Contacts of the strand formed by residues 14 - 18 (chain D) in PDB entry 1QO0
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 14 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU 3.5 9.0 + - - +
13D LEU* 1.3 72.7 - - - +
15D VAL* 1.3 63.2 - - - +
38D SER* 3.6 24.5 + - - +
40D ARG* 6.2 4.7 - - + -
51D VAL* 5.1 10.5 - - + +
52D PRO* 3.7 30.7 + - - +
53D VAL* 3.7 4.0 - - + -
54D ASP* 2.7 46.1 + - - +
55D VAL 3.1 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.3 9.6 - - + -
14D GLN* 1.3 78.7 - - - +
16D LEU* 1.3 66.2 + - - +
32D LEU* 3.9 15.7 - - + -
37D CYS* 3.6 36.3 - - + -
38D SER 2.8 12.0 + - - +
39D VAL* 3.3 7.0 - - + -
40D ARG* 2.8 29.2 + - - +
53D VAL* 5.0 0.2 - - - -
55D VAL* 3.3 20.6 - - + +
57D PHE* 3.5 33.9 - - + -
119D LEU* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLN 4.2 0.2 - - - -
15D VAL* 1.3 78.2 - - - +
17D VAL* 1.3 66.3 - - - +
18D LEU* 3.5 33.5 + - + +
40D ARG* 3.2 11.9 - - + +
42D CYS* 4.1 20.9 - - + -
49D PHE* 3.4 36.8 - - + -
53D VAL* 3.5 33.0 - - + -
55D VAL 2.8 7.6 + - - +
56D VAL* 3.4 5.5 - - + -
57D PHE* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 1.3 76.7 - - - +
18D LEU* 1.3 57.0 + - - +
19D ASN* 3.1 14.6 + - + -
25D SER* 4.0 30.3 - - - +
28D LEU* 4.1 25.1 - - + -
29D VAL* 3.9 23.1 - - + -
32D LEU* 3.9 25.8 - - + -
39D VAL* 4.2 2.7 - - + -
40D ARG 2.6 15.7 + - - +
41D GLN* 3.4 5.1 - - + +
42D CYS 3.0 22.3 + - - -
57D PHE* 3.8 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.5 19.3 + - + -
17D VAL* 1.3 69.0 - - - +
19D ASN* 1.3 60.5 + - - +
42D CYS* 3.7 15.0 - - + +
43D TRP* 3.7 9.0 - - + -
45D PRO* 3.8 27.6 - - + -
46D PRO* 4.1 9.6 - - + -
49D PHE* 4.7 2.9 - - + -
56D VAL* 3.9 13.9 - - + -
57D PHE 2.8 13.8 + - - +
58D THR* 3.0 23.4 + - - +
59D SER 4.2 0.2 + - - -
69D ILE* 3.5 38.6 - - + -
72D LEU* 3.8 20.4 - - + -
73D LEU* 5.6 0.9 - - + -
----------------------------------------------------------
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