Contacts of the helix formed by residues 400 - 408 (chain B) in PDB entry 4JYI
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 400 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 4.6 3.6 - - + +
222B SER* 4.0 22.4 - - - +
226B THR* 3.6 21.3 - - + +
398B SER 3.6 5.8 - - - +
399B MET* 1.3 99.7 - - + +
401B PRO* 1.3 76.9 - - + +
402B LEU 3.3 1.1 - - - +
403B ILE* 3.1 21.8 + - + +
404B GLN 3.1 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B MET 3.3 4.9 - - - +
400B PRO* 1.3 86.9 - - + +
402B LEU* 1.3 58.1 + - + +
404B GLN* 3.2 8.1 + - + +
405B GLU* 3.0 31.9 + - - +
632F ILE* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.8 21.8 - - + +
229B ILE* 3.6 28.5 - - + -
230B ILE* 3.6 29.6 - - + +
400B PRO* 3.3 0.8 - - - +
401B PRO* 1.3 78.8 - - + +
403B ILE* 1.3 65.6 + - + +
405B GLU* 3.3 3.6 + - - +
406B MET* 3.1 21.1 + - + +
632F ILE* 3.6 35.3 - - + +
633F LEU* 4.1 26.7 - - + -
636F LEU* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B SER* 4.0 12.1 - - - +
225B ALA* 4.1 6.5 - - + -
226B THR* 3.9 15.7 - - - +
229B ILE* 3.8 24.2 - - + -
388B VAL* 4.8 3.4 - - + -
399B MET* 3.6 19.1 - - + -
400B PRO* 3.1 35.6 + - + +
402B LEU* 1.3 76.6 - - - +
404B GLN* 1.3 62.7 + - - +
406B MET* 3.3 1.5 + - - +
407B MET* 3.0 36.1 + - + +
501B JYI 3.9 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LYS* 5.1 10.1 - - - +
399B MET* 4.5 14.5 - - + +
400B PRO 3.1 11.4 + - - +
401B PRO* 3.3 14.6 - - + +
403B ILE* 1.3 77.2 - - - +
405B GLU* 1.3 53.5 + - + +
407B MET* 5.1 2.0 - - - -
408B GLU* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LYS* 2.7 35.5 + - - +
401B PRO* 3.0 17.3 + - - +
402B LEU* 3.3 7.8 + - - +
404B GLN* 1.3 78.0 - - + +
406B MET* 1.3 50.7 + - - +
408B GLU* 3.4 10.5 - - - +
630F HIS* 3.4 27.6 + - - +
631F LYS* 3.5 7.8 + - - +
632F ILE* 3.0 39.7 + - - +
633F LEU* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.8 26.7 - - + +
232B ILE* 5.7 0.9 - - + -
233B VAL* 4.0 9.2 - - + -
254B LEU* 3.8 21.3 - - + -
255B LYS* 3.2 46.0 + - - +
258B CYS* 3.8 26.9 - - + -
402B LEU* 3.1 20.0 + - + +
403B ILE* 3.8 4.7 - - - +
405B GLU* 1.3 76.9 - - - +
407B MET* 1.3 79.1 + - + +
408B GLU 4.3 0.2 - - - +
633F LEU* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 5.4 3.4 - - + -
255B LYS 5.4 2.7 - - - +
258B CYS* 4.2 9.0 - - + -
259B LEU* 4.1 46.4 - - + +
262B LEU* 5.0 4.9 - - + -
385B ALA* 5.6 5.6 - - - -
388B VAL* 4.2 31.9 - - + -
389B ILE* 5.6 8.1 - - + +
403B ILE* 3.0 24.1 + - + +
404B GLN* 3.6 2.2 - - - +
406B MET* 1.3 99.3 - - + +
408B GLU* 1.3 69.0 + - - +
501B JYI 5.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LYS* 2.8 36.4 + - - +
404B GLN 2.7 19.4 + - - +
405B GLU* 3.4 8.5 - - - +
407B MET* 1.3 84.7 - - - +
630F HIS* 3.2 26.5 - - + -
----------------------------------------------------------
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