Contacts of the helix formed by residues 391 - 401 (chain A) in PDB entry 2FYU
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 PRO 391 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 6.4 1.8 - - + -
388A ARG* 5.7 1.3 - - - +
389A ARG* 3.4 15.9 - - + +
390A ILE* 1.4 86.2 - - - +
392A LEU* 1.3 59.9 + - - +
393A ALA* 3.2 7.9 - - + +
394A GLU* 3.0 41.9 + - + +
395A TRP* 3.3 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 28.5 + - + +
11A VAL* 3.7 35.7 - - + +
28A GLU* 6.0 0.4 - - - +
365A LEU* 3.8 32.0 - - + +
366A VAL* 4.0 26.0 - - + -
369A LEU* 4.3 25.6 - - + -
389A ARG* 5.6 2.7 - - - +
390A ILE 3.8 0.8 + - - -
391A PRO* 1.3 71.2 - - - +
393A ALA* 1.3 55.9 + - - +
395A TRP* 3.5 11.6 + - + +
396A GLU* 3.0 27.7 + - - +
43B PRO* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.4 19.5 + - + +
9A GLN* 3.7 27.6 - - - +
391A PRO* 3.2 5.7 - - + +
392A LEU* 1.3 74.5 - - - +
394A GLU* 1.4 60.2 + - - +
396A GLU* 3.4 8.8 - - - +
397A SER* 3.0 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 2.8 43.9 + - - -
390A ILE* 3.4 17.1 - - + +
391A PRO* 3.0 26.2 + - + +
393A ALA* 1.4 75.0 - - - +
395A TRP* 1.4 59.2 + - - +
397A SER* 3.2 9.6 + - - -
398A ARG* 2.9 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.9 25.8 - - + -
365A LEU* 3.7 35.9 - - + +
369A LEU* 6.1 2.0 - - + -
378A ASP* 5.5 5.1 + - - -
386A TYR* 3.8 29.2 - + - -
390A ILE* 3.3 61.8 + - + +
391A PRO 3.3 9.1 + - - -
392A LEU* 3.7 10.3 - - + +
394A GLU* 1.4 73.7 - - - +
396A GLU* 1.3 51.5 + - - +
398A ARG* 3.2 21.4 + - - +
399A ILE* 2.8 44.7 + - + +
56I ARG* 5.3 5.3 - - + +
57I GLY* 3.9 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 2.7 28.2 + - + +
5A ALA* 6.3 0.7 - - + -
8A LEU* 3.8 23.1 - - + -
362A ARG* 2.6 49.3 + - - +
365A LEU* 5.6 0.4 - - - +
392A LEU 3.0 15.2 + - - +
393A ALA* 3.4 11.2 - - - +
394A GLU 3.2 0.2 - - - -
395A TRP* 1.3 73.8 - - - +
397A SER* 1.3 52.5 + - - +
399A ILE* 3.2 4.9 + - - +
400A ALA* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA 3.0 14.7 + - - -
394A GLU* 3.4 12.3 - - - -
396A GLU* 1.3 73.2 - - - +
398A ARG* 1.3 60.3 + - - +
400A ALA* 3.9 6.1 - - - +
401A GLU* 3.3 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ALA 5.7 2.0 + - - -
265A PRO* 4.4 29.2 - - + +
268A VAL* 3.5 30.1 - - + +
388A ARG* 4.8 9.0 - - - +
390A ILE* 5.2 4.5 - - - +
394A GLU* 2.9 48.4 + - - +
395A TRP* 3.4 32.6 - - - +
397A SER* 1.3 69.8 - - - +
399A ILE* 1.3 64.6 + - - +
401A GLU* 3.8 20.4 - - - +
402A VAL* 3.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 5.9 0.4 - - - +
268A VAL* 3.8 12.1 - - + -
272A VAL* 4.8 1.6 - - + -
358A LYS* 3.2 52.8 - - + +
361A LEU* 3.8 33.7 - - + -
362A ARG* 4.1 25.6 - - + +
365A LEU* 4.7 11.0 - - + -
395A TRP* 2.8 37.9 + - + +
396A GLU* 3.8 7.2 - - - +
398A ARG* 1.3 69.8 - - - +
400A ALA* 1.4 59.8 + - - +
402A VAL* 2.9 25.1 + - - +
57I GLY* 5.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 2.8 27.2 + - - +
362A ARG* 3.8 16.8 - - - +
396A GLU* 2.8 26.7 + - - +
397A SER* 3.9 6.7 - - - +
399A ILE* 1.4 72.2 - - - +
401A GLU* 1.3 59.6 + - - +
402A VAL 3.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.3 30.6 + - - +
398A ARG* 3.8 20.1 - - - +
400A ALA* 1.3 75.5 - - - +
402A VAL* 1.3 65.3 + - + +
403A ASP* 3.3 9.5 + - - +
406A VAL* 3.9 11.2 - - - +
----------------------------------------------------------
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