Contacts of the strand formed by residues 8 - 12 (chain D) in PDB entry 3LUE
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 8 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA* 1.3 74.3 - - - +
9D VAL* 1.3 62.8 + - - +
10D VAL* 3.7 4.9 + - + +
20D GLY 3.1 11.0 - - - +
21D PHE* 3.2 32.1 - - + -
90D PHE* 3.3 39.7 - - + -
94D LEU* 4.7 10.8 - - + -
96D VAL* 3.3 17.0 - - + -
97D ALA 5.5 0.2 - - - +
98D PRO* 5.7 1.6 - - + -
101D HIS* 3.7 34.1 - - + +
102D PRO 3.1 6.0 + - - +
103D VAL* 3.6 11.8 - - + +
104D LEU 3.2 20.0 + - - +
----------------------------------------------------------
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 ALA 3.9 0.2 + - - -
8D LEU* 1.3 72.5 - - - +
10D VAL* 1.3 62.2 + - - +
11D ASP* 5.1 0.4 - - + +
19D ALA* 3.2 5.4 - - - -
20D GLY 2.9 27.2 + - - -
22D ALA* 4.2 16.6 - - + +
104D LEU* 3.7 30.3 - - + +
106D THR* 5.1 4.3 - - + -
340D TRP* 3.2 28.0 + - + +
343D GLY* 3.8 14.4 - - - +
344D SER* 3.4 33.2 - - - +
347D ALA* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.5 10.3 - - + +
9D VAL* 1.3 77.6 - - - +
11D ASP* 1.3 61.9 + - - +
12D ASN* 3.6 24.9 + - - +
17D CYS* 5.9 4.0 - - + -
18D LYS 3.7 3.8 - - - +
19D ALA* 4.4 3.4 - - + +
86D TRP* 3.7 18.8 - - + +
89D THR* 3.9 28.3 - - + +
90D PHE* 4.5 17.0 - - + -
103D VAL* 5.5 1.6 - - + -
104D LEU 3.0 6.9 + - - +
105D LEU* 3.4 18.9 - - + -
106D THR* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 4.1 0.8 - - + -
10D VAL* 1.3 74.0 - - - +
12D ASN* 1.3 65.7 + - - +
13D GLY* 3.7 0.7 + - - -
17D CYS* 3.3 9.7 - - - +
18D LYS* 2.8 65.3 + - + +
106D THR* 2.7 26.9 + - + +
137D GLN* 4.1 7.4 - - - +
339D VAL* 3.4 32.6 - - + +
340D TRP* 4.1 13.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.6 21.2 + - - +
11D ASP* 1.3 74.4 + - - +
13D GLY* 1.3 62.9 - - - +
14D SER 4.3 0.3 + - - -
17D CYS* 4.3 5.9 - - - -
71D ILE* 4.0 23.5 - - + +
74D GLY* 5.0 3.3 - - - +
76D VAL* 6.0 1.8 - - + -
82D MET* 3.2 11.2 - - + +
86D TRP* 2.9 41.8 + - - -
105D LEU* 4.3 5.1 - - - +
106D THR* 3.4 24.8 + - - +
119D MET* 5.7 1.4 - - - -
137D GLN* 4.0 17.8 + - - -
157D ASP* 5.9 0.2 - - - +
----------------------------------------------------------
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