Contacts of the helix formed by residues 149 - 168 (chain A) in PDB entry 3IFS
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 THR 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.0 6.5 - - + -
144A SER* 3.9 8.2 + - - -
145A LYS 5.7 0.2 + - - -
146A SER* 3.4 13.1 + - - -
147A GLY 3.9 0.2 - - - -
148A THR* 1.3 74.9 - - - +
150A THR* 1.3 68.3 + - - +
151A GLU* 3.4 15.4 + - - +
152A PRO* 3.4 18.8 - - + +
153A ALA* 3.1 20.1 + - - +
426A LYS* 5.2 9.5 + - - +
312B HIS* 3.8 21.3 - - + +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 5.2 3.1 - - + -
148A THR 3.0 6.7 + - - -
149A THR* 1.3 73.9 - - - +
151A GLU* 1.3 71.6 + - - +
153A ALA* 3.8 2.9 - - - +
154A LEU* 2.9 33.3 + - + +
429A MSE 3.3 33.4 - - + +
430A PHE* 3.5 16.6 - - - -
433A LEU* 4.9 7.0 - - + -
351B LEU* 4.6 14.0 - - + +
354B LEU* 5.8 3.6 - - + -
362B VAL* 4.3 23.8 - - + -
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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
----------------------------------------------------------
82A ILE* 3.4 12.9 - - + +
118A GLY* 3.3 14.8 - - - +
120A ASN 3.8 12.3 - - - +
121A ILE* 3.4 24.6 - - + +
126A MSE 5.3 1.0 - - - +
149A THR* 3.7 13.3 - - - +
150A THR* 1.3 81.6 + - - +
152A PRO* 1.3 62.9 - - + +
154A LEU* 3.5 5.7 + - - +
155A ALA* 3.0 28.4 + - - +
425A TYR* 4.3 5.1 + - - -
429A MSE 5.5 4.4 - - - +
308B SER* 2.7 34.0 + - - +
312B HIS* 2.9 25.3 + - - -
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Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.5 16.4 - - + +
81A GLY* 4.0 17.7 - - - -
82A ILE* 3.8 25.1 - - + +
118A GLY* 3.4 13.9 - - - +
142A VAL* 5.6 2.7 - - + -
143A ILE 4.8 3.4 - - - +
144A SER* 4.8 14.1 - - - +
149A THR* 3.4 22.0 - - + +
151A GLU* 1.3 93.4 - - + +
153A ALA* 1.3 59.1 + - - +
156A PHE* 2.8 32.9 + - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 6.2 0.2 - - - -
147A GLY 3.7 24.2 - - - +
148A THR* 4.2 5.6 - - - +
149A THR 3.1 21.7 + - - +
150A THR 3.8 2.7 - - - +
152A PRO* 1.3 77.0 - - - +
154A LEU* 1.3 56.9 + - - +
156A PHE* 3.8 6.5 - - - +
157A ARG* 3.1 27.9 + - - +
349B ASP* 4.0 11.8 - - + +
351B LEU* 3.8 17.0 - - + -
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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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121A ILE* 4.3 23.8 - - + -
126A MSE 5.4 4.5 - - + -
150A THR* 2.9 21.4 + - + +
151A GLU* 3.8 4.5 - - - +
153A ALA* 1.3 76.2 - - - +
155A ALA* 1.3 64.8 + - - +
157A ARG* 3.4 10.9 + - - +
158A ILE* 3.2 42.6 + - + +
341B ILE* 3.7 36.8 - - + -
351B LEU* 4.0 14.6 - - + +
354B LEU* 5.7 2.9 - - + -
359B VAL* 4.5 11.0 - - + -
362B VAL* 4.3 22.4 - - + -
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Residues in contact with ALA 155 (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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80A VAL* 4.1 7.6 - - + -
117A VAL* 4.2 13.2 - - + -
118A GLY* 3.3 37.7 - - - +
126A MSE 4.5 16.5 - - + +
151A GLU 3.0 9.1 + - - +
152A PRO 4.0 1.6 - - - +
154A LEU* 1.3 76.1 - - - +
156A PHE* 1.3 58.6 + - - +
158A ILE* 3.2 1.7 + - - -
159A PHE* 2.9 35.4 + - + +
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Residues in contact with PHE 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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80A VAL* 4.0 8.4 - - + +
140A ILE* 4.2 14.6 - - + -
142A VAL* 3.9 43.1 - - + -
152A PRO 2.8 19.8 + - - +
153A ALA* 3.8 6.7 - - - +
155A ALA* 1.3 74.7 - - - +
157A ARG* 1.3 61.0 + - - +
159A PHE* 4.5 0.7 - - - +
160A ARG* 2.8 68.8 + - + +
176A ILE* 4.2 20.6 - - + -
187A LEU* 4.1 11.4 - - + -
190A LEU* 3.3 31.2 - - + -
196A TYR* 4.4 1.8 - + - -
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Residues in contact with ARG 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 ALA 3.1 16.3 + - - +
154A LEU* 3.5 12.6 - - - +
155A ALA 3.3 0.2 - - - -
156A PHE* 1.3 79.5 - - - +
158A ILE* 1.3 66.7 + - + +
160A ARG* 4.2 6.3 + - - +
161A LYS* 3.4 21.1 + - - +
341B ILE* 4.5 13.4 - - - +
342B GLU* 2.9 30.4 + - + +
343B SER* 3.8 0.2 - - - +
344B GLU* 3.5 38.5 + - + +
347B ASP* 3.3 9.1 + - - -
349B ASP* 2.6 42.4 + - - +
