Contacts of the helix formed by residues 9 - 22 (chain B) in PDB entry 1FBA
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 9 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 3.7 1.2 + - - -
8B SER* 1.3 71.9 - - - +
10B GLU* 1.3 71.1 + - - +
12B GLN* 3.2 14.2 + - + +
13B ASP* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.7 19.5 - - - +
9B LYS* 1.3 86.0 + - - +
11B LEU* 1.3 60.7 + - - +
13B ASP* 3.9 5.2 - - - +
14B GLU* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.7 25.4 - - + -
7B PRO* 4.1 12.6 - - + -
8B SER* 3.1 19.8 + - - +
10B GLU* 1.3 78.0 - - - +
12B GLN* 1.3 66.2 + - - +
14B GLU* 3.3 5.6 + - + +
15B LEU* 3.0 42.1 + - + +
178B GLN 3.5 27.4 - - - +
179B SER 4.7 4.5 - - - +
181B ARG* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.2 15.0 - - - +
7B PRO* 2.7 35.2 + - + +
8B SER 2.9 17.2 + - - +
9B LYS* 3.2 11.3 + - - +
11B LEU* 1.3 76.6 - - - +
13B ASP* 1.3 60.4 + - - +
16B ARG* 2.9 39.1 + - - +
222B TYR* 3.5 48.2 + - + +
258C ARG* 5.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 2.9 54.6 + - - +
10B GLU* 3.9 6.2 - - - +
12B GLN* 1.3 79.5 - - - +
14B GLU* 1.3 56.9 + - - +
16B ARG* 2.9 32.6 + - - +
17B GLU* 2.9 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU 3.2 15.8 + - - +
11B LEU* 3.3 6.7 + - + +
12B GLN 3.3 0.2 - - - -
13B ASP* 1.3 78.8 - - - +
15B LEU* 1.3 63.6 + - + +
17B GLU* 3.4 10.2 + - - +
18B ILE* 3.1 35.4 + - + +
138B LYS* 2.7 28.6 + - - -
143B ASP* 4.6 0.2 - - - +
181B ARG* 2.8 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 5.8 2.2 - - + -
11B LEU* 3.0 37.3 + - + +
12B GLN* 3.9 2.7 - - - +
14B GLU* 1.3 73.1 - - + +
16B ARG* 1.3 66.2 + - - +
18B ILE* 3.4 2.1 + - + -
19B ALA* 3.1 21.3 + - - +
178B GLN* 3.7 38.6 - - + +
181B ARG* 3.8 10.5 - - + +
182B ILE 3.7 40.6 - - - +
183B VAL* 3.4 19.3 - - + +
222B TYR* 4.5 9.6 - - + -
225B GLY* 3.9 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 2.9 22.0 + - - +
13B ASP* 2.9 37.9 + - - +
15B LEU* 1.3 76.4 - - - +
17B GLU* 1.3 63.9 + - - +
19B ALA* 3.4 2.4 + - - +
20B GLN* 3.0 60.4 + - + +
222B TYR* 2.9 29.3 + - + +
224B GLU* 3.9 32.3 - - + +
225B GLY* 4.3 0.8 - - - -
265B THR* 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 2.9 34.5 + - - +
14B GLU* 3.7 8.8 - - - +
16B ARG* 1.3 84.9 + - - +
18B ILE* 1.3 62.1 + - + +
20B GLN* 3.7 12.6 - - - +
21B LYS* 3.1 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.1 32.1 + - + +
15B LEU* 4.9 0.7 - - - -
16B ARG 3.4 0.2 - - - -
17B GLU* 1.3 76.9 - - + +
19B ALA* 1.3 62.8 + - - +
21B LYS* 3.2 13.1 + - + +
22B ILE* 3.1 38.8 + - + +
103B ILE* 4.6 7.6 - - + -
138B LYS* 3.8 17.9 - - - +
143B ASP* 3.6 47.6 - - + +
181B ARG 4.3 3.1 - - - +
183B VAL* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 3.1 16.7 + - - +
16B ARG 3.8 2.5 - - - +
18B ILE* 1.3 78.4 - - - +
20B GLN* 1.3 62.4 + - - +
22B ILE* 3.2 13.1 + - - +
23B VAL* 3.4 15.6 + - - +
183B VAL* 4.2 8.7 - - + +
224B GLU 4.0 6.5 - - - +
226B THR 4.3 4.7 - - - +
227B LEU* 4.0 23.8 - - + +
265B THR* 3.5 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.0 51.0 + - + +
17B GLU* 3.7 12.9 - - - +
19B ALA* 1.3 75.6 - - - +
21B LYS* 1.3 63.5 + - + +
23B VAL* 3.4 6.8 + - - +
24B ALA* 3.2 19.8 + - - +
265B THR* 3.8 17.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.1 30.0 + - - +
18B ILE* 3.2 11.9 + - + +
20B GLN* 1.3 77.4 - - + +
22B ILE* 1.3 61.3 + - - +
24B ALA* 3.4 19.3 + - - +
27B LYS* 4.9 1.0 + - - +
74B SER* 3.7 9.9 - - - -
103B ILE* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.1 24.1 + - + +
19B ALA* 3.2 7.8 + - - +
21B LYS* 1.3 76.3 - - - +
23B VAL* 1.3 62.4 + - + +
24B ALA 3.4 0.8 + - - -
27B LYS 4.1 8.7 - - - +
28B GLY* 4.5 2.4 - - - -
29B ILE* 3.5 34.8 - - + -
74B SER* 2.6 29.2 + - - +
75B GLY 5.6 0.2 - - - +
103B ILE* 4.1 15.0 - - + -
144B PHE* 3.5 45.1 - - + -
183B VAL* 5.0 0.7 - - + -
227B LEU* 3.8 23.6 - - + -
268B THR* 4.8 0.4 - - + -
298B THR* 4.9 0.3 - - - +
----------------------------------------------------------
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