Contacts of the helix formed by residues 121 - 138 (chain A) in PDB entry 1P9W
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 ALA 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 1.3 73.6 - - + +
123A ILE* 3.2 15.7 - - + +
124A ILE* 3.5 40.3 + - + +
125A LYS* 3.6 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 6.0 0.7 - - - +
121A ALA* 1.3 85.3 - - + +
123A ILE* 1.3 65.8 + - + +
124A ILE 3.2 1.1 - - - -
125A LYS* 3.8 13.8 - - + +
126A LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 3.2 9.3 - - + -
122A PRO* 1.3 84.1 - - + +
124A ILE* 1.3 61.4 + - + +
126A LEU* 4.0 9.5 - - + +
127A ILE* 3.1 24.4 + - - +
171A LEU* 3.6 31.0 - - + -
174A LEU* 3.9 53.6 - - + +
175A LEU* 4.2 20.2 - - + +
178A ARG* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 3.5 35.8 + - + +
122A PRO 3.2 0.4 - - - -
123A ILE* 1.3 78.7 - - + +
125A LYS* 1.3 63.8 + - - +
127A ILE* 3.6 1.0 + - - +
128A ASN* 3.1 44.8 + - - +
178A ARG* 3.6 54.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 3.3 35.8 - - - +
104A LEU* 3.5 32.7 - - + +
121A ALA 3.6 10.0 + - - +
122A PRO* 3.5 13.9 + - + +
124A ILE* 1.3 80.3 - - - +
126A LEU* 1.3 56.6 + - - +
128A ASN* 4.2 6.2 - - - +
129A ALA* 3.1 30.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
101A PHE* 4.2 22.5 - - + -
104A LEU* 3.9 39.2 - - + +
105A ALA* 4.1 8.5 - - + +
122A PRO 2.9 17.4 + - - +
123A ILE* 4.3 14.6 - - + +
124A ILE 3.3 0.2 - - - -
125A LYS* 1.3 74.1 - - - +
127A ILE* 1.3 60.7 + - + +
129A ALA* 3.0 4.7 + - - +
130A MSE 2.8 32.7 + - + +
153A ILE* 5.6 4.0 - - + -
165A LEU* 5.5 7.4 - - + -
167A PRO* 6.1 4.5 - - + -
171A LEU* 5.4 5.4 - - + -
175A LEU* 3.9 26.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
123A ILE 3.1 21.3 + - - +
124A ILE 4.1 3.4 - - - +
125A LYS 3.6 0.2 - - - -
126A LEU* 1.3 75.9 - - + +
128A ASN* 1.3 57.0 + - - +
130A MSE 3.4 25.8 + - + +
131A LEU* 3.0 45.2 + - + +
144A ILE* 4.5 2.5 - - + -
175A LEU* 3.7 31.9 - - + +
178A ARG* 3.6 18.2 - - + -
179A VAL* 4.2 20.9 - - + -
182A MSE 3.8 22.0 - - - -
224A MSE 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.1 36.8 + - - +
125A LYS* 4.2 6.4 - - + +
127A ILE* 1.3 75.9 - - - +
129A ALA* 1.3 57.3 + - - +
131A LEU* 3.4 7.9 + - - +
132A GLY* 2.8 25.1 + - - -
178A ARG* 5.0 0.9 + - - +
182A MSE 3.7 26.7 - - - +
200A LEU* 5.5 1.3 - - - +
202A ILE* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 4.0 19.4 - - + +
101A PHE* 3.4 29.2 + - - +
104A LEU* 4.2 11.0 - - + -
125A LYS 3.1 19.7 + - - +
126A LEU* 3.0 6.1 + - - +
128A ASN* 1.3 75.5 - - - +
130A MSE 1.3 55.7 + - - +
132A GLY* 3.6 2.1 - - - +
133A GLU* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.6 26.0 - - + -
