Contacts of the strand formed by residues 1 - 13 (chain E) in PDB entry 1H48
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 MET 1 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1D LEU 5.0 9.2 - - - +
1D MET* 4.4 28.0 - - + +
0E GLU* 1.3 93.8 - - - +
2E ARG* 1.3 69.8 + - - +
153E LEU* 3.6 18.6 - - + -
154E LEU 3.2 12.1 - - - +
155E ILE* 4.6 19.3 - - + -
1F MET* 3.5 39.1 - - + +
92F GLY* 5.4 3.6 - - - -
93F ASN* 4.1 1.6 - - - +
153F LEU* 3.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 2 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E GLU* 4.4 16.8 + - - +
1E MET* 1.3 80.7 - - - +
3E ILE* 1.3 61.6 + - - +
50E GLY 5.1 0.6 + - - -
51E ALA* 2.7 36.4 + - + +
53E ALA* 3.7 13.5 - - - +
89E TYR* 3.3 38.0 + - + -
152E ALA 3.7 0.5 - - - +
153E LEU* 3.3 8.7 - - - +
154E LEU* 2.8 41.3 + - + +
92F GLY 4.5 2.1 + - - +
93F ASN* 3.2 30.8 - - + +
94F VAL 5.6 0.6 + - - -
125F ASP* 2.7 28.5 + - - -
126F ASP* 3.0 28.3 + - - +
127F VAL 5.7 0.2 - - - -
128F ASN* 5.9 0.4 - - - +
153F LEU* 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 3 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 3.9 15.3 - - + -
2E ARG* 1.3 73.0 - - - +
4E GLY* 1.3 64.2 + - - +
51E ALA* 3.3 9.8 - - - -
151E VAL* 5.5 2.2 - - + -
152E ALA 3.4 5.4 - - - +
153E LEU* 4.7 0.7 - - - -
3F ILE* 3.3 41.3 - - + -
93F ASN* 2.8 47.2 + - - +
94F VAL* 5.2 0.4 - - - -
95F ASP* 4.1 4.9 - - - +
151F VAL* 3.6 35.2 - - + +
152F ALA* 4.0 4.9 - - - +
153F LEU* 3.8 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 4 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 1.3 77.4 - - - +
5E HIS* 1.3 61.4 + - - +
47E ALA* 3.2 24.5 - - - -
51E ALA* 3.5 8.7 - - - +
151E VAL* 3.3 8.1 - - - +
152E ALA 3.0 30.2 + - - +
95F ASP* 3.7 5.4 - - - -
151F VAL* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D HIS* 5.1 1.8 - + - -
203D MN 4.5 0.7 - - - -
4E GLY* 1.3 75.2 - - - +
6E GLY* 1.3 75.1 + - - +
7E PHE* 4.0 9.9 - - + -
47E ALA* 3.5 7.9 - - - +
149E GLU* 2.9 25.5 + - + -
150E ALA 3.5 10.5 - - - -
151E VAL* 4.2 12.3 - - + -
5F HIS* 5.1 2.2 - + - -
95F ASP* 2.8 12.7 + - - +
97F THR* 3.3 16.5 + - - +
130F LYS* 2.7 33.2 + - - +
149F GLU* 3.3 38.5 + - + +
150F ALA 5.5 0.2 - - - -
151F VAL* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E HIS* 1.3 82.1 - - - +
7E PHE* 1.3 61.8 + - - +
43E ALA* 3.4 24.7 - - - -
46E ASP* 3.8 6.3 - - - -
47E ALA* 3.5 4.6 - - - +
149E GLU* 3.2 7.1 - - - +
150E ALA 2.9 30.4 + - - +
97F THR* 5.0 0.7 - - - -
130F LYS* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E HIS* 4.0 13.7 - - + -
