Contacts of the helix formed by residues 148 - 166 (chain A) in PDB entry 1A9Z
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 PRO 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.1 33.4 - - - +
90A VAL* 3.9 14.4 - - + +
93A PRO* 3.9 16.2 - - + -
96A TYR* 4.7 4.8 - - + +
97A TYR* 3.6 35.3 - - + +
146A GLN 4.6 1.3 - - - +
147A SER* 1.3 87.1 - - - +
149A PHE* 1.3 56.7 + - - +
151A LYS* 3.8 1.8 - - + +
152A SER* 2.9 31.5 + - - -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 3.4 26.5 - - - -
84A LYS* 3.7 16.2 - - + -
86A VAL* 3.6 24.5 - - + -
89A SER* 3.2 26.1 + - - +
96A TYR* 4.1 6.1 - + + -
100A ASN* 4.0 4.7 - - - -
124A ALA* 4.8 0.9 - - + -
126A THR* 4.4 11.0 - - + -
147A SER* 3.1 4.6 - - - +
148A PRO* 1.3 78.2 - - - +
150A GLY* 1.3 65.3 + - - +
152A SER* 2.8 21.8 + - - -
153A LYS* 3.3 28.5 + - + +
340A NAD 3.6 30.3 - + - -
341A UPG 3.3 31.4 - - - -
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.6 25.1 - - - +
127A VAL* 4.7 0.3 - - - +
145A PRO* 3.3 28.5 - - - +
147A SER* 3.0 14.2 + - - -
149A PHE* 1.3 78.0 - - - +
151A LYS* 1.3 63.0 + - - +
153A LYS* 3.2 4.9 + - - +
154A LEU 3.2 17.2 + - - -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 3.5 28.7 - - + +
144A THR* 4.3 15.0 - - + +
145A PRO* 2.8 41.1 + - + +
146A GLN* 4.1 17.0 + - - +
147A SER 2.9 15.0 + - - +
148A PRO* 3.8 1.2 - - + +
150A GLY* 1.3 76.9 - - - +
152A SER* 1.3 58.8 + - - +
154A LEU* 3.3 3.9 + - - +
155A MET* 2.8 44.6 + - + +
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR 4.5 3.3 - - - -
97A TYR* 4.0 12.8 - - - -
100A ASN* 3.1 32.1 + - - +
101A VAL* 3.5 24.5 - - - +
148A PRO 2.9 15.9 + - - -
149A PHE* 2.8 18.0 + - - -
151A LYS* 1.3 79.1 - - - +
153A LYS* 1.3 59.7 + - - +
155A MET* 4.4 0.2 - - - -
156A VAL* 3.2 29.2 + - - +
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS 5.4 0.2 + - - -
81A ALA 5.4 2.4 + - - -
82A GLY* 6.2 0.6 - - - -
100A ASN* 4.9 11.7 - - + +
121A PHE* 3.5 27.9 - - + -
122A SER* 2.7 27.2 + - - +
123A SER* 4.4 6.1 - - - +
124A ALA* 4.6 9.2 - - + +
126A THR* 4.9 1.6 - - + -
127A VAL* 4.1 15.9 - - + -
149A PHE* 3.3 32.3 + - + +
150A GLY* 3.2 7.9 + - - +
151A LYS 3.2 0.8 - - - -
152A SER* 1.3 76.0 + - - +
154A LEU* 1.3 67.2 + - - +
156A VAL* 3.2 3.7 + - + +
157A GLU* 3.0 26.0 + - - +
340A NAD 3.2 38.4 + - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.0 12.0 - - + +
142A THR* 3.7 34.3 - - + +
143A GLY 3.2 26.7 - - - +
144A THR* 5.0 0.2 - - - -
145A PRO* 3.8 17.5 - - + -
150A GLY 3.2 10.9 + - - +
151A LYS* 3.8 6.5 - - - +
153A LYS* 1.3 77.2 - - - +
155A MET* 1.3 66.3 + - - +
157A GLU* 3.1 11.6 + - + +
158A GLN* 3.0 44.4 + - + +
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Residues in contact with MET 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 3.5 44.4 - - + +
101A VAL* 4.1 18.6 - - + -
151A LYS* 2.8 28.1 + - + +
152A SER 3.7 5.2 - - - +
154A LEU* 1.3 78.1 - - + +
156A VAL* 1.3 57.8 + - - +
158A GLN* 3.3 15.3 + - - +
159A ILE* 3.0 33.8 + - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN* 3.5 26.0 - - + +
101A VAL* 3.9 14.8 - - + +
104A THR* 3.7 22.4 - - + +
121A PHE* 3.5 30.1 - - + -
152A SER 3.2 17.7 + - - +
153A LYS* 3.2 1.1 + - + +
154A LEU 3.2 0.2 - - - -
155A MET* 1.3 73.8 - - - +
