Contacts of the helix formed by residues 21 - 33 (chain G) in PDB entry 2HOI
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 ASP 21 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER* 1.3 85.9 + - - +
22G GLU* 1.3 61.0 + - + +
23G VAL 3.2 1.8 - - - -
24G ARG* 3.3 19.4 + - - +
25G LYS* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER 3.9 8.0 + - - +
21G ASP* 1.3 79.2 - - + +
23G VAL* 1.3 59.2 + - + +
25G LYS* 3.5 8.3 + - - +
26G ASN* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER* 3.2 37.6 - - - +
22G GLU* 1.3 79.4 - - + +
24G ARG* 1.3 63.0 + - + +
26G ASN* 3.5 2.8 + - - +
27G LEU* 3.2 30.4 + - + +
64G PHE* 5.4 9.0 - - + -
102G SER* 3.4 28.9 - - - +
103G GLY 5.2 2.0 - - - +
104G LEU* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER* 4.0 20.3 + - - +
21G ASP* 3.3 20.0 + - - +
23G VAL* 1.3 81.2 - - + +
25G LYS* 1.3 64.0 + - - +
27G LEU* 3.7 11.3 + - + +
28G MET* 3.3 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP 3.0 16.6 + - - +
22G GLU* 3.8 8.3 - - - +
24G ARG* 1.3 75.9 - - - +
26G ASN* 1.3 68.1 + - - +
28G MET* 3.3 8.7 + - - +
29G ASP* 3.0 53.0 + - - +
69H GLU* 4.5 15.4 + - - +
112H ALA* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLU* 2.8 25.5 + - - +
23G VAL 3.7 5.8 - - - +
25G LYS* 1.3 85.9 - - - +
27G LEU* 1.3 58.0 + - - +
29G ASP* 3.3 9.6 + - - +
30G MET* 3.0 23.3 + - - +
101G ARG 3.2 22.9 - - - +
102G SER* 2.9 24.7 + - - +
103G GLY* 4.0 5.6 - - - +
111H ASN* 3.5 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G VAL* 3.2 22.9 + - + +
24G ARG* 4.0 11.4 - - + +
25G LYS 3.3 0.2 - - - -
26G ASN* 1.3 77.6 - - - +
28G MET* 1.3 60.2 + - + +
30G MET* 3.2 19.3 + - + +
31G PHE* 3.0 25.3 + - - +
64G PHE* 4.5 19.1 - - + -
98G LEU* 4.5 17.9 - - + +
101G ARG 5.9 0.2 - - - -
102G SER* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ARG* 3.3 36.1 + - + +
25G LYS* 3.8 7.2 - - - +
26G ASN 3.3 0.4 - - - -
27G LEU* 1.3 75.1 - - + +
29G ASP* 1.3 61.0 + - - +
31G PHE* 3.4 7.8 + - + +
32G ARG* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LYS* 3.0 44.7 + - - +
26G ASN* 3.3 11.6 - - - +
27G LEU 3.3 0.2 - - - -
28G MET* 1.3 78.5 - - - +
30G MET* 1.3 60.2 + - - +
32G ARG* 3.2 32.4 + - - +
33G ASP* 3.2 21.3 + - - +
69H GLU* 4.4 0.3 - - - +
111H ASN* 3.9 24.4 + - + +
112H ALA* 4.2 12.5 + - - +
115H LEU* 3.5 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ASN 3.0 16.5 + - - +
27G LEU* 3.2 22.6 + - + +
29G ASP* 1.3 77.0 - - - +
31G PHE* 1.3 60.6 + - - +
33G ASP 3.5 2.8 - - - +
34G ARG* 3.3 22.7 + - - +
37G PHE* 3.9 20.1 - - - -
42G TRP* 3.8 33.8 - - + -
97G MET* 3.8 23.3 - - + -
98G LEU* 4.9 14.8 - - + +
101G ARG* 3.7 37.9 - - + +
111H ASN* 4.4 1.1 - - - +
115H LEU* 3.8 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU 3.0 12.3 + - - +
28G MET* 3.8 9.9 - - + +
29G ASP 3.4 0.2 - - - -
30G MET* 1.3 75.1 - - - +
32G ARG* 1.3 67.9 + - + +
34G ARG* 2.8 73.2 + - + -
42G TRP* 5.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G MET 3.0 18.1 + - - +
29G ASP* 3.2 26.1 + - - +
31G PHE* 1.3 82.4 - - + +
33G ASP* 1.3 59.7 + - - +
34G ARG* 3.7 11.3 + - - +
69H GLU* 3.0 38.8 + - - -
72H ARG* 3.6 50.6 - - - +
112H ALA* 3.7 7.3 - - - +
119H ARG* 3.6 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASP 3.2 12.8 + - - +
30G MET 3.5 5.9 - - - +
31G PHE 3.2 0.6 - - - -
32G ARG* 1.3 80.6 + - - +
34G ARG* 1.3 63.0 + - - +
35G GLN 3.2 3.1 - - - +
36G ALA* 3.1 19.8 + - - +
37G PHE* 5.2 1.4 - - - -
72H ARG* 2.9 29.6 + - - -
112H ALA* 3.8 4.3 - - - +
115H LEU* 3.9 20.0 - - + +
116H VAL* 3.7 18.6 + - - +
119H ARG* 2.4 47.5 + - - +
----------------------------------------------------------
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