Contacts of the helix formed by residues 344 - 356 (chain A) in PDB entry 1G59
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 344 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 3.3 16.7 - - - -
343A GLU* 1.3 83.7 - - - +
345A GLU* 1.3 60.2 + - - +
346A ALA* 3.0 19.4 + - - +
347A TYR* 3.1 13.6 + - - +
348A LEU 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 4.3 2.1 - - - +
332A LYS* 3.1 31.4 + - - -
342A TRP* 3.8 7.5 + - - +
344A SER* 1.3 71.0 + - - +
346A ALA* 1.3 61.3 + - - +
348A LEU* 3.2 10.3 + - - +
349A ARG* 2.8 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 3.0 8.6 + - - +
345A GLU* 1.3 79.0 - - - +
347A TYR* 1.3 64.4 + - - +
349A ARG* 3.3 7.7 + - - +
350A ARG* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 4.7 0.2 - - + -
343A GLU* 3.2 40.6 - - + +
344A SER* 3.1 22.7 + - - +
346A ALA* 1.3 81.0 - - - +
348A LEU* 1.3 64.7 + - - +
350A ARG* 3.3 4.4 + - - +
351A ALA* 2.9 26.0 + - + +
372A LEU* 2.6 46.5 + - - +
373A PHE* 4.0 19.5 - + - -
453A LEU* 3.6 40.5 - - + +
454A LEU* 4.7 5.4 - - - +
458A ARG* 3.9 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 3.3 28.7 - - + +
331A VAL* 4.1 4.7 - - + -
332A LYS* 3.7 15.9 - - + -
335A LEU* 3.4 31.2 - - + -
342A TRP* 3.7 13.0 - - + +
344A SER 2.9 18.1 + - - +
345A GLU* 3.6 20.4 - - - +
347A TYR* 1.3 81.1 - - - +
349A ARG* 1.3 52.6 + - - +
351A ALA* 3.1 7.4 + - - +
352A VAL* 2.7 51.9 + - + +
373A PHE* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.2 16.6 - - + +
325A GLU* 3.0 59.1 + - - +
328A ALA* 3.3 24.2 - - + +
329A GLU* 3.9 15.0 + - - -
345A GLU* 2.8 63.5 + - - +
346A ALA* 3.6 6.7 - - - +
348A LEU* 1.3 73.8 - - - +
350A ARG* 1.3 53.3 + - - +
352A VAL* 2.8 9.4 + - - +
353A GLU* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 5.6 0.2 - - - -
346A ALA 3.1 13.3 + - - +
347A TYR* 3.8 3.4 - - - +
349A ARG* 1.3 79.4 - - - +
351A ALA* 1.3 63.2 + - - +
353A GLU* 2.9 31.0 + - - -
354A LEU* 3.1 48.0 + - - +
409A GLU* 3.1 30.8 + - - -
449A GLU* 3.6 11.5 + - - +
453A LEU* 3.9 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TYR* 2.9 23.5 + - + +
348A LEU* 3.3 8.3 - - - +
350A ARG* 1.3 79.6 - - - +
352A VAL* 1.3 60.9 + - - +
354A LEU* 3.5 3.5 + - - +
355A MET* 3.4 26.5 + - - +
365A PHE* 3.9 2.2 - - - -
372A LEU* 4.0 20.5 - - + +
373A PHE* 3.7 28.0 - - + -
453A LEU* 4.3 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.1 7.4 - - + -
327A VAL* 3.1 38.1 - - + -
328A ALA* 3.8 26.5 - - + +
331A VAL* 4.3 4.3 - - + -
348A LEU* 2.7 37.1 + - + +
349A ARG* 3.4 5.4 - - - +
351A ALA* 1.3 71.6 - - - +
353A GLU* 1.3 60.2 + - - +
355A MET 3.2 0.5 + - - -
356A ARG* 2.8 30.2 + - + +
359A PHE* 4.4 8.3 - - + -
365A PHE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.4 34.7 - - + +
349A ARG 2.7 15.2 + - - +
350A ARG* 2.9 45.5 + - - +
352A VAL* 1.3 76.7 - - - +
354A LEU* 1.3 62.9 + - + +
355A MET 3.2 0.9 + - - -
356A ARG* 3.4 14.5 + - - +
357A PRO* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.1 51.0 + - - +
351A ALA* 3.5 4.7 + - - +
353A GLU* 1.3 77.4 - - + +
355A MET* 1.3 61.7 + - + +
357A PRO* 3.9 1.9 - - - +
358A ARG* 2.9 28.4 + - - -
372A LEU* 5.0 3.8 - - + -
445A PRO* 3.6 15.9 - - + +
449A GLU* 3.3 34.3 - - + +
450A ILE* 4.1 12.8 - - + -
453A LEU* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ALA 3.4 8.4 + - - +
352A VAL 3.2 1.2 + - - +
353A GLU 3.1 0.8 - - - -
354A LEU* 1.3 83.6 - - - +
356A ARG* 1.3 54.0 + - - +
357A PRO* 3.1 4.5 - - - -
358A ARG* 2.4 59.7 + - + -
359A PHE* 3.3 12.8 - - + -
365A PHE* 3.4 36.6 - - + +
368A LYS* 3.5 33.7 - - + +
369A ALA* 3.4 27.8 - - + +
371A TYR* 4.6 3.4 - - - +
372A LEU* 4.7 4.3 - - + -
445A PRO* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLY 5.2 0.2 - - - +
318A ILE* 3.0 35.1 + - + +
319A ARG* 3.2 44.5 + - + +
320A GLU* 4.6 0.6 - - - +
322A LEU 2.9 23.2 + - - -
323A SER* 3.6 3.0 - - - +
324A LEU* 3.0 52.8 - - + +
327A VAL* 4.6 3.1 - - + +
352A VAL* 2.8 22.1 + - + +
353A GLU 3.5 8.5 - - - +
355A MET* 1.3 74.5 - - - +
357A PRO* 1.3 65.8 - - + +
358A ARG 3.3 0.5 + - - -
359A PHE* 3.6 22.5 - - - +
----------------------------------------------------------
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