Contacts of the helix formed by residues 8 - 19 (chain B) in PDB entry 4UT2
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 8 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS 3.4 6.3 + - - +
7B LEU* 1.3 71.8 - - - +
9B ILE* 1.3 61.8 + - - +
10B ASP* 3.7 8.0 + - - +
11B SER* 3.2 32.1 + - - -
12B ILE* 3.2 29.1 + - + +
34B GLU* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.2 40.1 + - + +
8B ASN* 1.3 69.8 + - - +
10B ASP* 1.3 62.8 + - - +
12B ILE* 3.2 5.0 + - + +
13B ILE* 2.9 50.7 + - + +
38B LEU* 3.8 20.0 - - + -
109B ALA* 3.9 12.3 - - + +
112B ILE* 3.7 27.1 - - + -
113B LYS* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.4 7.5 + - - +
9B ILE* 1.3 76.7 - - - +
11B SER* 1.3 58.3 + - - +
13B ILE* 3.5 6.2 + - - +
14B GLN* 3.0 30.4 + - - +
113B LYS* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.2 33.3 + - - -
10B ASP* 1.3 75.9 - - - +
12B ILE* 1.3 66.5 + - - +
14B GLN* 3.4 12.1 + - - +
15B ARG* 3.1 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.4 35.2 - - + -
8B ASN 3.2 16.2 + - - +
9B ILE* 3.5 7.9 - - - +
11B SER* 1.3 78.1 - - - +
13B ILE* 1.3 62.4 + - - +
15B ARG* 3.4 21.0 + - - +
16B LEU* 3.0 39.5 + - + +
30B LEU* 4.1 17.3 - - + +
34B GLU* 4.0 22.4 - - + +
38B LEU* 4.2 25.1 - - + -
109B ALA* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 2.9 37.8 + - + +
10B ASP* 4.0 5.8 - - - +
12B ILE* 1.3 76.1 - - - +
14B GLN* 1.3 59.7 + - - +
16B LEU* 3.3 7.4 + - - +
17B LEU* 2.8 51.8 + - + +
106B LEU* 4.4 5.2 - - + -
109B ALA* 3.6 22.2 - - + -
110B TYR* 4.1 28.0 - - + +
113B LYS* 4.0 21.8 - - + -
114B TYR* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP 3.0 18.8 + - - +
11B SER* 3.7 14.0 + - - +
12B ILE 3.3 0.2 - - - -
13B ILE* 1.3 78.5 - - - +
15B ARG* 1.3 71.0 + - - +
17B LEU* 3.3 6.0 + - - +
18B GLU* 2.8 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 5.8 0.4 - - - +
11B SER* 3.1 38.5 + - - +
12B ILE* 3.6 20.2 - - - +
14B GLN* 1.3 85.3 - - - +
16B LEU* 1.3 65.7 + - - +
18B GLU* 3.2 29.4 + - - +
19B VAL* 4.2 1.2 + - - +
28B VAL* 3.6 26.4 - - + +
29B GLN 4.8 4.5 + - - -
30B LEU* 3.7 20.5 - - + +
31B GLN* 4.8 5.1 - - - +
34B GLU* 2.9 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.0 36.7 + - + +
13B ILE* 3.6 5.4 - - - +
15B ARG* 1.3 78.0 - - - +
17B LEU* 1.3 58.4 + - - +
19B VAL* 3.5 16.8 - - - +
28B VAL* 4.0 24.2 - - + +
30B LEU* 4.1 13.7 - - + -
69B TYR* 2.8 32.2 + - - +
73B LEU* 4.7 0.7 - - - +
102B GLU* 4.1 22.9 - - + +
105B CYS* 3.9 9.2 - - + +
106B LEU* 3.6 39.5 - - + +
109B ALA* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 2.8 34.3 + - + +
14B GLN* 3.6 5.6 - - - +
16B LEU* 1.3 72.4 - - - +
18B GLU* 1.3 64.2 + - - +
19B VAL 3.2 3.1 - - - -
20B ARG* 3.1 38.0 + - - +
73B LEU* 3.8 20.4 - - + -
81B PHE* 3.8 29.8 - - + -
106B LEU* 4.0 13.2 - - + -
110B TYR* 3.4 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 2.8 30.1 + - - +
15B ARG* 3.2 25.0 + - - +
17B LEU* 1.3 77.4 - - - +
19B VAL* 1.3 59.7 + - + +
20B ARG* 3.2 7.4 + - - +
22B SER* 5.0 0.3 + - - -
26B LYS* 5.7 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG 4.6 2.2 - - - +
16B LEU 3.5 17.5 - - - +
18B GLU* 1.3 77.2 - - + +
20B ARG* 1.3 63.0 + - - +
21B GLY 3.5 0.2 + - - -
22B SER* 2.7 31.4 + - - +
26B LYS* 4.2 23.6 - - + +
27B ASN 4.1 11.4 - - - +
28B VAL* 3.6 27.4 - - + -
69B TYR* 3.9 13.7 - - + -
70B TYR* 3.5 28.6 - - + +
73B LEU* 4.4 2.0 - - + -
----------------------------------------------------------
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