Contacts of the helix formed by residues 14 - 24 (chain A) in PDB entry 3L7N
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 PRO 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.6 30.5 - - + -
7A LEU* 4.0 19.3 - - + -
12A GLU 3.9 0.2 - - - -
13A ALA* 1.3 87.6 - - + +
15A GLY* 1.3 64.9 + - - +
16A ALA 3.2 0.7 + - - -
17A TYR* 2.8 26.7 + - - +
18A LEU* 3.7 32.5 - - + -
30A MET* 4.0 11.4 - - + -
52A MET* 3.9 14.3 - - + -
181A GLU* 3.9 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 2.9 9.3 + - - +
14A PRO* 1.3 74.8 - - - +
16A ALA* 1.3 64.1 + - - -
18A LEU* 2.9 18.4 + - - +
19A ALA* 3.1 10.9 + - - +
181A GLU 3.8 1.6 - - - -
183A THR* 5.1 3.6 - - - -
186A LEU* 3.4 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.2 1.0 + - - -
15A GLY* 1.3 71.0 - - - -
17A TYR* 1.4 57.4 + - - +
19A ALA* 3.7 9.4 - - - -
20A TRP* 2.9 30.1 + - - +
181A GLU* 3.1 30.2 + - - +
183A THR* 4.9 4.7 - - + +
222A ASN* 4.0 16.6 - - + +
225A LEU* 4.2 7.9 - - + -
226A TYR* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.8 21.2 - - + -
14A PRO 2.8 13.6 + - - +
16A ALA* 1.4 70.7 - - - +
18A LEU* 1.4 58.8 + - - +
20A TRP* 3.6 5.7 - - - +
21A ALA* 2.9 28.4 + - - +
50A ILE* 4.4 10.2 - - + +
52A MET* 3.3 18.2 - - + -
88A VAL* 4.0 18.4 - - + -
90A VAL* 3.5 26.8 - - + +
176A PHE* 3.9 20.7 - + - +
178A CYS 5.1 0.9 + - - -
180A LEU 5.3 2.1 + - - -
181A GLU* 3.4 44.4 + - + -
225A LEU* 3.7 30.4 - - + +
229A LEU* 3.9 27.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
5A PHE* 3.8 11.1 - - + -
14A PRO* 3.5 21.1 + - + -
15A GLY* 2.9 9.0 + - - +
17A TYR* 1.4 79.3 - - - +
19A ALA* 1.4 51.4 + - - +
21A ALA* 3.0 3.0 + - - +
22A ALA* 2.8 36.1 + - + +
28A VAL* 3.8 38.1 - - + -
30A MET* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 3.1 11.4 + - - +
16A ALA* 3.8 9.2 - - - +
17A TYR 3.4 0.2 - - - -
18A LEU* 1.4 72.9 - - - +
20A TRP* 1.3 55.2 + - - +
22A ALA* 3.0 8.0 + - - +
23A LEU* 2.8 47.7 + - + +
226A TYR* 3.8 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.6 24.0 - - + -
16A ALA 2.9 18.2 + - - +
17A TYR 3.6 6.3 - - - +
19A ALA* 1.3 76.4 - - - +
21A ALA* 1.3 79.6 + - + +
23A LEU* 3.8 4.9 - - - -
24A ARG* 2.9 64.9 + - + +
26A HIS* 3.5 24.9 - + - -
48A MET* 4.5 8.5 - - + -
50A ILE* 5.5 2.5 - - + -
226A TYR* 3.6 30.6 - + + -
229A LEU* 3.4 42.0 - - + +
230A ASP* 3.2 21.6 + - - -
233A THR* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.7 25.1 - - + -
5A PHE* 4.6 4.3 - - + -
17A TYR 2.9 16.1 + - - +
18A LEU* 3.0 9.8 + - - +
20A TRP* 1.3 84.3 - - + +
22A ALA* 1.3 60.6 + - - +
24A ARG 3.8 0.2 + - - -
25A GLY 3.4 1.4 + - - -
26A HIS* 2.9 36.4 + - + +
28A VAL* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.8 20.0 + - + +
19A ALA* 3.0 10.3 + - - +
21A ALA* 1.3 73.4 - - - +
23A LEU* 1.4 62.3 + - + +
25A GLY* 3.0 19.6 + - - -
26A HIS 5.0 2.9 - - - +
28A VAL* 5.1 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 2.8 35.2 + - + +
20A TRP* 3.9 3.4 - - - +
22A ALA* 1.4 74.4 - - + +
24A ARG* 1.3 81.8 + - - +
25A GLY* 3.1 5.4 + - - -
226A TYR* 4.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.7 2.3 - - - +
20A TRP* 2.9 43.6 + - + +
23A LEU* 1.3 102.1 - - - +
25A GLY* 1.3 62.4 + - - +
26A HIS* 3.4 28.9 + - + +
223A GLN* 5.5 2.8 - - - +
226A TYR* 3.6 27.3 - - - +
230A ASP* 2.8 35.8 + - - +
----------------------------------------------------------
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