Contacts of the helix formed by residues 17 - 24 (chain A) in PDB entry 4LZ6
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 LYS 17 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 3.8 12.3 - - + +
16A PRO* 1.3 91.5 - - + +
18A LEU* 1.3 60.9 + - - +
19A LEU 3.1 0.9 - - - -
20A ARG* 3.4 19.3 - - + -
21A SER* 2.6 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.3 33.4 - - + -
12A THR 3.3 19.7 - - - +
13A GLU* 4.1 7.0 - - - +
14A ALA* 3.5 21.5 + - + +
15A ILE* 3.7 27.8 - - + -
17A LYS* 1.3 78.8 - - - +
19A LEU* 1.3 49.6 + - - +
21A SER* 4.5 1.7 - - - -
22A LEU* 2.8 44.1 + - + +
302A ILE* 3.3 26.5 - - + -
305A TYR* 3.0 28.5 - - + +
306A ASN* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 5.6 1.3 - - + -
16A PRO* 4.1 8.4 - - + +
17A LYS 3.1 1.2 - - - +
18A LEU* 1.3 76.7 - - - +
20A ARG* 1.3 72.7 + - - +
22A LEU* 2.9 1.5 + - - -
23A SER* 2.8 29.4 + - - -
295A ILE* 5.5 2.9 - - + -
298A ALA* 3.4 25.4 - - + -
299A MET* 3.8 30.7 - - + +
302A ILE* 3.4 17.1 - - + +
318A THR* 3.8 23.1 - - + -
321A LEU* 3.2 35.7 - - + -
322A GLY* 4.5 2.0 - - - -
325A VAL* 4.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO 2.9 23.7 + - - +
17A LYS* 3.3 22.5 + - + +
19A LEU* 1.3 80.2 - - - +
21A SER* 1.3 60.7 + - - +
23A SER* 2.8 24.0 + - - -
24A ILE* 3.3 15.1 - - - +
295A ILE* 4.8 16.8 - - - +
321A LEU* 4.0 27.0 - - - +
325A VAL* 4.6 18.0 - - - +
329A PHE* 6.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 5.1 8.8 + - - -
10A LEU* 5.7 5.5 - - - +
17A LYS* 2.6 22.1 + - - -
18A LEU* 4.5 2.0 - - - -
20A ARG* 1.3 75.9 - - - +
22A LEU* 1.3 62.6 + - - +
24A ILE* 4.1 4.8 - - - +
25A PRO* 2.8 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 6.2 0.7 - - - +
10A LEU* 5.4 11.0 - - + -
18A LEU* 2.8 25.4 + - + +
19A LEU 2.9 3.0 + - - +
21A SER* 1.3 82.0 - - - +
23A SER* 1.3 72.6 + - - +
25A PRO* 3.2 10.4 - - + +
26A ALA* 4.0 3.1 + - - +
161A ARG 5.6 0.7 - - - +
164A GLY* 3.9 16.4 - - - +
166A ALA* 3.7 31.1 - - + +
297A GLN 4.7 2.6 - - - +
298A ALA* 3.2 37.5 + - + +
301A PRO* 4.1 16.2 - - + -
302A ILE* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 2.8 14.5 + - - -
20A ARG* 2.8 21.4 + - - -
22A LEU* 1.3 79.2 - - - +
24A ILE* 1.3 69.2 + - - +
25A PRO 2.7 12.1 - - - -
26A ALA* 2.7 17.3 + - - +
27A MET* 3.6 7.8 + - - -
294A GLY 3.7 15.3 - - - -
295A ILE* 3.7 29.7 - - - +
298A ALA* 3.6 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG 3.3 16.8 - - - +
21A SER* 4.1 5.4 - - - +
23A SER* 1.3 85.9 + - - +
25A PRO* 1.3 83.1 - - + +
27A MET* 3.0 16.2 - - + +
28A ILE* 2.7 50.9 + - + +
170A MET* 4.4 6.5 - - + -
----------------------------------------------------------
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