Contacts of the strand formed by residues 64 - 69 (chain D) in PDB entry 4UOW
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 LEU 64 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D THR* 6.4 0.4 - - + -
30D SER* 5.5 5.8 - - - -
31D CYS* 3.6 20.9 - - - +
32D GLN* 3.9 17.3 - - + +
60D GLN* 3.1 6.4 - - - +
61D ASP* 2.9 45.1 + - + +
62D GLY 3.1 0.4 - - - -
63D ASP* 1.3 92.0 - - - +
65D TYR* 1.3 61.0 + - - +
66D ARG* 5.5 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D SER* 3.3 3.6 - - - -
31D CYS* 2.9 39.0 + - - +
33D ILE* 3.3 46.1 + - + -
38D THR* 4.5 5.7 - - - -
39D PRO* 3.2 44.4 + - + +
41D VAL* 3.5 36.6 - - + -
43D TRP* 4.7 3.1 - - + +
59D ALA 3.8 3.4 - - - +
60D GLN* 3.1 41.3 + - + -
62D GLY 4.6 0.5 + - - -
63D ASP* 3.3 20.3 - - - -
64D LEU* 1.3 73.0 - - - +
66D ARG* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 3.8 27.2 - - - +
29D LEU 3.4 9.9 - - - +
30D SER* 4.2 10.1 - - - -
43D TRP* 4.8 5.7 - - - +
57D ARG 3.7 1.7 - - - +
58D LEU* 3.6 3.6 - - - +
59D ALA* 2.8 62.1 + - + +
64D LEU* 5.5 1.3 - - + +
65D TYR* 1.3 75.7 - - - +
67D LEU* 1.3 59.9 + - - +
68D THR* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ALA 3.9 0.2 - - - +
28D THR* 3.4 2.3 - - - -
29D LEU* 2.7 46.8 + - + +
43D TRP* 3.7 41.5 - - + +
50D VAL* 3.8 15.9 - - + -
56D PHE* 3.8 35.7 - - + -
57D ARG 3.5 4.5 - - - +
58D LEU* 4.0 19.1 - - + +
66D ARG* 1.3 71.7 - - - +
68D THR* 1.3 59.8 + - - +
69D ILE* 4.0 4.3 + - + +
80D TYR* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 4.2 15.5 - - + +
27D ALA 3.4 10.3 - - - +
28D THR* 3.5 11.8 - - + +
56D PHE* 3.3 7.1 - - - +
57D ARG* 2.7 47.5 + - - +
59D ALA* 6.0 0.3 - - - +
66D ARG* 3.3 32.1 + - - +
67D LEU* 1.3 70.8 - - - +
69D ILE* 1.3 63.9 + - - +
70D LEU* 3.7 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 3.4 1.7 - - - -
27D ALA* 2.7 52.8 + - + +
29D LEU* 3.9 28.9 - - + -
55D ARG* 3.6 5.8 - - + +
56D PHE* 3.6 27.1 - - + -
67D LEU* 4.6 6.7 - - + +
68D THR* 1.3 74.0 - - - +
70D LEU* 1.3 64.9 + - - +
72D LEU* 4.2 11.1 + - + -
76D ASP* 3.4 36.3 - - + +
80D TYR* 3.8 22.9 - - + +
----------------------------------------------------------
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