6E GLY* 1.3 74.0 - - - +
8E ASP* 1.3 63.9 + - - +
9E VAL* 3.7 31.2 - - + -
43E ALA* 4.2 2.9 - - - +
46E ASP* 4.1 12.8 + - - +
99E ILE* 5.2 0.2 - - + -
139E PHE* 5.3 1.6 - + - -
147E ALA* 4.2 12.8 - - + -
148E CYS 3.4 9.4 - - - -
149E GLU* 3.6 23.6 - - + -
904E GPP 3.5 46.9 - - + -
97F THR* 4.4 14.0 - - + +
99F ILE* 3.7 25.4 - - + -
132F THR* 3.7 24.4 - - + +
133F THR 5.5 0.2 - - - -
134F THR* 4.2 11.9 - - + -
149F GLU* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 1.3 80.9 - - - +
9E VAL* 1.3 82.4 + - - +
10E HIS* 3.6 2.1 + - - -
39E VAL* 3.4 22.6 - - - +
42E HIS* 2.7 19.0 + - + +
43E ALA* 3.9 11.2 - - + +
46E ASP* 5.6 1.8 - - - +
147E ALA* 3.2 4.5 - - - +
148E CYS 2.8 38.3 + - - +
902E CDI 3.4 6.7 + - - -
903E ZN 2.4 34.4 - - - -
132F THR* 4.2 5.1 + - - -
133F THR 5.1 0.3 - - - +
901F C5P 4.1 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 3.7 28.5 - - + -
8E ASP* 1.3 93.0 + - - +
10E HIS* 1.3 75.1 + - - +
39E VAL* 4.0 0.4 - - - -
139E PHE* 3.7 34.5 - - + -
146E ILE 3.4 6.3 - - - +
147E ALA* 3.7 5.4 - - + -
133F THR 4.5 3.7 + - - +
134F THR* 3.6 37.7 - - + +
135F GLU* 3.3 17.3 - - - +
137F LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ASP* 4.1 0.2 - - - -
9E VAL* 1.3 82.7 + - - +
11E ALA* 1.3 61.0 + - - +
31E LEU* 3.7 18.1 - - + +
32E LEU 3.4 20.9 + - - +
33E ALA* 4.0 5.1 - - + -
37E GLY* 3.5 24.3 - - - -
39E VAL* 3.7 18.6 - - + +
42E HIS* 3.2 9.1 + - - -
145E GLY* 3.3 1.0 - - - -
146E ILE 3.0 32.3 + - - +
902E CDI 3.2 29.4 - - - -
903E ZN 2.3 36.4 - - - -
135F GLU* 4.3 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E HIS* 1.3 75.3 - - - +
12E PHE* 1.3 65.7 + - - +
31E LEU* 3.5 6.2 - - - +
32E LEU* 3.1 40.0 + - + +
144E GLU 3.5 9.0 - - - +
135F GLU* 4.4 15.2 - - + +
137F LEU* 3.7 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ALA* 1.3 75.6 - - - +
13E GLY* 1.3 58.8 + - - +
18E ILE* 4.5 4.5 - - + -
27E TYR* 3.7 34.5 - + - -
29E LYS* 3.9 19.3 - - + -
30E GLY 3.3 9.9 - - - +
31E LEU* 3.5 23.8 - - + -
32E LEU* 4.1 9.1 - - - +
102E ALA 3.6 19.5 - - - -
143E GLY* 2.8 34.5 - - - +
144E GLU* 3.1 11.6 + - - +
145E GLY 3.5 24.7 - - - -
146E ILE* 3.4 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ALA 3.7 2.0 + - - -
12E PHE* 1.3 76.0 - - - +
14E GLY* 1.3 65.4 + - - -
15E GLU 3.6 0.5 + - - +
29E LYS* 4.6 5.5 - - - +
30E GLY* 2.8 33.2 + - - +
31E LEU 3.8 1.4 + - - -
32E LEU* 3.6 26.2 + - - +
----------------------------------------------------------
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