Contacts of the helix formed by residues 7 - 16 (chain B) in PDB entry 1XHU
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 ILE 7 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE 3.8 6.3 - - - +
4B ILE* 2.5 28.8 + - - +
5B LYS 2.7 0.2 + - - -
6B PRO* 1.3 82.7 - - + +
8B TYR* 1.3 63.5 + - - -
9B GLN 3.2 3.1 - - - -
10B ASP* 2.8 27.1 + - + +
11B ILE* 3.1 22.1 + - + +
44B PHE* 4.8 3.8 - - + -
45B LEU* 5.1 1.3 - - + -
48B ASN* 4.4 17.7 - - + +
49B LEU* 3.7 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.0 8.0 + - + -
5B LYS* 2.7 30.8 + - + +
7B ILE* 1.3 71.3 - - - +
9B GLN* 1.3 58.1 + - + +
11B ILE* 2.8 17.1 + - + +
12B ASN* 2.7 54.9 + - + -
169B LEU* 3.7 9.0 - - + -
185B THR* 2.6 61.1 + - + +
186B SER* 2.9 3.1 + - - -
187B PHE* 3.4 41.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS 4.7 0.4 + - - -
7B ILE* 3.1 1.2 + - - -
8B TYR* 1.3 87.4 - - + +
10B ASP* 1.3 60.2 + - - +
12B ASN* 3.6 6.5 + - - +
13B SER* 3.2 25.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
7B ILE* 2.8 23.5 + - + +
9B GLN* 1.3 75.8 - - - +
11B ILE* 1.3 64.0 + - - +
13B SER* 3.5 4.6 + - - -
14B ILE* 2.9 45.2 + - - +
44B PHE* 4.2 12.2 - - + -
48B ASN* 5.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.4 25.4 - - + -
7B ILE* 3.6 17.9 - - + +
8B TYR* 2.8 13.5 + - + +
10B ASP* 1.3 74.7 - - - +
12B ASN* 1.3 58.5 + - - +
14B ILE* 2.9 4.4 + - - +
15B LEU* 2.7 58.4 + - + +
41B VAL* 5.6 2.2 - - + -
44B PHE* 2.9 32.3 - - + -
45B LEU* 3.4 29.6 - - + -
169B LEU* 5.1 14.4 - - + -
185B THR* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 2.7 37.1 + - + +
9B GLN* 3.7 7.6 - - - +
11B ILE* 1.3 74.2 - - - +
13B SER* 1.3 57.1 + - - +
15B LEU* 4.7 0.9 - - - +
16B ILE* 2.9 55.5 + - - +
185B THR* 2.7 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN 3.2 12.6 + - - -
10B ASP* 3.6 12.6 - - - -
11B ILE 3.0 0.6 - - - -
12B ASN* 1.3 76.6 - - - +
14B ILE* 1.3 70.7 + - - +
16B ILE* 3.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 2.9 37.0 - - - +
11B ILE 2.9 6.9 + - - +
13B SER* 1.3 82.7 - - - +
15B LEU* 1.3 65.7 + - + +
16B ILE 4.2 1.6 - - - +
18B GLN* 3.0 38.1 + - - +
40B LEU 5.9 0.2 - - - +
44B PHE* 3.6 40.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
11B ILE* 2.7 38.9 + - + +
12B ASN 4.3 1.8 - - - +
14B ILE* 1.3 78.1 - - + +
16B ILE* 1.3 66.5 + - - +
17B GLY 3.0 4.2 + - - -
18B GLN* 3.1 19.4 + - + +
37B PHE* 5.0 7.4 - - + +
40B LEU* 3.9 36.6 - - + +
41B VAL* 3.6 30.7 - - + -
44B PHE* 5.6 2.2 - - + -
169B LEU* 4.4 7.0 - - + -
171B VAL* 4.9 10.1 - - + -
182B CYS* 3.3 15.9 - - - +
185B THR* 4.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 2.9 49.5 + - - +
13B SER* 3.3 16.1 - - - +
14B ILE 4.2 1.9 - - - +
15B LEU* 1.3 75.1 - - - +
17B GLY* 1.3 60.9 + - - +
18B GLN 3.5 0.2 - - - -
182B CYS* 4.1 11.0 - - - +
183B VAL* 4.2 9.0 - - - +
184B SER* 3.9 32.3 - - - +
185B THR* 4.3 1.6 - - - +
----------------------------------------------------------
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