - +
367B ALA* 1.3 74.0 + - - +
368B ARG* 3.3 2.4 + - - -
373B ALA* 3.6 12.3 - - + +
374B ALA* 3.5 39.3 - - + +
377B LEU* 3.5 13.5 - - + +
----------------------------------------------------------
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