Contacts of the strand formed by residues 195 - 201 (chain A) in PDB entry 1L0N
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 MET 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 4.1 1.9 - - - +
23A LEU* 3.3 17.7 - - + +
24A ARG* 3.5 6.2 + - - -
39A VAL* 3.8 18.4 - - + -
40A TRP 3.1 9.4 - - - +
41A ILE* 3.8 16.8 - - + -
117A VAL* 3.8 33.7 - - + +
190A TYR* 4.4 14.8 - - - +
191A LYS 4.0 3.4 - - - +
192A ALA* 2.9 34.9 + - - +
193A PRO 3.5 0.9 - - - -
194A ARG* 1.3 81.5 + - - +
196A VAL* 1.3 70.0 + - - +
216A PHE* 3.9 12.8 - - + -
219A LEU* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.9 0.9 - - - -
24A ARG* 3.3 49.1 - - + +
26A ALA* 5.0 3.6 - - + +
39A VAL* 4.4 2.0 - - - -
40A TRP* 2.8 38.6 + - + +
195A MET* 1.3 80.0 - - - +
197A LEU* 1.3 70.3 + - - +
198A ALA* 3.4 5.1 + - + +
380A GLY* 4.2 24.9 - - - +
383A LEU* 4.1 20.9 - - + -
384A LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.7 15.2 - - + +
24A ARG 2.9 10.1 + - - +
25A VAL* 3.4 8.1 - - + +
26A ALA 3.1 24.9 + - - +
37A VAL* 4.3 17.0 - - + -
38A GLY 3.4 20.6 - - - +
39A VAL* 4.2 14.4 - - + +
110A VAL* 4.4 9.4 - - + -
113A LEU* 4.6 4.7 - - + -
196A VAL* 1.3 71.8 - - - +
198A ALA* 1.3 59.3 + - - +
208A LEU* 3.8 26.4 - - + +
212A ALA* 4.0 24.9 - - + -
216A PHE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.4 4.7 - - - -
37A VAL* 3.4 3.6 - - - +
38A GLY 2.7 39.9 + - - +
40A TRP* 4.3 3.4 - - + -
196A VAL* 3.4 3.7 + - + -
197A LEU* 1.3 74.9 - - - +
199A ALA* 1.3 63.5 + - - +
208A LEU* 4.7 0.7 - - - -
376A CYS* 3.4 16.4 - - - +
379A ILE* 4.1 11.2 - - + -
380A GLY* 3.7 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 6.7 + - - -
27A SER* 3.4 18.9 - - - -
28A GLU 3.4 2.6 + - - -
36A THR 3.1 13.5 - - - +
37A VAL* 3.9 14.6 - - + -
198A ALA* 1.3 77.2 - - - +
200A ALA* 1.3 64.0 + - - +
203A LEU* 3.6 22.7 - - + -
208A LEU* 3.7 20.9 - - + -
376A CYS* 3.8 3.4 - - - -
379A ILE* 3.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.6 12.6 - - - +
35A CYS* 3.2 4.5 - - - -
36A THR 3.1 27.3 + - - -
199A ALA* 1.3 79.0 - - - +
201A GLY* 1.3 59.2 + - - +
203A LEU* 3.5 6.8 - - - +
372A THR* 3.3 29.4 - - - +
375A VAL* 4.0 17.7 - - + -
376A CYS* 4.0 11.0 - - - +
379A ILE* 4.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 3.3 9.1 + - - -
29A GLN* 3.4 4.9 - - - -
30A SER* 2.7 44.8 + - - +
34A THR 3.8 10.1 - - - -
35A CYS* 4.3 0.7 - - - -
200A ALA* 1.3 75.5 - - - +
202A GLY* 1.3 60.9 + - - -
203A LEU* 3.0 11.1 + - - +
372A THR* 4.1 6.1 - - - -
----------------------------------------------------------
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