Contacts of the helix formed by residues 3 - 15 (chain F) in PDB entry 5X6E
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 ALA 3 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR 4.6 2.4 - - - +
77A GLU* 3.9 29.4 + - + +
78A THR* 6.0 0.2 - - - -
100A ASN* 3.5 26.9 + - - +
2F ASN* 1.3 80.0 - - - +
4F GLN* 1.3 70.0 + - + +
5F ALA 3.4 0.3 + - - -
6F GLU* 3.7 4.6 + - - +
7F GLU* 3.7 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 4 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN* 5.7 3.4 - - - +
2F ASN 2.8 26.1 + - - +
3F ALA* 1.3 81.1 - - + +
5F ALA* 1.3 61.3 + - - +
7F GLU* 3.8 7.8 + - - +
8F PHE* 3.3 21.3 + - - +
112F HIS* 4.8 2.9 - - - -
115F TYR* 3.8 30.8 - - + +
118F GLN* 5.2 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 5 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ASN* 3.1 21.1 + - - +
4F GLN* 1.3 78.1 + - - +
6F GLU* 1.3 61.5 + - + +
8F PHE* 3.1 4.9 + - - +
9F LYS* 3.0 24.1 + - - +
40F PHE* 3.7 9.3 - - + -
42F TYR* 5.5 1.3 - - + -
66F ALA* 3.5 23.3 - - + -
115F TYR* 3.4 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP 4.6 5.7 - - - +
76A THR* 3.2 52.3 - - - +
77A GLU* 5.6 0.7 - - + +
78A THR* 5.5 1.6 - - - -
2F ASN* 3.2 26.1 + - - +
3F ALA* 4.1 4.0 - - - +
4F GLN 3.5 0.2 - - - -
5F ALA* 1.3 75.7 - - - +
7F GLU* 1.3 58.8 + - - +
9F LYS* 3.1 14.0 + - - +
10F LYS* 2.9 29.7 + - - +
42F TYR* 2.7 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 5.0 9.4 - - - +
36A GLU* 5.3 6.0 - - - +
76A THR 5.1 0.2 + - - -
78A THR* 4.6 19.1 + - - +
3F ALA 3.7 13.7 + - - +
4F GLN* 4.2 6.9 - - - +
5F ALA 3.3 0.4 - - - -
6F GLU* 1.3 79.7 - - - +
8F PHE* 1.3 55.0 + - - +
10F LYS* 3.9 14.2 - - + +
11F TYR* 2.9 19.2 + - - +
109F ASN* 5.4 1.7 + - - -
111F THR* 5.4 11.2 + - - +
112F HIS* 2.7 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLN 3.3 14.3 + - - +
5F ALA* 3.1 10.5 + - - +
7F GLU* 1.3 75.4 - - - +
9F LYS* 1.3 58.4 + - - +
11F TYR* 3.2 9.1 + + - +
12F LEU* 2.9 48.2 + - + +
38F CYS* 5.9 4.9 - - - -
40F PHE* 3.8 45.1 - + + -
68F VAL* 4.9 2.7 - - + -
97F ILE* 5.8 2.9 - - + -
102F LEU* 5.6 9.9 - - + -
105F LEU* 5.8 3.6 - - + -
106F LEU* 5.3 6.1 - - + -
112F HIS* 3.3 38.1 + + + -
115F TYR* 4.1 13.2 - + + -
116F VAL* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 5.8 4.6 - - - +
4B GLN* 6.1 1.6 - - - +
5F ALA 3.0 11.8 + - - +
6F GLU* 3.3 14.6 + - - +
8F PHE* 1.3 73.6 - - - +
10F LYS* 1.3 67.0 + - - +
12F LEU* 3.1 15.5 + - - +
13F GLU* 3.2 32.4 + - - +
40F PHE* 3.9 18.6 - - + -
42F TYR* 3.4 44.1 + - + -
95F TYR* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.1 46.0 + - - +
79A SER 4.2 1.2 + - - -
226B TYR* 3.7 15.3 - - + +
227B LEU* 2.4 46.8 + - + +
230B PRO* 3.7 20.3 - - + +
6F GLU 2.9 15.1 + - - +
7F GLU* 3.9 10.5 - - + +
9F LYS* 1.3 77.0 - - + +
11F TYR* 1.3 66.4 + - - +
13F GLU* 3.2 14.3 + - - +
14F THR* 3.2 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.0 20.4 - + - -
7F GLU 2.9 20.6 + - - +
8F PHE* 3.5 11.2 - + - +
9F LYS 3.2 0.2 - - - -
10F LYS* 1.3 79.8 - - - +
12F LEU* 1.3 66.0 + - + +
14F THR* 2.6 27.2 + - - -
15F ASN* 2.8 27.7 + - - -
105F LEU* 4.5 7.9 - - + -
108F LYS* 2.4 52.7 + - + +
109F ASN* 4.4 17.0 + - + -
112F HIS* 3.3 36.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PHE* 2.9 30.0 + - + +
9F LYS 3.3 9.6 - - - +
11F TYR* 1.3 82.2 - - + +
13F GLU* 1.3 55.2 + - - +
14F THR 3.3 0.3 + - - -
15F ASN* 3.4 9.1 + - - +
16F GLY 2.7 22.8 + - - +
17F ILE* 3.7 37.0 - - + +
40F PHE* 3.9 18.6 - - + -
95F TYR* 3.6 37.5 - - + -
97F ILE* 4.2 18.4 - - + -
105F LEU* 4.3 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PRO* 4.3 10.0 - - - +
231B ALA* 3.4 40.6 + - + +
234B GLY* 3.9 8.8 - - - -
9F LYS* 3.2 31.9 + - - +
10F LYS* 3.2 10.9 + - - +
12F LEU* 1.3 74.4 - - - +
14F THR* 1.3 63.8 + - - +
16F GLY* 3.0 21.7 + - - +
17F ILE 4.1 6.1 - - - +
19F PRO* 4.5 9.0 - - - +
95F TYR* 3.6 32.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.0 30.3 + - + +
230B PRO* 3.7 30.5 - - + +
233B TRP* 3.9 19.6 - - + -
234B GLY* 3.2 20.5 - - - +
237B ASN* 5.3 1.7 - - - +
10F LYS* 3.2 19.3 - - + +
11F TYR* 2.6 29.9 + - - -
13F GLU* 1.3 77.3 - - - +
15F ASN* 1.3 72.4 + - - +
16F GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 5.4 1.6 + - - -
233B TRP* 5.3 3.1 - - - -
234B GLY 5.6 0.2 - - - -
11F TYR* 2.8 43.8 + - - -
12F LEU 3.4 7.3 + - - +
13F GLU 3.2 0.6 - - - -
14F THR* 1.3 94.3 + - - +
16F GLY* 1.3 58.3 + - - +
17F ILE* 3.8 9.8 - - + +
105F LEU* 4.1 13.0 - - + +
108F LYS* 3.5 9.3 - - - +
----------------------------------------------------------
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