Contacts of the helix formed by residues 20 - 31 (chain C) in PDB entry 3LAW
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 GLY 20 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 3.3 0.4 - - - -
19C VAL* 1.3 81.3 - - - +
21C LYS* 1.3 68.0 + - - +
23C SER* 3.9 0.3 - - - -
24C LEU* 3.0 34.3 + - - +
87C VAL* 5.0 0.4 - - - -
125C ASN* 3.8 0.7 - - - -
1400C GNP 3.0 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 3.7 34.5 - - + +
14C LEU 3.6 5.8 - - - -
15C GLY* 2.9 34.2 + - - +
16C ASP 2.7 25.3 + - - -
19C VAL* 3.4 8.9 - - + +
20C GLY* 1.3 78.2 - - - +
22C THR* 1.3 64.0 + - - +
24C LEU* 3.4 6.9 + - - +
25C MET* 3.3 20.4 + - - +
63C ASP* 3.9 12.0 - - - +
64C THR* 4.1 19.1 - - - -
66C GLY 4.5 2.7 - - - +
87C VAL* 4.0 7.6 - - + -
1400C GNP 2.6 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 1.3 73.3 - - - +
23C SER* 1.3 56.4 + - - +
25C MET* 2.9 10.6 + - + +
26C ASN* 2.7 46.7 + - - +
38C LYS 5.1 5.0 + - - +
40C THR* 3.2 1.2 + - - -
63C ASP* 2.7 21.6 + - - +
1400C GNP 3.0 15.5 + - - -
1401C MG 2.0 31.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLY 3.9 0.7 - - - -
22C THR* 1.3 78.0 - - - +
24C LEU* 1.3 57.0 + - - -
26C ASN* 3.9 5.8 - - - +
27C GLN* 2.8 33.4 + - - +
32C LYS 4.4 1.9 - - - +
33C PHE* 4.0 14.2 - - - +
34C SER 4.9 3.0 + - - -
156C ALA* 3.8 12.9 - - - +
1400C GNP 2.7 54.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 5.6 2.7 - - + -
20C GLY 3.0 23.6 + - - +
21C LYS* 3.7 5.2 - - - +
22C THR 3.2 0.4 - - - -
23C SER* 1.3 76.2 - - - +
25C MET* 1.3 56.4 + - - +
27C GLN* 3.8 3.0 - - - +
28C TYR* 3.1 30.0 + - - +
87C VAL* 3.8 24.5 - - + -
123C LEU* 4.1 16.8 - - + -
125C ASN* 3.5 35.7 - - + +
154C THR* 3.8 11.0 - - - +
156C ALA* 3.8 12.6 - - + -
162C VAL* 4.0 24.4 - - + +
166C PHE* 4.1 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.6 5.3 - - + +
21C LYS 3.3 9.5 + - - +
22C THR* 2.9 11.3 + - + +
24C LEU* 1.3 78.9 - - - +
26C ASN* 1.3 69.1 + - - +
28C TYR* 3.4 3.7 + - - -
29C VAL* 2.8 43.8 + - + +
44C ASP 5.0 1.3 - - - +
45C PHE 5.6 0.4 - - - -
46C LEU* 3.7 31.9 - - + +
61C ILE* 3.7 44.9 - - + +
63C ASP* 3.7 37.7 - - + +
166C PHE* 5.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 2.7 30.8 + - - +
23C SER* 3.9 5.8 - - - +
25C MET* 1.3 87.1 - - - +
27C GLN* 1.3 59.7 + - - +
29C VAL* 5.1 0.2 - - - -
30C ASN* 2.9 48.3 + - - +
31C LYS 3.1 6.2 + - - -
32C LYS* 3.4 28.2 + - - +
46C LEU* 4.3 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER 2.8 22.4 + - - +
24C LEU* 3.8 6.5 - - - +
26C ASN* 1.3 71.1 - - - +
28C TYR* 1.3 59.0 + - - +
31C LYS* 2.9 41.9 + - - +
32C LYS 3.3 22.1 + - - +
33C PHE* 4.1 4.4 - - - +
156C ALA* 3.0 27.9 + - - +
157C LYS 4.3 3.2 + - - -
159C ALA* 3.3 35.9 - - + +
162C VAL* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU 3.1 18.6 + - - +
25C MET* 3.8 2.7 - - - +
27C GLN* 1.3 79.0 - - - +
29C VAL* 1.3 63.2 + - + +
31C LYS* 4.7 3.6 + - - +
48C LYS* 2.8 59.1 + - + +
50C VAL* 4.0 16.1 - - - +
59C MET* 3.3 34.1 - - + +
61C ILE* 4.1 13.0 - - + -
162C VAL* 3.9 16.6 - - + -
163C GLU* 3.4 28.1 + - - +
166C PHE* 3.4 47.1 + + + +
167C GLN* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C MET* 2.8 23.3 + - + +
28C TYR* 1.3 80.6 - - + +
30C ASN* 1.3 73.9 + - - +
31C LYS* 3.7 4.5 + - - +
46C LEU* 3.9 28.9 - - + -
47C THR 3.6 21.1 - - - +
48C LYS* 4.4 18.2 - - + +
61C ILE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASN* 2.9 21.2 + - - +
29C VAL* 1.3 85.3 - - - +
31C LYS* 1.3 74.2 + - - +
32C LYS* 3.1 42.1 + - - +
46C LEU* 3.7 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 2.9 37.1 + - - +
28C TYR 5.2 3.4 - - - +
29C VAL 5.1 4.0 - - - +
30C ASN* 1.3 81.8 - - - +
32C LYS* 1.3 60.2 + - - +
----------------------------------------------------------
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