Contacts of the strand formed by residues 7 - 14 (chain E) in PDB entry 1N34
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 GLU 7 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ASP 3.8 3.3 + - - +
6E PHE* 1.3 73.3 - - - +
8E GLU* 1.3 88.1 + - - +
9E LYS* 5.0 3.8 - - - +
34E VAL* 3.4 2.1 - - - +
35E GLY 3.0 28.6 + - - +
36E ASP* 4.8 6.2 - - - +
37E ARG* 2.7 53.5 + - - +
112E LEU* 4.1 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E PHE 4.8 4.0 - - - +
7E GLU* 1.3 89.8 - - - +
9E LYS* 1.3 72.6 + - - +
10E MET 4.6 0.7 + - - -
32E VAL* 4.1 9.5 - - + +
33E VAL 2.7 24.5 - - - +
34E VAL* 3.0 19.3 - - + +
59E GLY* 6.5 0.7 - - - -
63E ARG* 5.3 8.9 + - - +
112E LEU* 4.1 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASP* 3.9 24.6 + - - -
57D ARG* 5.0 4.2 - - - +
7E GLU* 5.0 2.9 - - - +
8E GLU* 1.3 81.9 - - - +
10E MET* 1.3 61.5 + - - +
11E ILE 3.2 3.6 + - - +
32E VAL* 2.8 19.3 - - - +
33E VAL* 3.2 23.9 + - + +
37E ARG* 4.3 8.3 - - - +
107E ARG* 5.1 1.0 - - - +
108E ALA* 4.7 18.1 - - + +
111E GLU* 3.0 29.3 + - - +
112E LEU* 3.9 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ARG* 4.3 31.7 + - - +
8E GLU* 4.6 1.2 + - - -
9E LYS* 1.3 70.5 - - - +
11E ILE* 1.3 65.9 + - - +
12E LEU* 3.3 20.6 - - - +
13E ILE* 3.1 42.4 - - + +
31E LEU 3.3 8.3 - - - +
32E VAL* 3.9 7.4 - - + -
55E VAL* 4.3 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS 3.2 6.1 + - - -
10E MET* 1.3 74.4 - - - +
12E LEU* 1.3 81.8 + - + +
31E LEU* 2.6 53.5 + - + +
33E VAL* 3.2 28.7 - - + +
104E ALA 4.3 2.9 - - - +
105E VAL* 3.8 44.0 - - + +
108E ALA* 3.9 14.4 - - + -
109E ILE* 4.7 3.1 - - + -
128E PRO* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E MET* 3.3 6.0 - - - -
11E ILE* 1.3 89.3 - - + +
13E ILE* 1.3 90.0 + - - +
14E ARG* 4.1 15.5 - - + +
31E LEU* 2.5 48.8 + - + +
45E PHE* 4.8 3.8 - - + -
105E VAL* 5.9 1.1 - - + -
128E PRO* 4.3 20.4 - - + -
129E ILE* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E MET* 3.1 39.6 - - + +
12E LEU* 1.3 80.7 - - - +
14E ARG* 1.3 66.9 + - - +
28E PHE* 5.5 2.2 - - + -
29E GLY 2.4 25.4 - - - +
30E ALA* 3.1 21.1 - - + -
31E LEU 3.5 0.2 - - - +
51E VAL* 4.1 23.6 - - + -
55E VAL* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A U 4.3 22.9 + - - +
18A C 4.0 14.5 + - - -
1079A G 3.3 36.0 + - - -
1080A A 3.9 16.1 + - - -
12E LEU* 4.4 16.2 - - + -
13E ILE* 1.3 77.4 - - - +
15E ARG* 1.3 60.2 + - - +
16E THR* 3.9 17.6 - - - +
28E PHE* 3.3 12.5 - - - -
29E GLY* 2.3 46.8 + - - +
45E PHE* 3.8 24.5 - - + -
129E ILE* 4.0 17.2 - - - +
----------------------------------------------------------
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