Contacts of the helix formed by residues 5 - 15 (chain C) in PDB entry 1YCY
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 SER 5 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 4.9 5.2 - - - -
6C LEU* 1.3 67.6 + - - +
7C LEU* 4.0 6.5 - - - +
8C GLU* 2.7 28.2 + - - +
9C LYS* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 4.7 14.6 - - + +
36A PHE* 4.6 19.7 - - - +
37A ASP* 3.5 33.6 + - + +
40A VAL* 4.1 8.3 - - + -
42A LEU* 4.9 7.9 - - + +
58A LEU* 5.4 0.2 - - + -
5C SER* 1.3 68.9 - - - +
7C LEU* 1.3 58.0 + - - +
9C LYS* 4.3 6.9 - - - +
10C VAL* 2.8 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 5.1 0.8 + - - -
39A GLU* 6.0 4.0 - - + -
40A VAL* 4.1 25.2 - - + +
58A LEU* 3.4 35.9 - - + -
5C SER* 2.9 6.3 - - - +
6C LEU* 1.3 79.0 - - - +
8C GLU* 1.3 62.6 + - - +
10C VAL* 4.0 0.5 - - - +
11C LEU* 2.9 44.9 + - + +
38C GLU* 6.3 1.3 - - - -
61C LEU* 3.9 28.5 - - + -
67C ILE* 5.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 2.7 27.3 + - - +
7C LEU* 1.3 73.5 - - - +
9C LYS* 1.3 65.2 + - + +
11C LEU* 2.9 13.2 + - - +
12C LYS* 2.9 21.1 + - + +
36C PHE* 3.8 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER 2.7 31.2 + - - +
6C LEU* 3.7 7.9 - - - +
8C GLU* 1.3 73.8 - - + +
10C VAL* 1.3 64.6 + - + +
12C LYS* 3.4 19.8 - - - +
13C GLU* 3.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.8 24.9 - - + -
56A GLN* 4.6 2.9 - - - +
58A LEU* 3.8 18.6 - - + -
6C LEU* 2.8 37.5 + - + +
7C LEU 4.0 2.0 - - - +
9C LYS* 1.3 76.0 - - + +
11C LEU* 1.3 61.5 + - - +
13C GLU* 3.3 11.8 + - - +
14C TRP* 2.9 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.7 21.3 - - + -
7C LEU* 2.9 41.5 + - + +
8C GLU 2.9 1.8 + - - -
10C VAL* 1.3 74.5 - - - +
12C LYS* 1.3 66.3 + - - +
14C TRP* 3.2 15.5 + - + +
15C LYS* 3.1 21.8 + - - +
33C LEU* 3.9 16.7 - - + +
36C PHE* 3.5 50.0 - - + -
41C ILE* 4.3 12.8 - - + -
61C LEU* 5.3 4.3 - - + -
67C ILE* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLU* 2.9 21.0 + - + +
9C LYS* 3.4 12.6 - - - +
11C LEU* 1.3 74.7 - - - +
13C GLU* 1.3 65.8 + - + +
15C LYS* 3.1 26.4 + - - +
36C PHE* 3.5 17.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 5.5 1.6 - - - +
9C LYS* 3.5 23.8 - - - +
10C VAL* 3.3 12.6 + - - +
11C LEU 3.3 0.8 - - - -
12C LYS* 1.3 77.1 - - + +
14C TRP* 1.3 66.0 + - + +
15C LYS 4.2 0.3 - - - +
17C HIS* 3.2 23.7 + - - -
69C LEU* 5.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.1 4.5 - - + -
56A GLN* 3.2 34.2 + - + -
57A MSE 4.0 3.6 - - - -
58A LEU* 3.7 30.5 - - + -
10C VAL* 2.9 46.3 - - + +
11C LEU* 3.2 14.2 + - + +
13C GLU* 1.3 86.0 + - + +
15C LYS* 1.3 61.1 + - - +
16C GLY 3.3 0.2 + - - -
17C HIS* 2.9 36.8 + - - +
19C VAL* 4.5 10.1 - - + -
33C LEU* 4.1 11.9 - - + +
67C ILE* 3.9 18.6 - - + -
68C MSE 3.8 12.6 - - - -
69C LEU* 3.4 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 3.1 9.5 + - - +
12C LYS* 3.1 18.8 + - - +
13C GLU 4.2 1.4 - - - +
14C TRP* 1.3 76.9 - - - +
16C GLY* 1.3 58.4 + - - +
17C HIS* 3.4 12.6 + - - -
33C LEU* 3.3 15.7 - - + +
34C GLU 3.2 25.4 - - - +
35C ASP* 3.3 31.4 + - - -
36C PHE* 4.0 18.1 - - - -
----------------------------------------------------------
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