Contacts of the helix formed by residues 374 - 381 (chain D) in PDB entry 3IAD
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 SER 374 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D VAL* 1.3 76.3 - - - +
375D ASN* 1.3 65.8 + - - +
376D GLN* 3.4 21.9 - - - +
377D PHE* 3.0 23.2 + - - +
378D LEU* 3.1 22.3 + - - +
395D LEU* 4.2 1.6 - - - -
509D GLN* 3.1 18.6 + - - +
521D SER* 5.6 0.7 + - - -
901D 15X 3.4 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D SER* 1.3 71.6 - - - +
376D GLN* 1.3 68.7 + - - +
378D LEU* 3.0 10.1 + - - +
379D ILE* 2.8 38.4 + - + +
391D ASP 6.1 0.2 - - - +
393D SER* 4.2 4.0 - - - +
394D VAL* 3.4 15.9 - - + +
395D LEU* 2.7 40.1 + - - +
396D GLU* 3.0 29.1 + - - -
438D ASP* 4.6 7.7 + - - -
901D 15X 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D SER* 3.4 19.9 - - - +
375D ASN* 1.3 90.0 + - - +
377D PHE* 1.3 55.9 + - - +
379D ILE* 3.2 12.3 + - + +
380D ASN* 2.8 43.3 + - - +
521D SER* 5.6 5.6 - - - +
602D ASN* 3.7 28.7 + - - +
603D THR* 5.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D VAL* 3.7 29.8 - - + -
374D SER* 3.0 25.2 + - - +
376D GLN* 1.3 74.9 - - - +
378D LEU* 1.3 63.7 + - + +
380D ASN* 3.9 5.9 - - - +
381D THR* 2.9 57.8 + - + +
509D GLN* 3.7 29.8 - - + +
512D ARG* 4.4 21.1 - - + -
513D GLU* 3.8 31.0 - - + +
516D ARG* 4.3 16.4 - - - -
518D MET* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D PRO* 4.6 6.1 - - + -
373D VAL* 3.7 23.1 - - + -
374D SER 3.1 15.8 + - - +
375D ASN* 3.0 9.3 + - - +
377D PHE* 1.3 78.8 - - + +
379D ILE* 1.3 59.5 + - - +
381D THR* 3.2 6.4 + - - +
383D SER* 3.0 52.8 + - - +
385D LEU* 4.6 10.8 - - + -
386D ALA* 3.6 8.8 - - + +
394D VAL* 4.3 14.4 - - + -
395D LEU* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D ASN* 2.8 26.8 + - + +
376D GLN* 3.2 11.0 + - + +
378D LEU* 1.3 75.3 - - - +
380D ASN* 1.3 66.6 + - - +
382D ASN* 3.0 20.1 + - - +
386D ALA* 3.7 13.0 - - + +
391D ASP* 3.7 57.2 - - + +
394D VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLU* 3.7 17.5 - - - +
376D GLN* 2.8 33.1 + - - +
377D PHE* 4.0 3.9 - - - +
379D ILE* 1.3 79.3 - - - +
381D THR* 1.3 58.7 + - - +
382D ASN* 3.2 1.5 + - - +
518D MET* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 3.3 18.2 + - - +
410B GLU* 2.9 27.6 + - + -
377D PHE* 2.9 49.3 + - + +
378D LEU* 3.2 13.2 + - - +
380D ASN* 1.3 77.0 - - - +
382D ASN* 1.3 64.1 + - - +
383D SER* 3.3 8.1 + - - -
516D ARG* 3.8 24.2 - - - +
518D MET* 4.5 10.1 - - - -
----------------------------------------------------------
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