Contacts of the helix formed by residues 394 - 401 (chain B) in PDB entry 3RAW
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 394 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO 3.5 5.7 - - - +
393B ILE* 1.4 93.5 - - + +
395B SER* 1.3 66.4 + - - +
396B HIS* 3.1 27.6 - - + +
397B MET* 3.0 24.5 + - - -
398B ILE* 3.5 6.4 + - - +
454B GLU* 5.7 1.1 - - - +
455B PHE* 3.5 31.2 - - + -
456B ASP* 4.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ILE 3.5 4.7 + - - -
394B PRO* 1.3 71.6 - - - +
396B HIS* 1.3 59.7 + - - +
398B ILE* 3.1 13.0 + - - +
399B HIS* 2.9 47.9 + - - -
410B GLY* 5.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B PRO* 3.1 27.7 + - + +
395B SER* 1.3 81.5 + - - +
397B MET* 1.3 68.3 + - + +
399B HIS* 3.5 8.9 + - - +
400B ARG* 2.9 36.9 + - + +
456B ASP* 2.8 36.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PRO* 4.6 5.2 - - + -
344B GLU* 4.3 13.7 - - - +
347B LEU* 4.3 11.0 - - + +
349B LEU* 3.6 33.3 - - + +
393B ILE* 4.3 7.9 - - + -
394B PRO* 3.0 28.7 + - - +
396B HIS* 1.3 95.8 - - + +
398B ILE* 1.3 58.3 + - - +
400B ARG* 3.9 3.9 - - - +
401B THR* 3.1 29.1 + - - +
455B PHE* 3.3 36.8 - - + +
456B ASP* 3.8 9.0 - - - +
457B PRO* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 5.4 0.4 - - + -
387B GLU* 5.3 3.4 - - - +
393B ILE* 3.8 32.1 - - + +
394B PRO 3.5 2.0 + - - +
395B SER* 3.1 13.1 + - - +
397B MET* 1.3 76.0 - - - +
399B HIS* 1.3 65.6 + - + +
400B ARG 3.3 0.7 + - - -
401B THR* 3.4 9.7 - - - +
404B GLN* 2.4 40.0 - - - +
407B PHE* 3.3 52.7 - - + -
410B GLY* 3.3 33.9 - - - +
411B GLY* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B SER* 2.9 35.7 + - - +
396B HIS* 3.8 8.7 - - - +
397B MET 3.4 0.2 - - - -
398B ILE* 1.3 84.0 - - + +
400B ARG* 1.3 63.0 + - + +
401B THR 4.2 3.5 - - - +
404B GLN* 4.3 4.0 - - - +
410B GLY* 5.8 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 4.0 16.5 - - + +
396B HIS* 2.9 31.6 + - + +
397B MET* 4.0 4.7 - - - +
398B ILE 3.2 0.6 - - - -
399B HIS* 1.3 77.6 - - + +
401B THR* 1.3 69.0 + - - +
402B ARG* 3.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 2.4 39.7 + - + +
349B LEU* 3.7 8.7 - - - +
397B MET 3.1 15.2 + - - +
398B ILE* 3.4 20.0 - - - +
399B HIS 4.2 2.4 - - - +
400B ARG* 1.3 80.3 - - - +
402B ARG* 1.3 60.1 + - - +
403B LYS* 3.0 31.8 + - + +
404B GLN* 3.4 21.6 - - - +
407B PHE* 4.2 9.4 - - + -
----------------------------------------------------------
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