126A LEU* 2.8 17.4 + - - +
127A ILE* 3.9 32.8 - - + +
129A ALA* 1.3 74.9 - - - +
131A LEU* 1.3 60.2 + - + +
133A GLU* 3.3 1.1 + - - +
134A ALA* 2.9 29.8 + - - +
142A ILE* 4.0 19.3 - - + -
144A ILE* 4.0 6.7 - - + -
153A ILE* 4.0 26.9 - - - -
155A PHE* 3.7 23.3 - - + -
175A LEU* 6.0 0.4 - - - -
224A MSE 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.0 40.9 + - + +
128A ASN* 3.6 6.7 - - - +
130A MSE 1.3 78.4 - - + +
132A GLY* 1.3 55.3 + - - +
134A ALA* 3.2 3.3 + - - +
135A ILE* 3.0 34.5 + - + +
142A ILE* 4.2 11.2 - - + -
182A MSE 4.5 16.8 - - + -
198A ILE* 6.1 2.2 - - + -
200A LEU* 4.5 13.5 - - + -
202A ILE* 5.0 8.1 - - + -
209A VAL* 4.5 12.3 - - + -
224A MSE 4.2 24.9 - - + -
226A LEU* 3.5 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASN 2.8 19.2 + - - -
129A ALA* 3.6 5.2 - - - -
130A MSE 3.3 0.2 - - - -
131A LEU* 1.3 72.2 - - - +
133A GLU* 1.3 56.0 + - - +
135A ILE* 3.6 4.4 + - - +
136A LYS* 3.1 27.1 + - - +
202A ILE* 4.6 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP* 3.6 20.4 - - - +
101A PHE* 3.8 23.9 + - + +
102A PHE* 4.2 14.8 - - + -
129A ALA 2.8 19.8 + - - +
130A MSE 3.7 4.5 - - - +
132A GLY* 1.3 69.9 - - - +
134A ALA* 1.3 61.6 + - - +
136A LYS* 3.3 25.0 + - - +
137A GLU* 2.9 69.9 + - - +
155A PHE* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MSE 2.9 18.3 + - - +
131A LEU 3.4 5.8 - - - +
133A GLU* 1.3 77.6 - - - +
135A ILE* 1.3 56.6 + - - +
137A GLU* 3.3 2.1 + - - -
138A GLY 3.0 6.9 + - - -
139A ALA* 2.9 36.1 + - + +
142A ILE* 3.5 28.0 - - + -
155A PHE* 3.9 13.7 - - + -
226A LEU* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.0 17.9 + - + +
132A GLY 3.9 4.7 - - - +
134A ALA* 1.3 74.1 - - - +
136A LYS* 1.3 66.1 + - + +
138A GLY* 3.1 13.9 + - - +
139A ALA 5.0 3.8 - - - +
202A ILE* 3.9 34.5 - - + -
207A VAL* 3.8 33.9 - - + -
226A LEU* 3.7 25.8 - - + +
227A LEU 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 3.1 18.3 + - - +
133A GLU* 3.3 28.9 + - - +
135A ILE* 1.3 77.9 - - - +
137A GLU* 1.3 61.7 + - + +
138A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.4 7.8 - - - -
133A GLU* 2.9 45.3 + - - +
134A ALA* 3.3 5.8 + - - +
135A ILE 3.2 0.2 - - - -
136A LYS* 1.3 79.7 - - + +
138A GLY* 1.3 62.5 + - - +
139A ALA* 4.6 2.7 - - + +
155A PHE* 3.9 12.8 - - - -
157A VAL* 4.0 18.8 - - + +
162A ARG* 2.5 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA 3.0 2.8 + - - -
135A ILE* 3.1 14.9 + - - -
136A LYS 3.3 0.6 + - - -
137A GLU* 1.3 80.9 - - - +
139A ALA* 1.3 63.9 + - - +
140A SER* 3.8 1.0 + - - -
157A VAL* 4.6 5.0 - - - +
158A ASP* 4.5 13.0 + - - +
----------------------------------------------------------
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