157A GLU* 1.3 67.3 + - - +
159A ILE* 3.1 8.8 + - + +
160A LEU* 2.8 41.1 + - + +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.4 4.3 - - + -
123A SER* 2.6 33.0 + - - +
127A VAL* 3.9 8.9 - - - +
142A THR* 4.5 0.3 - - - +
153A LYS 3.0 19.6 + - - +
154A LEU* 3.1 16.0 + - + +
156A VAL* 1.3 77.9 - - - +
158A GLN* 1.3 58.3 + - + +
160A LEU* 3.4 2.7 + - - +
161A THR* 2.9 33.2 + - - -
174A LEU* 3.9 32.1 - - + +
176A ARG* 2.7 45.2 + - - +
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Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 5.1 2.6 + - - -
154A LEU* 3.0 39.5 + - + +
155A MET* 3.6 17.4 - - - +
157A GLU* 1.3 74.3 - - + +
159A ILE* 1.3 60.3 + - + +
161A THR* 3.2 7.0 + - - -
162A ASP* 3.0 36.8 + - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.8 30.5 - - + +
105A LEU* 4.8 19.1 - - + -
108A ILE* 4.0 24.5 - - + -
155A MET* 3.0 23.7 + - + +
156A VAL* 3.6 10.8 - - + +
158A GLN* 1.3 77.3 - - + +
160A LEU* 1.3 64.7 + - + +
162A ASP* 3.4 7.5 + - - +
163A LEU* 2.9 22.7 + - + +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 4.7 1.8 - - + -
108A ILE* 3.8 39.0 - - + -
119A PHE* 3.8 28.9 - - + -
121A PHE* 3.9 16.4 - - + -
156A VAL* 2.8 42.3 + - + +
157A GLU 3.7 4.3 - - - +
159A ILE* 1.3 75.0 - - + +
161A THR* 1.3 56.7 + - - +
163A LEU* 3.2 5.4 + - + +
164A GLN* 2.9 29.3 + - - +
170A TRP* 5.5 0.2 - - + -
172A ILE* 3.6 26.9 - - + +
174A LEU* 3.9 14.4 - - + -
256A VAL* 5.2 0.9 - - + -
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU 2.9 18.4 + - - -
158A GLN* 3.2 7.3 + - - -
160A LEU* 1.3 75.2 - - - +
162A ASP* 1.3 68.8 + - - +
164A GLN* 3.2 3.6 + - - +
165A LYS* 3.0 23.5 + - + +
174A LEU* 4.2 5.0 - - - +
256A VAL* 4.0 31.2 - - + +
258A ILE* 5.8 0.5 - - - +
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Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLN* 3.0 21.1 + - - +
159A ILE* 3.7 7.6 - - - +
161A THR* 1.3 83.0 - - - +
163A LEU* 1.3 61.3 + - - +
165A LYS* 3.3 14.3 + - - +
166A ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 4.2 25.4 - - + -
112A ARG* 4.0 17.3 - - + +
159A ILE* 2.9 18.1 + - + +
160A LEU* 3.6 5.8 - - + +
162A ASP* 1.3 76.8 - - - +
164A GLN* 1.3 61.8 + - - +
166A ALA* 3.1 6.4 + - + -
167A GLN* 2.8 47.5 + - + +
170A TRP* 4.0 39.3 - - + -
172A ILE* 4.9 3.6 - - + -
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU 2.9 11.7 + - - +
161A THR 3.7 1.5 - - - +
163A LEU* 1.3 77.7 - - - +
165A LYS* 1.3 69.2 + - - +
167A GLN 3.1 4.3 - - - -
168A PRO* 3.0 59.6 + - - +
170A TRP* 3.3 30.0 + - + +
172A ILE* 3.9 9.4 - - + -
254A PRO 4.4 0.2 - - - -
255A GLY* 3.5 23.8 - - - +
256A VAL* 3.5 31.7 - - + +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 3.0 14.8 + - + +
162A ASP* 3.6 17.5 - - - +
163A LEU 3.2 0.2 - - - -
164A GLN* 1.3 85.5 + - - +
166A ALA* 1.3 59.4 + - - +
168A PRO* 4.2 12.1 - - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP 3.1 16.6 + - - +
163A LEU* 3.7 7.6 - - + +
165A LYS* 1.3 76.7 - - - +
167A GLN* 1.3 76.4 + - + +
168A PRO* 3.6 6.1 - - - +
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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) + - + + + + + -
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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