Contacts of the helix formed by residues 148 - 170 (chain A) in PDB entry 3IIL
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 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASN* 1.3 87.2 - - + +
149A PRO* 1.4 76.2 - - + +
150A GLU* 3.5 26.3 + - - +
151A GLU* 3.0 30.0 + - + +
152A LEU 3.2 0.7 + - - -
174A ADP 2.9 18.7 + - - -
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Residues in contact with PRO 149 (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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148A LYS* 1.4 85.9 - - + +
150A GLU* 1.3 74.0 + - + +
152A LEU* 3.1 13.3 + - + +
153A GLU* 3.0 22.0 + - - +
174A ADP 3.2 19.7 - - + +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 3.2 25.3 + - + +
149A PRO* 1.3 98.5 - - + +
151A GLU* 1.3 59.2 + - + +
153A GLU* 3.6 13.2 + - - +
154A ASN* 3.0 26.7 + - - +
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 3.6 38.4 - - + +
146A SER* 3.8 1.2 + - - -
147A ASN* 2.8 36.6 + - - +
148A LYS* 3.0 27.7 + - + +
150A GLU* 1.3 77.4 - - + +
152A LEU* 1.3 58.7 + - - +
154A ASN* 3.2 5.2 + - + -
155A ASN* 2.8 38.6 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.7 23.1 - - + -
19A LEU* 3.9 40.2 - - + +
22A GLU* 3.7 20.4 - - - +
148A LYS 3.2 4.9 + - - -
149A PRO* 3.1 14.2 + - + +
151A GLU* 1.3 76.3 - - - +
153A GLU* 1.3 58.5 + - - +
155A ASN* 3.2 10.1 + - - +
156A VAL* 2.9 40.5 + - + +
174A ADP 3.6 25.6 + - + +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 5.4 2.7 - - - +
149A PRO 3.0 11.9 + - - +
150A GLU* 3.7 13.9 - - - +
152A LEU* 1.3 75.5 - - - +
154A ASN* 1.3 59.6 + - - +
156A VAL* 3.4 7.8 + - + +
157A ASP* 2.9 29.8 + - + +
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Residues in contact with ASN 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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145A PRO* 6.1 2.8 - - - +
150A GLU 3.0 17.9 + - - +
151A GLU* 3.2 8.3 + - + +
153A GLU* 1.3 75.7 - - - +
155A ASN* 1.3 64.5 + - - +
157A ASP* 3.7 5.8 - - - +
158A GLN* 2.9 58.3 + - - +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.9 16.9 - - + +
95A LEU* 5.1 1.6 - - - +
144A LEU* 3.8 41.1 - - + +
145A PRO* 2.9 31.8 + - - +
146A SER* 4.5 8.7 + - - -
151A GLU* 2.8 24.1 + - - +
152A LEU* 3.2 8.7 + - - +
154A ASN* 1.3 79.2 + - - +
156A VAL* 1.3 66.1 + - - +
158A GLN* 3.4 3.2 + - - -
159A ILE* 3.0 33.7 + - - +
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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
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19A LEU* 3.6 21.3 - - + +
22A GLU* 3.6 33.4 - - + +
23A LEU* 4.0 9.5 - - + +
26A LYS* 3.9 21.3 - - + +
152A LEU* 2.9 22.6 + - + +
153A GLU* 3.7 7.0 - - + +
155A ASN* 1.3 75.0 - - - +
157A ASP* 1.3 65.5 + - - +
159A ILE* 3.9 0.3 - - - -
160A LEU* 2.9 50.9 + - + +
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Residues in contact with ASP 157 (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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153A GLU* 2.9 21.0 + - + +
154A ASN* 3.7 9.1 - - - +
156A VAL* 1.3 79.1 - - - +
158A GLN* 1.3 75.1 + - - +
160A LEU* 3.5 7.5 + - - +
161A LYS* 2.7 66.4 + - - +
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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
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93A PHE* 6.1 0.2 - - - -
144A LEU* 6.1 4.9 - - + -
154A ASN* 2.9 42.8 + - - +
155A ASN* 4.1 4.3 - - - +
157A ASP* 1.3 100.6 + - - +
159A ILE* 1.3 59.7 - - + +
161A LYS* 3.5 17.1 + - - +
162A TRP* 3.0 26.2 + - - +
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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
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6A ILE* 3.9 21.5 - - + -
8A LEU* 4.6 0.4 - - + -
19A LEU* 3.9 11.9 - - + -
23A LEU* 3.7 39.5 - - + -
93A PHE* 3.6 36.3 - - + -
144A LEU* 3.8 26.2 - - + -
155A ASN 3.0 22.3 + - - +
158A GLN* 1.3 76.0 - - + +
160A LEU* 1.3 60.0 + - - +
162A TRP* 3.0 8.5 + - + +
163A ILE* 2.8 30.0 + - + +
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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
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23A LEU* 3.9 16.4 - - + +
