Contacts of the strand formed by residues 6 - 12 (chain D) in PDB entry 3LNX
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 6 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D PRO* 5.3 0.5 - - - +
5D ASP* 1.3 78.1 - - - +
7D PHE* 1.3 68.8 + - - +
59D LEU* 3.6 29.6 - - + -
88D LEU* 3.6 27.1 - - + -
89D LEU 3.3 5.2 - - - +
90D GLU* 4.4 1.6 - - + -
59F LEU 4.7 1.3 - - - +
60F ALA* 3.4 34.3 - - + -
63F GLY* 2.9 19.6 + - - +
65F SER* 4.0 17.7 - - - +
88F LEU* 4.0 6.3 - - + -
100F SCN 3.9 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D PRO* 4.0 27.4 - - + -
5D ASP 4.0 2.5 - - - -
6D ILE* 1.3 80.3 - - - +
8D GLU* 1.3 63.8 + - - +
9D VAL* 3.8 26.7 - - + -
51D ARG* 3.4 34.3 - - + -
52D ILE* 4.2 1.1 - - + -
56D ASP* 3.6 14.8 - - - -
88D LEU* 3.7 2.3 - - - +
89D LEU* 2.8 61.5 + - + +
91D LYS* 3.7 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS* 6.0 0.2 + - - -
6D ILE* 6.4 0.2 - - + -
7D PHE* 1.3 78.2 - - - +
9D VAL* 1.3 70.6 + - - +
51D ARG* 4.0 8.7 + - - -
86D HIS* 2.7 36.6 + - - +
87D LEU 3.3 11.4 - - - +
88D LEU* 4.4 12.9 - - + +
89D LEU* 5.0 0.2 - - - -
102D SCN 5.1 2.4 + - - -
8F GLU* 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 3.8 26.2 - - + -
8D GLU* 1.3 82.0 - - - +
10D GLU* 1.3 62.3 + - - +
11D LEU* 4.3 9.6 - - + -
49D ASP* 4.7 2.2 - - - +
51D ARG* 3.9 38.1 - - + +
52D ILE* 3.9 21.3 - - + -
85D VAL 3.5 0.3 - - - +
86D HIS* 3.4 6.4 - - - -
87D LEU* 3.0 55.8 + - + +
89D LEU* 4.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 3.6 34.2 + - + +
51B ARG* 5.3 1.6 + - - -
10C GLU* 3.4 35.0 + - + +
84C VAL* 4.0 17.4 - - + +
9D VAL* 1.3 72.7 - - - +
11D LEU* 1.3 61.3 + - - +
12D ALA 3.9 1.4 + - - -
49D ASP* 4.8 0.3 - - - +
51D ARG* 3.9 15.5 + - - +
84D VAL* 3.5 24.6 - - + +
85D VAL 3.4 0.4 - - - -
86D HIS* 3.5 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY* 6.3 0.7 - - - -
9D VAL* 4.3 11.7 - - + -
10D GLU* 1.3 73.6 - - - +
12D ALA* 1.3 68.0 + - - +
18D LEU* 3.7 49.2 - - + +
20D ILE* 5.4 1.1 - - + -
45D ALA* 3.8 14.4 - - + +
46D ALA* 4.2 6.3 - - + -
49D ASP* 3.7 34.8 - - + +
51D ARG* 5.7 0.2 - - - +
52D ILE* 4.2 14.1 - - + -
84D VAL* 3.4 2.0 - - - -
85D VAL 2.8 37.5 + - - +
87D LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B IOD 4.2 0.2 - - + -
83C GLN* 3.7 31.4 + - + +
84C VAL* 3.6 34.4 + - + +
10D GLU 3.9 3.4 + - - -
11D LEU* 1.3 76.4 - - - +
13D LYS* 1.3 65.1 + - - +
45D ALA* 3.1 19.3 - - - +
83D GLN* 3.4 9.6 - - - +
84D VAL* 3.9 7.2 - - + -
----------------------------------------------------------
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