Contacts of the strand formed by residues 32 - 35 (chain D) in PDB entry 3QIR
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 ILE 32 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ASN* 1.3 81.4 - - - +
33D VAL* 1.3 60.3 + - - +
41D THR* 3.5 31.6 - - + +
42D TYR 3.3 10.5 - - - +
43D ARG* 4.2 34.3 - - + +
116D THR* 2.7 44.1 + - - +
117D GLY 2.9 12.0 + - - +
118D ILE 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.6 3.4 - - + -
31D ASN* 4.0 0.4 + - - +
32D ILE* 1.3 75.9 - - - +
34D ILE* 1.3 60.4 + - - +
35D THR* 5.4 0.9 - - + -
40D ARG 3.8 0.5 - - - +
41D THR* 3.3 7.6 + - - -
42D TYR* 2.8 41.9 + - + +
44D ILE* 3.1 37.7 - - + -
87D LEU* 4.6 3.1 - - + -
108D LEU* 4.0 21.1 - - + -
113D SER* 4.0 23.6 - - - +
114D PHE 3.1 13.9 - - - +
115D MET* 4.1 17.5 - - + -
116D THR* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 1.3 72.6 - - - +
35D THR* 1.3 70.3 + - - +
36D ARG* 3.6 7.6 - - + +
39D ASN* 4.5 17.9 - - - +
40D ARG 3.3 15.0 - - - +
41D THR* 4.5 6.5 - - - +
113D SER* 3.4 1.8 - - - -
114D PHE* 2.7 45.0 + - + +
116D THR* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 5.4 0.9 - - + -
34D ILE* 1.3 70.5 - - - +
36D ARG* 1.3 61.9 + - - +
37D TYR* 3.2 25.3 + - + +
38D ASN* 2.6 26.5 + - - +
39D ASN* 2.9 24.8 + - - -
40D ARG* 3.0 14.6 + - - +
42D TYR* 4.1 6.1 - - + -
108D LEU* 3.9 28.5 - - + -
109D LEU 5.8 0.4 - - - +
112D LEU* 3.3 10.3 - - + +
113D SER* 3.8 22.4 - - - +
----------------------------------------------------------
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