Contacts of the helix formed by residues 17 - 25 (chain E) in PDB entry 4GOM
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 LEU 17 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LYS* 3.0 20.5 + - + +
16E PRO* 1.3 82.7 - - + +
18E LEU* 1.3 65.2 + - - +
19E ASP 3.5 0.4 - - - -
20E ASP* 3.1 16.0 + - + +
21E ILE* 3.0 38.9 + - + +
179E TYR* 5.2 0.7 - - - +
181E ASP* 6.4 0.9 - - - -
184E TYR* 4.5 5.2 - - - +
226E SER* 4.5 12.3 - - - +
245E VAL* 5.1 11.7 - - + -
247E VAL* 6.3 2.9 - - + -
263E GLU* 3.5 48.7 - - + +
265E LEU* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LYS* 5.9 3.4 - - + -
4E ASN 5.8 0.2 - - - +
14E LYS* 4.0 7.9 - - + +
15E TYR* 3.4 40.8 + - + +
16E PRO 3.3 3.0 - - - -
17E LEU* 1.3 76.6 - - - +
19E ASP* 1.3 59.1 + - - +
21E ILE* 3.2 8.5 + - + +
22E LYS* 2.8 45.6 + - + +
40E SER* 3.7 41.5 - - - +
41E VAL* 4.4 13.9 - - + -
44E ASN* 4.0 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E TYR 5.2 1.7 - - - +
16E PRO 4.5 8.3 + - - +
17E LEU 3.5 0.6 - - - -
18E LEU* 1.3 77.5 + - - +
20E ASP* 1.3 60.6 + - - +
22E LYS* 3.6 9.6 + - - +
23E ARG* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PRO 4.1 13.5 - - - +
17E LEU* 3.1 13.5 + - + +
19E ASP* 1.3 76.5 - - - +
21E ILE* 1.3 65.0 + - - +
23E ARG* 2.9 18.6 + - - +
24E HIS* 3.1 23.8 + - - +
245E VAL* 4.4 21.2 - - + +
265E LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LYS* 4.7 6.7 - - + -
17E LEU* 3.0 41.9 + - + +
18E LEU* 3.7 10.1 - - + +
20E ASP* 1.3 73.2 - - - +
22E LYS* 1.3 60.4 + - + +
24E HIS 3.3 1.7 + - - -
25E LEU* 2.9 46.5 + - + +
41E VAL* 4.1 24.2 - - + -
179E TYR* 3.3 46.0 - - + +
224E LEU* 3.9 12.4 - - + +
226E SER* 5.1 0.2 - - - +
265E LEU* 4.2 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 2.8 32.5 + - + +
19E ASP* 4.0 9.2 - - - +
21E ILE* 1.3 74.2 - - + +
23E ARG* 1.3 67.2 + - - +
24E HIS 3.2 0.5 + - - -
25E LEU* 3.5 17.7 + - + +
41E VAL* 6.2 0.2 - - + -
44E ASN* 2.8 36.9 + - - +
45E THR* 4.3 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASP 2.9 17.4 + - - +
20E ASP* 2.9 12.5 + - - +
22E LYS* 1.3 76.1 - - - +
24E HIS* 1.3 78.2 + - + +
25E LEU 3.8 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ASP* 3.1 28.3 + - - +
21E ILE 4.3 0.9 - - - +
23E ARG* 1.3 88.2 - - + +
25E LEU* 1.3 63.8 + - - +
26E PRO* 3.5 1.9 - - - +
224E LEU* 4.2 20.9 - - + -
243E HIS* 3.5 53.6 + + + +
265E LEU* 3.7 16.1 - - + +
267E LEU* 3.5 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ILE* 2.9 25.4 + - + +
22E LYS* 3.5 14.4 + - + +
23E ARG 4.8 1.0 - - - +
24E HIS* 1.3 76.3 - - - +
26E PRO* 1.3 77.9 - - + +
31E LEU* 4.5 3.6 - - + -
41E VAL* 4.1 26.0 - - + -
45E THR* 4.4 7.9 - - + -
47E PHE* 4.2 21.1 - - + -
177E VAL* 3.9 23.8 - - + -
179E TYR* 4.1 21.1 - - + -
224E LEU* 4.2 16.8 - - + -
----------------------------------------------------------
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