Contacts of the helix formed by residues 14 - 22 (chain A) in PDB entry 3FA9
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 ASN 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 1.3 80.5 + - + +
15A PHE* 1.3 58.1 + - - +
17A GLU* 3.0 26.2 + - - +
18A LEU* 3.0 28.2 + - - +
128A VAL* 3.7 12.9 - - - +
129A VAL 2.9 24.8 + - - +
130A CYS* 3.9 2.2 - - - +
34B ALA* 3.3 15.4 + - + +
37B SER* 3.4 5.5 + - - -
57B THR* 2.7 24.8 + - - -
58B VAL* 2.7 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.9 16.1 + - - +
13A GLU 3.3 1.4 - - - -
14A ASN* 1.3 74.1 - - - +
16A GLU* 1.3 66.1 + - - +
17A GLU* 3.5 1.0 + - - -
18A LEU* 3.2 7.0 + - + +
19A LEU* 3.0 49.0 + - + +
32A ALA* 3.9 24.5 - - + -
33A VAL* 3.8 18.6 - - + -
76A VAL* 4.2 23.6 - - + -
123A MET* 4.7 4.3 - - - -
130A CYS* 3.6 28.0 - - + -
132A LYS* 3.7 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 1.3 79.9 - - - +
17A GLU* 1.3 64.4 + - + +
19A LEU* 3.2 10.0 + - - +
20A LYS* 2.7 33.2 + - + +
29A ARG* 3.1 42.4 + - + +
30A LYS* 3.2 35.7 + - - -
33A VAL* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.0 41.3 + - - +
15A PHE 3.5 0.5 + - - -
16A GLU* 1.3 87.7 + - + +
18A LEU* 1.3 61.8 + - - +
20A LYS* 3.3 10.6 + - + +
21A VAL* 3.1 31.2 + - + +
128A VAL* 5.1 1.3 - - - -
57B THR* 3.2 30.1 - - - +
58B VAL* 3.9 14.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
14A ASN* 3.0 19.8 + - - +
15A PHE* 3.4 9.0 - - + +
17A GLU* 1.3 72.6 - - - +
19A LEU* 1.3 67.2 + - + +
21A VAL* 3.2 5.8 - - + +
22A LEU* 3.2 38.8 + - + +
76A VAL* 4.3 23.6 - - + -
123A MET* 4.2 17.5 - - + +
124A THR 5.6 0.2 - - - -
125A ALA* 3.8 28.5 - - + -
128A VAL* 3.9 31.4 - - + +
130A CYS* 3.7 24.2 - - + +
----------------------------------------------------------
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 PHE* 3.0 36.6 + - + +
16A GLU* 3.5 10.1 - - - +
18A LEU* 1.3 76.0 - - + +
20A LYS* 1.3 63.3 + - - +
22A LEU* 3.2 14.8 + - + +
24A VAL* 3.1 49.9 + - + +
29A ARG* 4.0 17.5 - - - +
32A ALA* 3.8 29.6 - - + -
76A VAL* 3.9 33.4 - - + +
77A ASP* 5.4 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 2.7 21.4 + - + +
17A GLU* 3.5 12.3 - - + +
18A LEU 3.2 0.2 - - - -
19A LEU* 1.3 73.4 - - - +
21A VAL* 1.3 61.0 + - + +
23A GLY* 2.9 20.6 + - - -
24A VAL 4.2 0.7 + - - +
29A ARG* 3.6 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.1 15.1 + - + +
18A LEU* 3.2 19.3 - - + +
20A LYS* 1.3 78.3 - - + +
22A LEU* 1.3 65.8 + - + +
23A GLY 3.2 0.4 + - - -
125A ALA 5.9 0.4 - - - +
128A VAL* 3.8 27.6 - - + -
38B LYS* 5.0 12.8 - - - +
57B THR* 4.6 18.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
18A LEU* 3.2 31.9 - - + +
19A LEU* 3.5 13.5 - - + +
20A LYS 3.1 1.2 - - - -
21A VAL* 1.3 82.3 - - + +
23A GLY* 1.3 59.5 + - - +
24A VAL* 3.5 5.1 - - + +
76A VAL* 3.5 32.3 - - + -
77A ASP* 4.3 25.2 - - + +
105A PRO* 3.9 22.4 - - + -
125A ALA* 3.8 23.8 - - + -
----------------------------------------------------------
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