Contacts of the strand formed by residues 399 - 401 (chain A) in PDB entry 1IR1
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 VAL 399 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.3 24.9 - - + +
171A GLY 4.2 6.7 - - - +
199A PHE* 4.4 4.0 - - + -
239A TYR* 3.8 19.3 - - - +
325A HIS* 4.2 11.7 - - + -
375A LEU* 4.1 23.1 - - + -
376A PRO 3.0 6.3 + - - +
377A VAL* 3.3 23.7 - - + +
378A ALA 2.8 26.9 + - - +
398A SER* 1.3 80.5 - - - +
400A LEU* 1.3 63.2 + - - +
401A GLN* 4.0 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 4.1 26.0 - - + -
169A LEU 2.9 9.2 + - - +
170A LEU* 3.4 12.3 - - + +
171A GLY 2.9 20.6 + - - +
378A ALA* 3.6 22.2 - - + -
382A ILE* 5.0 0.2 - - + -
387A MET* 3.9 25.1 - - - -
390A LEU* 4.2 28.0 - - + +
391A THR* 4.6 4.3 - - - +
394A PHE* 4.6 5.4 - - + -
398A SER* 4.0 13.7 - - - +
399A VAL* 1.3 79.7 - - - +
401A GLN* 1.3 60.4 + - - +
402A PHE* 3.8 16.2 - - + -
424A LEU* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY* 3.3 19.6 - - - -
172A CYS* 4.2 3.4 - - - +
173A THR* 4.3 2.4 + - - +
201A KCX 3.4 20.4 - - - +
239A TYR* 3.0 43.9 + - - -
292A HIS* 4.0 1.0 - - - -
327A HIS* 3.8 6.6 - - - -
377A VAL* 3.4 26.6 - - + +
378A ALA 2.9 9.5 + - - -
379A SER* 3.6 33.0 + - - +
380A GLY 4.3 1.7 + - - -
382A ILE* 3.4 21.0 - - - +
399A VAL* 4.0 3.7 - - + +
400A LEU* 1.3 76.5 - - - +
402A PHE* 1.3 64.7 + - - +
403A GLY 4.1 1.4 + - - -
501A CAP 4.4 1.1 + - - -
----------------------------------------------------------
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