Contacts of the strand formed by residues 41 - 47 (chain D) in PDB entry 3DOY
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 LYS 41 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 3.7 31.9 + - + +
37D GLN* 2.9 56.3 + - + +
40D GLN* 1.3 83.9 - - + +
42D ILE* 1.3 67.9 + - - +
43D VAL* 4.5 10.8 - - + +
81D LEU* 3.5 11.4 - - - +
122D HIS* 5.8 1.2 + - - -
123D LEU 3.0 14.4 - - - +
124D GLU* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.7 29.8 - - + -
35D GLU 3.3 15.5 - - - +
36D LEU* 3.8 18.2 - - + -
41D LYS* 1.3 78.5 - - - +
43D VAL* 1.3 71.5 + - - +
44D ALA 4.2 0.4 - - - +
77D SER* 3.6 40.4 - - - +
80D PHE* 3.9 10.3 - - + -
81D LEU* 4.0 15.0 - - + -
121D TYR 3.5 1.7 - - - +
123D LEU* 2.8 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.7 1.7 - - - +
34D THR* 2.9 38.6 + - - +
35D GLU* 2.8 40.8 + - + +
41D LYS* 4.5 12.8 - - + +
42D ILE* 1.3 77.7 - - - +
44D ALA* 1.3 64.0 + - - +
120D GLU* 4.0 17.3 - - + +
121D TYR 3.1 5.8 - - - +
122D HIS* 3.7 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.8 4.7 - - + -
32D ARG 3.2 15.9 - - - +
33D ILE* 3.6 22.7 - - + +
34D THR* 4.2 2.2 - - - +
42D ILE* 4.2 2.0 - - + +
43D VAL* 1.3 75.9 - - - +
45D TYR* 1.3 68.1 + - - +
77D SER* 3.7 23.8 - - - +
120D GLU* 3.5 6.9 - - - +
121D TYR* 2.7 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLY* 2.7 36.8 + - - -
30D VAL* 3.9 0.3 - - - -
31D ASP* 2.9 22.1 + - + -
32D ARG* 3.0 56.2 + - + -
34D THR* 3.9 15.9 - - + -
44D ALA* 1.3 83.2 - - - +
46D LYS* 1.3 63.9 + - - +
47D ASN* 3.6 17.0 - - - -
118D ARG* 3.3 51.4 - - + +
119D LEU 3.1 15.9 - - - +
120D GLU* 3.8 8.1 - - + -
121D TYR* 4.0 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.2 11.1 + - - +
51A ASN* 4.1 3.8 - - - -
29D LEU* 3.2 61.9 - - + +
30D VAL* 4.2 0.2 - - - -
31D ASP* 3.2 15.3 - - - +
45D TYR* 1.3 78.0 - - - +
47D ASN* 1.3 77.8 + - - +
48D ILE* 3.6 8.3 + - + +
52D GLU* 2.8 31.6 + - - -
65D PHE* 3.9 17.2 - - + -
119D LEU* 2.9 33.4 + - + +
121D TYR* 3.5 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.7 25.8 + - + +
48A ILE 3.1 25.6 + - - +
49A THR* 3.1 10.3 - - - -
116A GLY 3.2 17.3 + - - +
117A ASP 2.8 30.1 + - - -
118A ARG* 4.2 1.3 - - - +
31D ASP* 2.8 9.2 + - - +
45D TYR* 3.6 17.9 - - - -
46D LYS* 1.3 94.6 + - - +
48D ILE* 1.3 60.3 + - - +
52D GLU* 3.7 0.2 - - - +
117D ASP 4.0 1.1 - - - -
118D ARG* 4.0 12.5 - - - +
----------------------------------------------------------
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