Contacts of the helix formed by residues 352 - 373 (chain B) in PDB entry 4RG1
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 ARG 352 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.3 32.9 + - - -
99A GLN* 5.5 1.6 - - - +
102A ARG* 3.9 18.5 - - - +
172A LEU 3.0 17.2 + - - -
173A ASN* 2.9 30.6 + - - +
174A PRO* 4.9 3.4 - - - +
86B ASN* 6.4 1.8 - - - -
314B LEU* 6.4 1.6 - - - -
350B THR* 5.2 2.7 - - - +
351B ILE* 1.3 74.0 - - - +
353B THR* 1.3 68.0 + - - +
354B GLU* 2.9 30.5 + - - +
355B GLU* 2.8 28.8 + - - +
356B ALA* 2.8 20.3 + - - +
401B SAH 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.2 25.4 - - + -
83B ILE* 3.6 25.9 - - + +
311B PHE* 4.1 16.6 - - + -
312B GLY 2.7 29.7 + - - +
313B GLY* 3.7 2.8 - - - -
351B ILE 3.8 1.2 + - - -
352B ARG* 1.3 72.9 - - - +
354B GLU* 1.3 60.4 + - - +
356B ALA* 3.2 3.3 + - - +
357B ILE* 3.0 31.7 + - + +
401B SAH 3.5 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.9 3.8 + - - -
83B ILE* 4.9 2.1 - - - +
96B LEU* 3.4 26.2 - - + +
99B GLN* 3.6 32.1 - - + +
100B ILE* 3.7 26.4 - - + +
103B ALA* 4.8 3.3 - - - +
352B ARG* 2.9 52.4 + - - +
353B THR* 1.3 75.4 + - - +
355B GLU* 1.3 69.0 + - + +
357B ILE* 3.7 4.5 + - - +
358B LEU* 3.6 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLN* 5.3 2.9 - - - +
102A ARG* 2.8 58.6 + - - +
103A ALA 5.1 0.6 + - - -
106A ILE* 3.7 13.9 - - + +
173A ASN* 4.7 0.7 - - - +
358A LEU* 4.1 24.1 - - + +
351B ILE* 3.7 9.4 - - + -
352B ARG* 2.8 36.0 + - + +
354B GLU* 1.3 84.1 - - + +
356B ALA* 1.3 65.8 + - - +
358B LEU* 3.2 6.1 + - - +
359B ILE* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE* 3.8 6.3 - - + -
351B ILE* 3.6 11.8 - - + +
352B ARG 2.8 16.1 + - - +
353B THR 3.2 4.2 + - - +
355B GLU* 1.3 72.1 - - - +
357B ILE* 1.3 59.9 + - - +
359B ILE* 4.4 5.4 - - - -
360B SER* 2.7 36.8 + - - +
401B SAH 3.4 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.5 7.4 - - + -
79B LEU* 4.1 14.4 - - + -
100B ILE* 3.7 36.6 - - + -
103B ALA* 3.8 20.9 - - + -
104B CYS* 4.6 8.5 - - - -
311B PHE* 3.7 35.4 - - + -
353B THR* 3.0 21.4 + - + +
354B GLU 4.0 5.4 - - - +
355B GLU 3.2 0.4 - - - -
356B ALA* 1.3 74.9 - - - +
358B LEU* 1.3 58.9 + - - +
361B LEU* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU* 4.1 26.7 - - + +
358A LEU* 3.8 32.8 - - + -
359A ILE* 4.0 27.3 - - + +
99B GLN 5.8 0.7 - - - +
103B ALA* 3.6 33.0 - - + -
106B ILE* 4.6 7.2 - - + -
107B PHE* 3.9 14.3 - - + -
354B GLU 3.6 9.3 + - - +
355B GLU 3.2 7.4 + - - +
357B ILE* 1.3 77.3 - - - +
359B ILE* 1.3 62.2 + - - +
362B ALA* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 4.0 13.5 - - + -
107A PHE* 3.8 39.3 - - + -
358A LEU* 4.0 19.3 - - + +
362A ALA* 3.8 10.5 - - + +
342B THR* 3.7 28.3 - - - +
343B CYS* 4.1 6.7 - - + -
351B ILE* 4.0 26.0 - - + -
355B GLU 3.0 17.2 + - - +
356B ALA* 3.9 4.0 - - - +
358B LEU* 1.3 74.8 - - - +
360B SER* 1.3 59.1 + - - +
362B ALA* 3.4 2.9 + - - +
363B ALA* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B THR* 4.0 9.2 - - - +
311B PHE* 3.6 23.5 - - - -
342B THR* 2.8 36.6 + - - +
356B ALA* 2.7 29.2 + - - -
359B ILE* 1.3 70.6 - - - +
361B LEU* 1.3 59.7 + - - +
363B ALA* 3.2 0.5 + - - +
364B LEU* 2.9 40.8 + - - +
401B SAH 4.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.5 12.6 - - + -
77B VAL* 4.0 11.4 - - + -
103B ALA 4.4 2.9 - - - +
104B CYS* 4.9 0.4 - - - -
107B PHE* 3.6 42.4 - - + -
109B VAL* 3.9 18.2 - - + -
309B VAL* 4.2 31.4 - - + -
311B PHE* 4.7 2.5 - - + -
357B ILE* 2.9 40.3 + - + +
360B SER* 1.3 72.5 - - - +
362B ALA* 1.3 59.1 - - - +
364B LEU* 3.8 3.0 - - + -
365B GLN* 2.9 31.5 + - - +
