Contacts of the strand formed by residues 344 - 352 (chain A) 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 GLY 344 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 4.0 18.3 - - - +
260A LYS 3.4 13.9 - - - -
262A LYS* 5.3 2.2 - - - -
342A ASP 3.5 1.3 + - - -
343A PRO* 1.3 76.2 - - - +
345A LEU* 1.3 65.1 + - - +
346A MET* 4.0 3.8 - - - -
399A ARG 3.7 2.0 - - - +
400A TYR* 3.6 2.8 - - - -
401A THR* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 4.5 5.6 - - + -
260A LYS 3.0 8.2 + - - -
261A LEU* 3.6 27.5 - - + +
262A LYS* 3.3 21.1 + - - +
271A VAL* 4.0 26.0 - - + -
273A ILE* 4.2 14.6 - - + -
344A GLY* 1.3 73.6 - - - -
346A MET* 1.3 64.6 + - - +
347A LEU* 3.5 1.4 + - - -
368A VAL* 4.8 2.2 - - + -
398A CYS* 4.2 18.7 - - + +
399A ARG 3.8 2.2 - - - -
400A TYR* 3.3 36.3 - - + -
411A VAL* 4.2 4.9 - - + -
413A LEU* 4.5 12.1 - - + -
434A LEU* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 4.0 25.4 - - + +
341A ASP* 2.9 37.0 - - + +
342A ASP 5.8 1.1 - - - +
344A GLY 5.4 1.8 - - - -
345A LEU* 1.3 72.9 - - - +
347A LEU* 1.3 64.6 + - - +
348A MET* 3.8 4.9 - - - +
398A CYS* 3.0 6.6 - - - -
399A ARG* 2.8 67.4 + - + +
517B ASN* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.2 2.7 - - + -
262A LYS 3.1 20.2 + - - +
263A LEU* 3.5 38.0 - - + +
345A LEU 3.5 1.4 + - - +
346A MET* 1.3 74.7 - - - +
348A MET* 1.3 71.9 + - - +
349A GLY 3.6 20.2 - - - +
350A PHE* 3.8 13.7 - - + -
396A ALA* 3.9 18.8 - - + -
397A LEU 3.4 10.8 - - - +
398A CYS* 3.9 9.4 - - - -
457B LEU* 5.0 0.2 - - + -
461B MET* 3.2 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A MET* 3.8 12.6 - - - +
347A LEU* 1.3 80.6 - - - +
349A GLY* 1.3 55.1 + - - +
397A LEU* 2.6 26.3 + - + +
398A CYS* 3.9 2.5 - - - -
399A ARG* 3.8 32.3 - - - +
410A PHE* 3.9 5.4 - - + -
461B MET* 5.0 2.9 - - - -
463B LEU* 3.5 17.9 - - + +
477B PHE* 3.3 27.1 - - + -
516B LEU 3.0 28.5 - - - +
517B ASN* 3.7 1.3 - - - +
518B PRO* 3.2 45.4 - - + +
522B VAL* 4.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.6 8.0 - - - +
348A MET* 1.3 80.4 - - - +
350A PHE* 1.3 61.9 + - - -
396A ALA* 3.5 4.0 - - - -
397A LEU 2.8 29.3 + - - +
461B MET* 3.2 26.0 - - - -
463B LEU* 3.7 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.8 20.6 - - + -
349A GLY* 1.3 74.2 - - - -
351A LYS* 1.3 60.7 + - - +
352A PRO* 4.3 1.2 - - - +
385A LEU* 3.9 21.8 - - + -
389A CYS* 4.0 6.1 - - - -
394A VAL* 3.5 28.5 - - + +
395A ALA 3.3 4.0 - - - -
396A ALA* 3.8 24.0 - - + -
457B LEU* 4.4 4.0 - - + -
458B ILE* 3.5 49.6 - - + +
461B MET* 2.8 50.1 + - + +
462B SER* 3.4 6.6 + - - -
463B LEU* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 1.3 74.7 - - - +
352A PRO* 1.3 68.8 - - + +
353A LEU 3.3 0.3 + - - -
355A LEU* 3.5 33.7 - - + +
356A LEU* 4.7 17.7 - - + +
394A VAL* 3.1 4.0 - - - -
395A ALA* 2.9 33.8 + - + +
397A LEU* 3.7 24.8 - - + +
437A LEU* 5.9 1.6 - - - +
463B LEU* 4.2 16.2 - - + +
475B ASP* 2.7 35.6 + - - +
477B PHE 2.7 25.5 + - - -
478B PRO* 4.3 2.0 - - - +
479B THR* 4.5 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE 4.3 2.0 - - - +
351A LYS* 1.3 88.5 - - + +
353A LEU* 1.3 58.3 + - - +
354A VAL* 2.7 21.1 + - + +
355A LEU* 2.9 24.2 + - + +
356A LEU* 4.3 1.4 + - - +
392A LYS 5.8 0.2 - - - +
393A GLU 3.6 5.2 - - - +
394A VAL* 3.1 16.1 - - + -
462B SER* 5.1 3.4 - - - +
464B ALA* 3.7 18.4 - - + +
473B LEU* 3.6 32.5 - - + -
----------------------------------------------------------
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