Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 4DGX
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 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 5.3 0.6 + - - -
117A LEU* 1.3 78.8 - - - +
119A GLY* 1.3 61.0 + - - +
120A LYS* 3.1 24.8 + - - +
121A GLU* 2.9 42.2 + - - +
122A ALA* 3.2 28.2 + - - +
138A ARG* 4.0 0.4 - - - -
141A GLN* 3.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 1.3 73.1 - - - +
120A LYS* 1.3 57.2 + - - +
122A ALA* 4.0 2.3 - - - +
123A GLU* 3.3 25.9 + - - +
138A ARG* 3.5 28.5 - - - -
141A GLN* 3.6 10.1 + - - -
169A HIS* 4.5 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.9 21.0 + - - +
119A GLY* 1.3 77.7 - - - +
121A GLU* 1.3 76.7 + - + +
122A ALA 3.1 1.6 - - - -
123A GLU* 3.1 32.3 - - - +
124A LYS* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.5 21.5 - - + +
118A SER* 2.9 29.7 + - - +
120A LYS* 1.3 94.7 - - + +
122A ALA* 1.3 59.0 + - - +
124A LYS* 3.7 8.5 + - + +
125A LEU* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.9 15.2 - - + +
118A SER 3.2 17.9 + - - +
119A GLY 4.1 3.8 - - - +
120A LYS 3.1 0.4 - - - -
121A GLU* 1.3 74.7 - - - +
123A GLU* 1.3 58.9 + - - +
124A LYS 3.1 1.8 - - - -
125A LEU* 3.2 8.2 + - - +
126A LEU* 3.0 33.0 + - - +
136A LEU* 4.1 13.5 - - + +
138A ARG* 3.9 21.1 - - - +
150A SER* 5.0 5.2 - - - +
169A HIS* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 3.3 15.5 + - - +
120A LYS* 3.1 28.1 - - - +
122A ALA* 1.3 76.0 - - - +
124A LYS* 1.3 57.4 + - + +
126A LEU* 3.9 9.3 - - - +
127A THR* 2.5 39.0 + - - +
167A VAL* 4.9 7.5 - - + +
169A HIS* 4.6 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS 3.1 16.5 + - - +
121A GLU* 3.8 9.4 - - + +
122A ALA 3.1 0.2 - - - -
123A GLU* 1.3 76.2 - - - +
125A LEU* 1.3 59.1 + - + +
126A LEU 3.2 0.2 + - - -
127A THR* 3.3 4.2 + - - -
128A GLU* 2.6 75.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 4.2 17.7 - - + +
117A LEU* 4.2 16.4 - - + -
121A GLU* 3.1 16.1 + - + +
122A ALA* 3.2 7.3 + - - +
124A LYS* 1.3 80.6 - - + +
126A LEU* 1.3 54.4 + - - +
128A GLU* 4.6 7.2 - - - +
129A LYS* 2.7 56.1 + - - +
130A GLY 3.3 4.2 + - - -
136A LEU* 5.0 0.7 - - + -
216A LEU* 3.2 29.4 - - + +
218A THR* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.0 20.6 + - - +
123A GLU* 4.1 1.6 - - - +
125A LEU* 1.3 73.1 - - - +
127A THR* 1.3 63.7 + - - +
130A GLY* 2.9 27.4 + - - +
134A SER* 3.7 37.5 - - - +
135A PHE* 4.6 2.0 - - - +
136A LEU* 3.9 18.2 - - + -
150A SER* 3.6 37.5 - - - +
151A VAL 4.3 0.7 - - - +
152A ARG* 3.1 16.1 + - + +
167A VAL* 3.7 31.9 - - + -
169A HIS* 5.5 0.2 - - - +
216A LEU* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.5 24.8 + - - +
124A LYS* 3.6 4.7 - - - -
126A LEU* 1.3 77.6 - - - +
128A GLU* 1.3 64.0 + - - +
152A ARG* 2.8 25.6 + - - +
158A GLY* 3.3 14.2 - - - +
159A GLU* 4.2 26.0 - - - +
160A SER 5.1 5.2 - - - +
167A VAL* 4.7 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 2.6 61.6 + - + +
125A LEU* 4.1 6.5 + - - +
127A THR* 1.3 78.1 - - - +
129A LYS* 1.3 65.9 + - + +
158A GLY* 3.5 17.7 - - - -
159A GLU* 2.8 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 2.7 45.6 + - - +
128A GLU* 1.3 83.0 - - + +
130A GLY* 1.3 62.4 + - - +
131A LYS* 5.1 1.2 - - - +
157A LYS* 5.2 5.3 - - - +
216A LEU* 3.8 10.8 - - + +
217A ASN* 2.6 30.3 + - + +
218A THR* 3.5 21.2 - - - +
220A ARG* 4.3 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 3.3 3.4 + - - -
126A LEU* 2.9 23.7 + - - -
128A GLU 3.5 0.2 - - - -
129A LYS* 1.3 81.9 - - - +
131A LYS* 1.3 59.4 + - - -
134A SER* 3.8 8.5 - - - -
152A ARG* 3.8 5.6 + - - -
157A LYS* 3.3 19.5 - - - +
158A GLY 3.6 8.8 + - - -
216A LEU* 3.7 14.1 - - - -
----------------------------------------------------------
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