Contacts of the helix formed by residues 430 - 435 (chain B) in PDB entry 5IY8
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 ASN 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B TYR* 4.2 7.4 + - - +
428B ASP 4.1 1.2 + - - -
429B PHE* 1.3 83.1 - - - +
431B LEU* 1.3 53.4 + - - +
432B GLU* 3.0 28.1 + - - +
433B LEU* 2.6 63.1 + - + +
434B ALA 3.2 8.5 + - - -
182M ALA 4.7 6.3 + - - -
152T ASN* 5.7 0.6 + - - -
155T PRO* 5.2 8.7 - - - +
158T ASN* 3.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.1 27.6 - - + -
128B ILE* 3.8 36.5 - - + +
130B LYS* 3.8 31.9 - - + -
145B GLN* 4.4 18.8 - - + +
147B THR* 5.9 0.7 - - + +
415B VAL* 5.4 4.7 - - + -
429B PHE* 3.4 27.6 - - + -
430B ASN* 1.3 71.4 + - - +
432B GLU* 1.3 63.4 + - + +
433B LEU 3.5 0.2 + - - -
434B ALA* 3.6 14.7 + - + +
435B ILE* 3.9 16.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 3.9 20.6 - - - +
147B THR* 4.7 25.9 + - + +
430B ASN* 3.0 14.3 + - - +
431B LEU* 1.3 78.7 - - + +
433B LEU* 1.3 63.4 + - + +
435B ILE* 4.1 10.4 + - - +
127M ARG* 3.6 15.9 + - - -
151T THR* 4.4 16.6 - - - +
152T ASN* 3.7 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B TYR* 3.3 25.3 - - + +
430B ASN* 2.6 45.0 + - + +
432B GLU* 1.3 73.9 - - + +
434B ALA* 1.3 62.7 + - - +
435B ILE 3.3 1.1 - - - -
436B LYS* 4.6 4.7 - - - -
127M ARG* 2.7 40.7 + - - +
182M ALA 3.9 9.2 - - - +
183M VAL 3.7 27.4 - - - +
184M SER* 3.5 26.5 - - - +
185M ARG* 4.2 7.0 - - + +
158T ASN* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU 4.6 1.6 - - - +
415B VAL* 3.4 32.4 - - + +
418B TYR* 3.3 42.2 - - + +
419B ALA* 6.4 0.2 - - + -
429B PHE* 5.3 4.0 - - + -
430B ASN 3.2 4.9 + - - +
431B LEU* 3.9 13.9 - - + +
432B GLU 3.5 0.4 - - - -
433B LEU* 1.3 79.5 - - - +
435B ILE* 1.3 61.4 + - + +
436B LYS* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 5.2 9.2 - - + -
128B ILE* 4.3 22.0 - - + -
147B THR* 4.9 7.2 - - + -
148B PHE 4.2 3.4 - - - +
149B ILE* 4.0 34.3 - - + +
411B LEU* 4.5 12.3 - - + -
415B VAL* 3.9 21.1 - - + -
431B LEU* 3.9 17.4 + - + +
432B GLU 4.1 8.0 + - - +
433B LEU 3.3 2.5 - - - -
434B ALA* 1.3 75.3 - - - +
436B LYS* 1.3 59.7 + - - +
437B THR* 3.1 32.0 + - + +
127M ARG* 3.7 17.2 + - - -
----------------------------------------------------------
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