368B LEU* 5.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR 5.7 0.4 - - - +
359A ILE* 3.8 18.6 - - + +
362A ALA* 3.8 17.7 - - + -
363A ALA* 4.7 10.0 - - + +
107B PHE* 3.6 19.2 - - + -
358B LEU 3.1 21.2 + - - +
359B ILE 3.5 4.5 - - - +
361B LEU* 1.3 77.3 - - - +
363B ALA* 1.3 61.7 + - - +
365B GLN* 3.3 14.1 + - - +
366B PRO* 3.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA* 4.6 11.2 - - + +
363A ALA* 6.1 0.2 - - - +
296B VAL* 4.3 18.8 - - + +
342B THR* 4.0 28.7 - - + +
359B ILE 2.8 20.6 + - - +
360B SER 3.2 4.9 + - - +
362B ALA* 1.3 73.5 - - - +
364B LEU* 1.3 59.9 + - - +
365B GLN 3.7 0.2 + - - -
366B PRO* 3.8 8.8 - - - +
367B GLY 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 4.2 31.0 - - + -
289B THR* 5.4 0.4 - - + -
296B VAL* 3.8 24.7 - - + -
299B ALA* 5.7 1.1 - - + -
301B LEU* 4.6 16.4 - - + -
309B VAL* 4.2 31.0 - - + -
338B LEU* 6.1 0.4 - - + -
340B VAL* 4.8 3.8 - - + -
342B THR* 4.9 5.6 - - + -
360B SER* 2.9 27.3 + - - +
361B LEU* 3.8 3.4 - - - +
363B ALA* 1.3 75.0 - - - +
365B GLN* 1.3 58.7 + - - +
366B PRO 3.4 2.0 - - - -
367B GLY* 3.2 5.1 + - - +
368B LEU* 2.8 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR 4.1 4.0 - - - +
343A CYS* 4.0 9.7 - - - -
344A PRO* 3.2 51.6 + - + +
345A GLY 5.6 0.2 - - - -
106B ILE 5.5 0.6 + - - -
107B PHE* 3.8 31.1 + - + +
361B LEU 2.9 18.1 + - - +
362B ALA* 3.3 6.6 + - - +
364B LEU* 1.3 76.2 - - - +
366B PRO* 1.3 71.2 - - + +
368B LEU* 3.9 7.1 - - - +
369B THR* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 5.6 12.1 - - + -
362B ALA 3.6 10.8 - - - +
363B ALA 3.8 7.9 - - - +
364B LEU 3.6 3.4 - - - -
365B GLN* 1.3 96.3 - - + +
367B GLY* 1.3 56.6 + - - +
369B THR* 3.5 6.2 + - - +
370B GLN* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 3.6 19.1 - - - +
363B ALA 5.3 0.4 + - - -
364B LEU* 3.2 6.9 + - - +
366B PRO* 1.3 77.5 - - - +
368B LEU* 1.3 59.0 + - - +
370B GLN* 3.8 6.4 - - - +
371B ALA* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.0 11.7 - - + +
75B LEU* 4.0 29.8 - - + -
285B LEU* 4.5 3.8 - - + -
287B ILE* 4.5 6.7 - - + -
301B LEU* 3.6 18.8 - - + +
304B PHE* 3.4 31.1 - - + -
307B ALA* 3.9 17.0 - - + -
309B VAL* 4.8 7.0 - - + -
361B LEU* 5.0 5.4 - - + +
364B LEU* 2.8 39.6 + - + +
365B GLN* 3.9 6.1 - - - +
367B GLY* 1.3 72.1 - - - +
369B THR* 1.3 58.6 + - - +
372B GLY* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO* 6.0 0.7 - - - +
73B TYR* 3.8 20.5 + - + +
365B GLN* 2.9 28.8 + - - +
366B PRO* 3.6 6.7 - - - +
368B LEU* 1.3 77.2 - - - +
370B GLN* 1.3 62.6 + - - +
372B GLY* 4.2 0.5 - - - -
373B ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 4.4 6.8 - - - +
303B ASN* 4.4 10.2 + - - +
366B PRO 3.1 18.2 + - - +
367B GLY* 3.8 6.1 - - - +
368B LEU 3.2 0.2 - - - -
369B THR* 1.3 80.1 - - - +
371B ALA* 1.3 75.9 + - - +
372B GLY 3.5 0.3 + - - -
373B ALA* 3.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 3.8 20.6 - - + +
302B PRO 3.4 22.7 - - - +
303B ASN* 3.3 14.1 - - - +
304B PHE* 3.2 29.9 + - + +
367B GLY 2.9 18.6 + - - +
370B GLN* 1.3 86.5 - - - +
372B GLY* 1.3 58.7 + - - +
373B ALA 3.4 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 3.6 12.5 - - - +
73B TYR* 3.4 33.3 - - - +
304B PHE* 3.3 27.6 - - - +
368B LEU 2.9 11.6 + - - -
371B ALA* 1.3 75.0 - - - +
373B ALA* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 4.8 3.8 - - - -
73B TYR* 5.0 2.0 - - - -
303B ASN* 5.8 2.8 + - - +
369B THR 3.3 17.2 + - - +
370B GLN* 3.6 12.0 - - - +
371B ALA 3.4 5.2 - - - +
372B GLY* 1.3 81.5 - - - +
374B ARG* 1.3 69.6 + - - +
----------------------------------------------------------
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