Contacts of the helix formed by residues 41 - 51 (chain A) in PDB entry 1LWP
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 ALA 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 4.2 0.2 - - - -
40A THR* 1.3 75.9 - - - +
42A ARG* 1.3 66.8 + - + +
43A SER* 3.2 18.4 - - - +
44A SER* 2.7 23.5 + - - +
45A GLU* 3.0 11.2 + - - +
172A TYR* 6.1 0.4 - - - +
209A TYR* 5.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 1.3 75.2 - - + +
43A SER* 1.3 96.9 + - - +
45A GLU* 2.4 44.6 - - - +
46A LYS* 3.0 13.0 + - - +
63A LEU* 4.2 2.2 - - + +
360A GLU* 3.1 56.0 + - - +
361A ARG* 3.5 41.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 3.8 9.5 - - - +
42A ARG* 1.3 116.5 - - - +
44A SER* 1.3 66.2 + - - +
46A LYS* 3.0 7.8 + - - +
47A GLN* 2.9 26.2 + - - +
172A TYR* 4.8 2.9 + - - -
209A TYR* 3.8 31.7 + - - -
360A GLU* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.5 13.2 - - - +
41A ALA* 2.7 36.9 + - - -
43A SER* 1.3 79.0 + - - +
45A GLU* 1.3 63.9 + - - +
47A GLN* 2.6 51.4 + - - +
48A ALA* 3.1 5.9 + - - +
171A ASN* 5.8 4.7 - - - -
172A TYR* 5.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 6.2 3.1 - - - -
40A THR* 5.3 10.4 + - - +
41A ALA 3.0 7.4 + - - +
42A ARG* 2.4 44.1 - - - +
44A SER* 1.3 82.7 + - - +
46A LYS* 1.3 61.1 + - - +
48A ALA* 3.4 5.7 + - - +
49A LEU* 3.0 25.4 + - - +
63A LEU* 3.9 10.5 - - + +
65A VAL* 3.0 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.0 11.6 + - - +
43A SER* 3.0 14.1 + - - +
45A GLU* 1.3 79.2 - - - +
47A GLN* 1.3 56.9 + - - +
49A LEU* 3.2 2.6 + - - +
50A MET* 2.6 80.7 + - + +
61A PRO 3.3 3.2 + - - -
62A HIS* 3.2 11.3 - - - +
63A LEU* 2.8 68.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 2.9 11.5 + - - +
44A SER* 2.6 50.7 + - - +
46A LYS* 1.3 78.6 - - - +
48A ALA* 1.3 73.8 + - + +
50A MET* 3.3 12.8 + - - +
51A SER* 3.4 10.9 + - - -
171A ASN* 5.9 3.2 - - - +
172A TYR* 4.9 8.8 + - - -
210A GLN* 4.3 20.6 + - - +
238A GLY 5.3 6.2 - - - +
239A LYS* 5.9 8.7 - - - +
240A LEU* 4.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 6.1 4.9 - - + -
44A SER 3.1 7.1 + - - +
45A GLU* 3.8 9.0 - - - +
47A GLN* 1.3 86.0 - - + +
49A LEU* 1.3 58.4 + - - +
51A SER* 2.9 27.3 + - - -
53A LEU* 4.7 1.7 - - - +
54A LYS* 5.4 0.9 - - - +
108A LYS* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU 3.0 18.2 + - - +
46A LYS* 3.7 4.9 - - - +
48A ALA* 1.3 77.2 - - - +
50A MET* 1.3 62.8 + - - +
51A SER* 3.2 7.8 + - - +
54A LYS* 3.7 35.5 - - + +
57A SER 4.6 1.3 - - - +
58A HIS* 2.2 71.2 + - + +
63A LEU* 3.1 23.3 - - + -
64A ASN 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 2.6 69.6 + - + +
47A GLN* 3.7 8.5 - - - +
48A ALA 3.2 0.2 - - - -
49A LEU* 1.3 73.4 - - - +
51A SER* 1.3 67.7 + - - +
52A GLU* 3.4 2.8 + - - -
58A HIS* 4.0 19.4 + - - -
61A PRO* 3.3 24.2 - - + +
239A LYS* 6.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 3.4 6.8 + - - -
48A ALA* 2.9 18.9 + - - -
49A LEU 3.2 6.3 - - - +
50A MET* 1.3 80.6 - - - +
52A GLU* 1.3 72.8 + - - +
53A LEU* 2.6 45.9 + - - +
54A LYS 3.3 10.6 + - - +
238A GLY* 5.8 8.1 - - - -
----------------------------------------------------------
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