Contacts of the helix formed by residues 5 - 16 (chain B) in PDB entry 1UK0
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 PRO 5 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS 3.8 7.6 - - - +
4B LEU* 1.3 97.8 - - + +
6B LYS* 1.3 71.2 + - - +
7B PRO* 2.8 16.6 - - + -
8B VAL* 3.0 18.6 + - + -
9B GLN 3.1 2.6 + - - -
140B ILE 5.6 2.0 - - - +
142B VAL* 4.5 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU 3.3 3.0 + - - -
5B PRO* 1.3 73.2 - - - +
7B PRO* 1.4 72.5 - - + +
9B GLN* 3.1 11.1 + - - +
10B ASP* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.4 7.0 - - + +
6B LYS* 1.4 92.4 - - + +
8B VAL* 1.3 69.7 + - + +
10B ASP* 3.2 9.8 - - + +
11B LEU* 2.9 21.3 + - - +
142B VAL* 3.5 35.2 - - + -
174B ASP* 4.3 25.8 - - + +
176B PHE* 4.7 7.1 - - + -
343B LYS* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.2 31.6 - - + -
5B PRO* 3.0 14.5 + - + +
7B PRO* 1.3 79.8 - - - +
9B GLN* 1.4 63.8 + - - +
11B LEU* 3.2 3.7 + - + +
12B ILE* 3.0 31.9 + - + +
133B TYR* 4.8 2.0 - - + -
140B ILE* 3.5 38.4 - - + +
142B VAL* 4.4 10.8 - - + -
176B PHE* 3.7 23.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
1B LYS* 3.7 16.8 + - - +
2B SER* 2.6 56.3 + - - -
3B LYS 4.1 0.2 - - - -
4B LEU* 2.9 36.0 + - - +
5B PRO 3.1 8.9 + - - +
6B LYS* 3.5 14.8 - - - +
8B VAL* 1.4 71.6 - - - +
10B ASP* 1.3 75.5 + - - +
12B ILE* 3.8 2.1 - - - +
13B LYS* 3.2 26.5 + - - +
129B ILE* 3.6 15.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
6B LYS* 3.1 18.9 + - - +
7B PRO* 3.2 11.3 - - + +
9B GLN* 1.3 91.6 - - - +
11B LEU* 1.3 69.2 + - - +
13B LYS* 2.7 25.3 + - - +
14B MET* 2.9 16.2 + - + -
343B LYS* 5.1 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 2.9 17.3 + - - +
8B VAL* 3.2 4.2 + - + +
10B ASP* 1.3 75.1 - - - +
12B ILE* 1.4 72.5 + - + +
14B MET* 3.0 18.2 + - - +
15B ILE* 3.0 22.4 + - + +
140B ILE* 4.3 26.0 - - + -
176B PHE* 3.6 36.1 - - + -
212B LEU* 4.9 6.1 - - + -
257B LEU* 3.8 31.6 - - + -
341B LEU* 3.9 26.0 - - + -
343B LYS* 4.9 6.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
4B LEU* 3.8 10.8 - - + -
8B VAL* 3.0 24.4 + - + +
9B GLN 3.8 2.9 - - - +
10B ASP 2.9 1.2 + - - -
11B LEU* 1.4 74.3 - - + +
13B LYS* 1.3 70.3 + - - +
15B ILE* 3.1 19.0 - - - +
16B PHE* 3.3 10.0 - - + -
129B ILE* 4.0 17.7 - - + -
132B ASN* 3.7 15.3 - - + -
133B TYR* 3.2 46.0 - - + +
136B LEU* 3.1 33.0 - - + -
140B ILE* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS* 6.1 6.1 - - - +
9B GLN* 3.2 11.7 + - - +
10B ASP* 2.7 31.2 + - - +
12B ILE* 1.3 81.8 - - - +
14B MET* 1.3 67.7 + - - +
16B PHE* 3.1 8.1 + - - +
17B ASP* 3.0 17.7 + - - -
129B ILE* 3.2 39.5 - - + -
132B ASN* 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 2.9 12.8 + - + +
11B LEU* 3.1 13.9 - - - +
13B LYS* 1.3 78.6 - - - +
15B ILE* 1.4 56.3 + - + +
17B ASP* 2.6 36.8 + - + +
20B SER* 4.8 0.7 + - - -
205B THR* 4.7 18.4 + - + -
255B ILE* 4.3 19.3 - - + +
257B LEU* 4.1 21.5 - - + -
343B LYS* 3.6 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.4 16.8 - - + +
12B ILE* 3.1 15.5 - - - +
14B MET* 1.4 74.7 - - - +
16B PHE* 1.3 91.2 + - + +
17B ASP* 2.9 7.1 + - - +
20B SER* 5.7 0.2 + - - -
21B MET* 4.0 10.6 - - - +
113B ALA* 4.1 6.5 - - - +
136B LEU* 4.0 14.4 - - + -
205B THR* 3.5 20.1 + - - +
206B THR* 4.6 2.6 - - - +
208B PHE* 3.6 14.8 - - + -
209B ALA* 3.5 26.9 - - - +
212B LEU* 4.2 10.3 - - + -
257B LEU* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE 3.3 13.0 - - - +
13B LYS* 3.1 12.9 + - - +
15B ILE* 1.3 87.8 - - + +
17B ASP* 1.4 57.1 + - - +
18B VAL* 3.0 16.4 + - - +
21B MET* 4.4 5.4 - - - -
113B ALA* 4.6 6.7 - - + -
116B LEU* 4.3 11.2 - - + -
117B LEU* 3.3 43.1 - - + +
132B ASN* 3.4 54.5 - - + +
135B LYS* 4.6 2.9 - - - -
136B LEU* 3.9 14.4 - - + -
209B ALA* 3.4 27.1 - - + -
----------------------------------------------------------
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