26A LYS* 3.5 40.6 - - + +
27A SER* 3.7 21.3 - - - -
156A VAL* 2.9 38.3 + - + +
157A ASP* 3.8 7.2 - - - +
159A ILE* 1.3 75.3 - - - +
161A LYS* 1.3 58.7 + - + +
163A ILE* 3.4 7.3 + - + +
164A GLU* 3.1 27.8 + - - +
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Residues in contact with LYS 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 ASP* 2.7 55.5 + - - +
158A GLN* 3.6 17.1 - - - +
160A LEU* 1.3 75.7 - - + +
162A TRP* 1.3 64.1 + - - +
164A GLU* 3.4 9.7 + - - +
165A GLN* 3.1 22.9 + - - +
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Residues in contact with TRP 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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4A PRO* 3.7 39.0 - - + -
6A ILE* 4.0 11.2 - - + -
90A HIS* 4.0 12.6 - - + -
91A ILE* 3.4 57.0 - - + +
93A PHE* 5.4 3.1 - - + -
158A GLN 3.0 13.9 + - - +
159A ILE* 3.0 12.8 + - + +
161A LYS* 1.3 71.7 - - - +
163A ILE* 1.3 73.0 + - + +
165A GLN* 3.3 6.5 + - + +
166A TRP* 2.9 49.0 + + + +
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Residues in contact with ILE 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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4A PRO* 4.4 7.6 - - + -
6A ILE* 3.6 31.6 - - + -
23A LEU* 4.6 4.0 - - + -
27A SER* 4.1 22.0 - - - +
29A LEU* 3.8 22.4 - - + -
75A ILE* 5.3 1.1 - - + -
159A ILE* 2.8 27.2 + - + +
160A LEU* 3.6 12.6 - - + +
162A TRP* 1.3 89.3 - - + +
164A GLU* 1.3 63.4 + - - +
166A TRP* 3.3 3.0 + - - +
167A ILE* 2.9 45.8 + - + +
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Residues in contact with GLU 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 3.1 17.8 + - - +
161A LYS* 3.7 9.8 - - - +
162A TRP 3.3 0.2 - - - -
163A ILE* 1.3 78.3 - - - +
165A GLN* 1.3 60.2 + - - +
167A ILE* 3.4 7.8 + - - +
168A LYS* 3.1 23.8 + - + +
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Residues in contact with GLN 165 (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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161A LYS 3.1 16.7 + - - +
162A TRP* 3.8 7.2 - - + +
163A ILE 3.3 0.4 - - - -
164A GLU* 1.3 76.0 - - - +
166A TRP* 1.3 57.8 + - - +
168A LYS* 3.3 25.1 + - - +
169A ASP* 2.9 64.7 + - - +
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Residues in contact with TRP 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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2A LEU* 3.4 31.4 - - + -
3A LEU 3.5 13.2 - - - -
4A PRO* 3.4 32.8 - - + -
90A HIS* 3.6 39.6 + + - +
162A TRP* 2.9 52.3 + + + +
163A ILE* 3.3 4.2 + - - +
165A GLN* 1.3 75.8 - - - +
167A ILE* 1.3 67.5 + - - +
169A ASP* 3.2 4.5 + - - -
170A HIS* 2.8 80.1 + + + -
182A SO4 3.8 12.3 + - - -
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Residues in contact with ILE 167 (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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1A MET* 3.4 31.0 - - + -
2A LEU 4.1 2.7 - - - +
3A LEU* 3.8 22.0 - - + -
4A PRO* 4.0 17.7 - - + -
29A LEU* 5.2 3.6 - - + -
163A ILE* 2.9 40.5 + - + +
164A GLU* 3.8 7.2 - - - +
166A TRP* 1.3 80.5 - - - +
168A LYS* 1.3 63.2 + - - +
171A ASN* 2.9 34.5 + - - +
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Residues in contact with LYS 168 (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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164A GLU* 3.1 15.4 + - + +
165A GLN* 3.5 29.6 + - - +
167A ILE* 1.3 79.5 - - - +
169A ASP* 1.3 63.9 + - - +
170A HIS 3.2 1.0 + - - -
171A ASN* 3.4 16.4 + - - +
172A SER* 4.0 4.5 + - - -
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 2.9 48.5 + - - +
166A TRP* 3.7 6.1 - - - +
168A LYS* 1.3 80.3 - - - +
170A HIS* 1.3 73.8 + - + +
171A ASN 3.6 0.4 - - - -
172A SER* 3.8 12.3 + - - -
182A SO4 5.7 1.8 + - - +
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Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.5 22.4 - - + +
166A TRP* 2.8 86.5 + + + +
167A ILE 4.3 0.4 - - - +
169A ASP* 1.3 91.3 - - + +
171A ASN* 1.3 70.4 + - - +
172A SER 3.7 1.6 - - - -
182A SO4 2.7 32.9 + - - -
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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