Contacts of the helix formed by residues 398 - 405 (chain A) in PDB entry 1I43
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 GLN 398 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.5 27.5 + - - +
373A THR* 3.4 22.0 - - + +
374A ALA* 3.3 25.5 - - - +
377A VAL* 4.1 7.3 - - + +
397A ASP* 1.3 74.0 - - - +
399A PRO* 1.3 55.2 - - - +
400A ALA* 2.6 7.2 + - + +
401A ILE* 2.6 50.9 + - + +
402A MET* 2.8 12.9 + - - +
419A ASP* 3.2 23.2 + - - +
421A LEU 3.6 15.3 - - - +
422A VAL* 4.2 4.0 - - + -
92C THR* 3.9 6.6 + - - +
95C LEU* 5.5 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO* 4.5 12.6 - - + -
397A ASP* 3.1 24.6 - - - +
398A GLN* 1.3 80.8 - - - +
400A ALA* 1.3 61.0 + - - +
401A ILE 3.3 0.2 - - - -
402A MET* 4.3 0.4 - - + -
403A SER* 3.0 31.2 + - - +
404A TYR* 3.1 20.5 - - + -
417A ILE* 4.0 12.3 - - + -
421A LEU* 3.6 31.6 - - + +
423A ARG* 3.9 23.3 - - + +
600A PMC 5.8 1.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
370A LEU* 4.8 2.9 - - + -
398A GLN* 2.6 8.6 + - + +
399A PRO* 1.3 75.8 - - - +
401A ILE* 1.3 63.0 + - + +
404A TYR* 3.2 7.3 - - - +
405A TRP* 3.1 29.5 + - - -
412A ARG* 3.8 16.1 - - - +
417A ILE* 3.6 15.9 - - + +
418A MET 3.6 23.9 + - - +
419A ASP* 4.0 16.2 - - - +
421A LEU 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.8 34.5 - - + -
398A GLN* 2.6 31.1 + - + +
400A ALA* 1.3 73.0 - - - +
402A MET* 1.3 64.3 + - - +
403A SER 3.4 0.5 + - - -
405A TRP* 3.3 39.2 + - + +
92C THR* 3.5 28.9 - - + -
95C LEU* 3.8 27.1 - - + -
96C ILE* 4.0 23.1 - - + -
99C LYS* 3.8 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE 4.3 1.1 - - - +
386A ALA* 3.5 16.4 - - - +
387A PRO* 3.4 46.0 - - + -
397A ASP* 3.1 36.8 - - + +
398A GLN 2.8 12.4 + - - +
401A ILE* 1.3 78.6 - - - +
403A SER* 1.3 58.9 + - - +
600A PMC 3.3 9.3 + - - +
89C PHE* 3.5 23.8 - - + -
95C LEU* 3.9 24.0 - - + -
99C LYS* 2.7 28.6 + - - +
107C GLU* 4.2 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 3.0 28.7 + - - -
399A PRO* 3.0 13.1 + - - +
402A MET* 1.3 79.5 - - - +
404A TYR* 1.3 80.3 + - - +
405A TRP 3.8 0.4 - - - -
406A ASP* 4.7 1.1 - - - -
600A PMC 3.1 49.5 + - - -
99C LYS* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS 5.2 2.4 + - - -
164A ARG* 3.4 39.7 + - + +
211A ASN* 5.5 6.2 + - - -
212A PRO* 5.7 3.1 - - + +
399A PRO* 3.1 27.3 + - + +
400A ALA* 3.2 11.2 - - - +
403A SER* 1.3 100.0 - - - +
405A TRP* 1.3 64.8 - - - +
406A ASP* 3.1 10.5 - - - -
407A LEU* 3.1 30.8 + - + +
412A ARG* 3.3 31.2 + - + +
415A TYR* 5.7 6.7 - + + -
417A ILE* 3.9 36.1 - - + +
600A PMC 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 4.4 24.7 - - + -
400A ALA 3.1 11.4 + - - -
401A ILE* 3.3 38.8 + - + +
403A SER 3.8 0.2 - - - -
404A TYR* 1.3 78.9 - - - +
406A ASP* 1.3 60.3 + - - +
407A LEU 3.2 7.8 + - - +
412A ARG* 3.4 38.5 + - - +
96C ILE* 3.9 22.1 - - + +
99C LYS* 3.6 38.5 - - + +
100C GLU* 3.1 33.7 + - + +
----------------------------------------------------------
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