Contacts of the helix formed by residues 120 - 135 (chain A) in PDB entry 4I6H
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 LYS 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 1.3 85.6 + - - +
121A PRO* 1.4 77.2 - - + +
122A HIS* 3.2 22.3 + - + +
123A GLN* 3.3 29.1 - - + +
124A ARG* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER 3.7 5.1 - - - +
120A LYS* 1.4 91.4 - - + +
122A HIS* 1.3 58.6 + - - +
124A ARG* 3.5 7.2 - - + +
125A GLU* 3.1 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.8 30.8 - - + +
121A PRO* 1.3 79.8 - - + +
123A GLN* 1.3 68.4 + - - +
125A GLU* 3.7 14.1 + - - +
126A LYS* 3.0 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.1 31.3 - - + -
117A ARG 3.0 24.2 + - - -
118A VAL* 3.5 12.7 - - - +
119A SER* 3.5 3.0 + - - +
120A LYS* 3.3 50.5 - - + +
122A HIS* 1.3 87.9 + - + +
124A ARG* 1.3 62.8 + - - +
126A LYS* 3.5 18.8 - - - +
127A ILE* 3.3 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 4.0 9.9 - - - -
118A VAL* 3.4 24.9 - - + +
119A SER 5.6 1.1 - - - +
120A LYS 3.1 16.3 + - - +
121A PRO* 3.5 9.4 - - + +
123A GLN* 1.3 80.5 - - - +
125A GLU* 1.3 61.6 + - + +
127A ILE* 3.7 5.6 + - - +
128A ASP* 3.0 45.6 + - - +
131A ILE* 5.7 1.6 - - - +
148A TYR* 5.3 1.8 + - - -
150A GLU* 2.9 38.2 + - - -
155A ILE* 3.7 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.1 31.9 + - - +
122A HIS* 3.7 14.9 - - - +
124A ARG* 1.3 75.0 - - + +
126A LYS* 1.3 63.8 + - - +
128A ASP* 3.2 9.4 + - + +
129A LYS* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 5.8 5.7 - - + -
122A HIS* 3.0 49.0 + - - +
123A GLN* 3.5 17.9 - - + +
124A ARG 3.3 0.4 - - - -
125A GLU* 1.3 76.9 - - - +
127A ILE* 1.3 62.8 + - + +
129A LYS* 3.6 3.6 + - - +
130A GLU* 3.3 21.5 + - - +
225A GLY 4.8 14.0 - - - +
226A LEU* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 5.0 7.0 - - + -
111A LYS* 6.0 0.4 - - - +
113A ILE* 3.9 27.1 - - + -
118A VAL* 3.5 29.6 - - + -
123A GLN 3.3 12.5 + - - +
124A ARG* 4.3 6.5 - - - +
126A LYS* 1.3 76.1 - - + +
128A ASP* 1.3 58.9 + - - +
130A GLU* 3.3 18.6 + - - +
131A ILE* 2.9 40.8 + - + +
155A ILE* 4.0 18.6 - - + -
157A ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.0 43.1 + - - +
125A GLU* 3.2 14.3 + - - +
127A ILE* 1.3 78.0 - - - +
129A LYS* 1.3 59.4 + - - +
131A ILE* 4.1 8.1 - - - +
132A GLU* 3.0 30.3 + - - +
148A TYR* 5.2 4.2 + - - -
----------------------------------------------------------
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 GLU 3.0 14.6 + - - +
126A LYS* 4.1 4.5 - - - +
128A ASP* 1.3 73.1 - - - +
130A GLU* 1.3 60.6 + - - +
132A GLU* 4.1 23.4 + - - +
133A LEU* 2.9 62.5 + - + +
227A ALA 4.5 9.0 - - - +
228A ALA* 5.4 6.1 - - + -
229A ARG 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 2.7 34.0 + - - +
126A LYS 3.3 12.9 + - - +
127A ILE* 3.3 26.2 + - + +
129A LYS* 1.3 79.8 - - - +
131A ILE* 1.3 57.1 + - + +
133A LEU* 4.6 2.0 - - - +
134A HIS* 3.0 37.2 + - + +
157A ILE* 4.9 6.9 - - + +
159A LEU* 5.9 1.0 - - - +
223A ASP* 4.7 0.9 - - - +
224A PHE* 3.6 33.9 + - + +
225A GLY* 4.0 18.7 - - - +
227A ALA* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 5.7 1.6 - - - +
127A ILE* 2.9 29.9 + - + +
128A ASP* 4.1 9.9 - - - +
130A GLU* 1.3 74.7 - - + +
132A GLU* 1.3 65.8 + - - +
135A ARG* 3.1 43.2 + - - +
145A PHE* 3.8 22.9 - - + -
148A TYR* 3.6 53.8 - - + -
155A ILE* 4.6 4.7 - - + -
157A ILE* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP 3.0 20.9 + - - +
129A LYS* 3.8 23.5 + - - +
131A ILE* 1.3 78.5 - - - +
133A LEU* 1.3 80.4 + - + +
135A ARG* 3.8 21.8 - - - +
136A ILE* 3.9 12.5 - - - +
229A ARG* 4.5 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 2.9 35.1 + - + +
130A GLU* 4.6 2.0 - - - +
132A GLU* 1.3 103.7 - - + +
134A HIS* 1.3 63.2 + - - +
136A ILE* 3.3 23.9 - - - +
137A LEU* 3.6 11.8 - - - +
201A ILE* 4.2 16.2 - - + +
224A PHE* 5.9 2.2 - - + -
227A ALA* 3.7 35.2 - - + +
228A ALA* 3.7 20.6 - - - +
229A ARG* 3.9 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.0 26.8 + - - +
131A ILE 3.5 0.2 + - - -
133A LEU* 1.3 73.6 - - - +
135A ARG* 1.3 58.3 + - - +
136A ILE 3.0 10.5 + - - -
137A LEU* 3.2 24.8 + - + +
143A VAL* 2.9 35.9 + - + -
145A PHE* 3.8 23.7 + + + +
157A ILE* 5.9 0.4 - - - +
159A LEU* 3.6 27.9 - - + +
223A ASP* 5.1 4.0 - - - -
224A PHE* 3.5 44.4 + + + +
401A 1C8 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 3.1 37.2 + - - +
132A GLU* 3.8 15.9 - - - +
134A HIS* 1.3 75.4 - - - +
136A ILE* 1.3 67.9 + - + +
137A LEU 3.4 2.5 + - - +
144A GLN* 5.6 0.9 - - - +
145A PHE* 3.5 40.9 - - + +
147A HIS* 5.6 4.6 + - - -
148A TYR* 4.1 30.5 + - - +
----------------------------------------------------------
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