Contacts of the strand formed by residues 68 - 73 (chain D) in PDB entry 3W13
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 PHE 68 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 4.5 9.4 - - - -
53D LEU* 4.0 22.0 - - + -
54D ILE* 4.0 12.9 - - + +
60D ARG* 2.9 30.0 + - - -
64D VAL* 3.9 20.4 - - + -
65D PRO* 3.2 34.9 + - + +
66D ASP 3.1 0.8 - - - -
67D ARG* 1.3 85.3 - - + +
69D THR* 1.3 59.0 + - - +
79D LEU* 5.5 3.8 - - + -
80D THR 3.7 2.2 - - - -
81D ILE* 3.6 35.4 - - + -
88D ASP* 4.0 27.4 - - - -
92D TYR* 3.9 17.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LYS* 4.4 2.6 + - - +
54D ILE* 4.1 1.5 - - - +
60D ARG* 3.4 18.2 - - - +
66D ASP 4.0 10.5 - - - +
68D PHE* 1.3 78.2 - - - +
70D GLY* 1.3 64.1 + - - +
71D SER* 3.9 1.0 + - - -
79D LEU* 4.2 1.5 - - - +
80D THR* 2.7 58.0 + - - +
82D SER* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TRP* 5.1 2.7 - - - -
54D ILE* 3.4 19.9 - - - +
57D ALA 3.3 21.4 - - - +
58D SER* 4.5 10.3 - - - +
60D ARG* 5.0 1.6 - - - +
69D THR* 1.3 75.0 - - - +
71D SER* 1.3 62.4 + - - -
78D THR 4.2 1.8 - - - -
79D LEU* 4.1 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TRP* 5.0 0.7 + - - +
57D ALA* 3.7 6.6 + - - +
58D SER* 6.2 0.4 - - - -
69D THR 3.9 0.9 + - - -
70D GLY* 1.3 76.1 - - - -
72D GLY* 1.3 67.4 + - - +
77D PHE* 3.5 15.2 - - - +
78D THR* 3.1 38.8 + - - +
80D THR* 3.6 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASN* 4.5 3.5 + - - -
57D ALA* 4.8 3.5 - - - +
71D SER* 1.3 82.3 - - - +
73D SER* 1.3 62.7 + - - -
76D ASP 3.5 13.7 - - - -
77D PHE* 3.7 13.0 - - - -
78D THR* 4.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 4.5 10.4 - - - +
37D ASN* 2.8 27.5 + - - -
72D GLY* 1.3 75.1 - - - -
74D GLY* 1.3 67.5 + - - +
75D THR 3.5 3.3 + - - -
76D ASP* 3.3 16.5 + - - +
77D PHE* 4.0 4.3 - - - -
----------------------------------------------------------
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