Contacts of the strand formed by residues 410 - 414 (chain A) in PDB entry 1IAX
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 TRP 410 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A SER* 3.4 22.9 - - - -
178A PHE* 3.7 12.6 - + - -
357A CYS 5.1 1.1 - - - -
358A LEU* 4.1 18.2 - - + -
367A TRP* 3.0 69.1 - + + -
368A MET 3.3 14.1 - - - -
369A ASP* 3.2 23.3 - - + -
371A ARG* 3.4 23.8 - - - +
382A GLU* 3.9 2.1 + - - +
400A GLY* 2.6 35.4 + - - -
405A CYS* 4.3 2.9 - - - -
407A GLU* 3.4 45.8 + - + -
408A PRO 3.5 4.6 - - - -
409A GLY* 1.3 77.9 - - - +
411A PHE* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A CYS 3.3 0.7 - - - +
367A TRP* 3.7 4.7 - - - -
368A MET* 2.8 50.5 + - + +
370A LEU* 3.6 29.2 - - + -
382A GLU* 3.7 30.1 - - + -
385A LEU* 4.2 7.4 - - + -
386A TRP* 3.5 32.8 - + + -
389A ILE* 4.3 6.5 - - + -
397A VAL* 3.6 21.8 - - + -
398A SER 3.1 19.3 - - - +
399A PRO* 3.6 12.3 - - + -
400A GLY 4.3 0.4 - - - +
409A GLY* 3.6 22.9 - - - -
410A TRP* 1.3 77.2 - - - +
412A ARG* 1.3 61.4 + - - +
413A VAL* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET 3.9 3.8 - - - +
52A GLY* 3.0 22.1 + - - -
54A ALA* 3.6 5.6 - - - +
209A ASN* 3.0 22.5 + - - +
210A PRO* 3.6 20.6 - - + +
365A PHE* 3.9 24.1 - - + -
366A CYS 3.5 4.0 - - - +
367A TRP* 3.9 10.2 - - + -
397A VAL* 3.6 1.7 - - - +
398A SER* 3.1 33.9 + - - -
403A PHE* 3.6 36.7 - - + -
411A PHE* 1.3 71.7 - - - +
413A VAL* 1.3 63.6 + - - +
414A CYS* 3.6 21.3 - - - -
600A SO4 2.8 47.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 3.4 42.8 - - + -
346A PHE* 3.9 19.1 - - + -
365A PHE* 3.3 19.3 - - - -
366A CYS* 3.2 15.4 + - - +
368A MET* 3.8 30.7 - - + -
395A LEU* 6.1 0.4 - - + -
397A VAL* 3.9 17.3 - - + -
411A PHE* 4.0 8.3 - - + +
412A ARG* 1.3 79.2 - - - +
414A CYS* 1.3 59.5 + - - +
415A PHE* 3.5 6.9 - - - -
430A ILE* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 2.8 38.9 + - - +
52A GLY 3.9 1.8 - - - -
53A LEU 3.2 41.7 - - - +
54A ALA* 3.5 10.3 - - - -
55A GLU 5.9 0.2 - - - +
364A LEU 3.3 9.9 - - - +
365A PHE* 3.9 9.0 - - - -
412A ARG* 3.6 28.3 - - - -
413A VAL* 1.3 69.3 - - - +
415A PHE* 1.3 58.1 + - - +
416A ALA 3.7 1.6 - - - +
417A ASN* 3.7 4.7 - - - +
418A MET* 3.6 10.4 - - - +
----------------------------------------------------------
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