Contacts of the helix formed by residues 124 - 131 (chain H) in PDB entry 2GD4
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 GLU 124 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 1.3 75.5 + - - +
125H ARG* 1.3 72.5 + - - +
126H ASP* 3.5 2.0 + - - +
127H TRP* 3.0 10.4 + - - -
128H ALA* 2.8 15.3 + - - +
235H LEU* 5.8 0.2 - - - -
99L PHE* 3.7 40.7 - - - -
101L HIS* 4.9 14.2 - - - -
110L SER* 4.9 1.9 - - - -
111L CYS 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H GLU* 1.3 73.4 + - - +
126H ASP* 1.3 75.9 + - - +
128H ALA* 2.8 21.3 + - - +
129H GLU* 2.9 13.3 + - - +
232H THR* 4.4 6.0 + - - +
235H LEU* 4.2 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H GLU* 3.1 3.3 + - - +
125H ARG* 1.3 86.9 - - - +
127H TRP* 1.3 67.6 + - - +
129H GLU* 3.0 17.3 + - - +
130H SER* 3.1 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H GLU* 3.0 21.6 + - + +
126H ASP* 1.3 74.1 - - - +
128H ALA* 1.3 57.5 + - - +
130H SER* 2.9 10.5 + - - -
131H THR* 2.7 88.3 + + + -
203H PHE* 3.7 35.9 - + + -
208H PHE* 3.8 21.8 - + - -
93L ASN* 2.9 23.6 + - - -
98L GLN 2.8 24.8 + - - -
99L PHE* 3.4 29.6 - + + -
100L CYS* 3.3 34.8 - - + +
101L HIS* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H GLU* 2.8 40.2 + - + +
125H ARG* 2.8 16.9 + - - +
127H TRP* 1.3 77.4 - - - +
129H GLU* 1.3 51.8 + - - +
130H SER 2.7 12.5 + - - -
131H LEU* 2.9 44.9 + - + -
232H THR* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H ARG* 2.9 13.2 + - - +
126H ASP* 3.0 11.1 + - - +
128H ALA* 1.3 74.5 - - - +
130H SER* 1.3 57.0 + - - +
131H MET* 3.8 22.1 - - + -
132H THR* 4.0 6.8 - - - +
230H LYS* 2.7 29.5 + - - +
232H THR* 3.3 25.8 + - - +
233H ALA* 4.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ASP 3.1 7.3 + - - -
127H TRP* 2.9 17.9 + - - -
128H ALA 2.7 6.1 + - - -
129H GLU* 1.3 76.5 - - - +
131H THR* 1.3 65.0 + - - +
132H THR* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H TRP* 2.7 46.1 + - + +
128H ALA 2.9 1.2 + - - -
130H SER* 1.3 86.9 + - - +
131H LEU* 1.3 53.2 + - - -
132H THR* 3.8 8.1 + - - -
133H GLN* 2.6 33.2 + - - +
203H PHE* 3.3 39.7 - - + -
93L ASN* 4.3 5.0 + - + +
----------------------------------------------------------
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