351B LEU* 3.8 17.0 + - - +
352B ASN* 2.9 33.5 + - - +
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Residues in contact with ILE 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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126A MSE 4.1 15.7 - - - -
130A MSE 3.5 31.9 - - + -
154A LEU* 3.2 24.5 + - + +
155A ALA 3.6 6.1 - - - +
156A PHE 3.2 0.4 - - - -
157A ARG* 1.3 83.4 - - + +
159A PHE* 1.3 71.9 + - + +
161A LYS* 3.4 5.8 + - - +
162A LEU* 3.3 21.1 + - + +
339B LEU* 4.5 8.7 - - + -
340B THR 6.0 1.8 - - - +
341B ILE* 5.6 6.5 - - + -
359B VAL* 4.0 26.9 - - + -
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.7 27.8 - - + -
80A VAL* 5.5 1.3 - - + -
117A VAL* 3.7 24.9 - - + -
126A MSE 3.6 34.5 - - + -
129A LEU* 4.0 18.4 - - + -
130A MSE 3.8 24.5 - - + -
133A LEU* 3.8 20.0 - - + -
138A PHE* 4.6 2.2 - + + -
140A ILE* 3.7 10.2 - - + +
155A ALA 2.9 27.3 + - - +
156A PHE* 4.7 1.6 - - - +
158A ILE* 1.3 80.3 - - + +
160A ARG* 1.3 60.5 + - - +
161A LYS 3.2 1.8 - - - -
162A LEU* 3.2 13.8 + - + +
163A LEU* 3.0 27.9 + - - +
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Residues in contact with ARG 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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140A ILE* 4.1 10.8 - - - +
156A PHE* 2.8 51.8 + - + +
157A ARG* 4.2 5.5 + - - +
159A PHE* 1.3 71.4 - - - +
161A LYS* 1.3 59.5 + - - +
163A LEU* 3.3 3.1 + - - +
164A GLU* 2.9 67.3 + - - +
169A LYS* 6.2 0.6 - - - +
176A ILE* 4.0 9.0 - - + -
190A LEU* 3.9 26.8 - - - +
194A GLU* 5.0 4.2 + - - -
196A TYR* 3.4 23.6 + - - -
344B GLU* 3.1 37.6 + - - +
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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 ARG 3.4 16.7 + - - +
158A ILE* 3.6 5.6 - - - +
159A PHE 3.2 0.4 - - - -
160A ARG* 1.3 82.2 - - - +
162A LEU* 1.3 62.1 + - + +
164A GLU* 3.9 10.7 - - + +
165A GLU* 2.4 66.8 + - + +
342B GLU* 3.4 39.7 + - + +
343B SER 5.8 2.0 - - - -
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Residues in contact with LEU 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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130A MSE 3.7 44.2 - - + -
133A LEU* 4.9 5.2 - - + -
138A PHE* 4.6 9.6 - - + -
158A ILE* 3.3 13.2 + - + +
159A PHE* 3.2 25.2 + - + +
161A LYS* 1.3 78.3 - - + +
163A LEU* 1.3 58.5 + - - +
165A GLU* 3.3 18.4 + - - +
166A LYS* 2.9 30.6 + - - +
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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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138A PHE* 3.7 37.3 - - + +
140A ILE* 4.0 10.5 - - + -
159A PHE 3.0 13.4 + - - +
160A ARG 3.6 8.3 - - - +
162A LEU* 1.3 77.3 - - - +
164A GLU* 1.3 55.9 + - - +
166A LYS* 3.2 3.9 + - - +
167A TYR* 2.9 64.7 + - + +
172A ALA* 3.9 15.7 - - + +
175A ARG* 4.1 11.2 - - + +
176A ILE* 3.3 38.8 - - + -
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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 ARG* 2.9 65.5 + - + +
161A LYS* 3.9 11.4 - - + +
163A LEU* 1.3 72.7 - - - +
165A GLU* 1.3 57.9 + - + +
168A GLY* 2.7 32.0 + - - -
169A LYS* 4.1 36.3 + - + +
172A ALA* 3.8 25.0 - - + +
176A ILE* 5.1 1.4 - - + +
194A GLU* 5.0 6.1 - - - +
196A TYR* 4.4 4.2 + - - -
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Residues in contact with GLU 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* 2.4 62.4 + - + +
162A LEU* 3.7 20.9 - - - +
164A GLU* 1.3 79.4 - - + +
166A LYS* 1.3 63.5 + - - +
168A GLY* 4.3 1.6 + - - -
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Residues in contact with LYS 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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133A LEU 5.1 1.0 + - - +
135A GLY* 4.9 6.5 - - - +
136A LYS 3.1 36.8 + - - +
137A ASP* 4.2 2.9 + - - +
138A PHE* 3.6 18.4 - - + -
162A LEU 2.9 17.9 + - - +
163A LEU 3.2 4.9 + - - +
165A GLU* 1.3 78.9 - - - +
167A TYR* 1.3 98.7 + - + +
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Residues in contact with TYR 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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137A ASP* 2.7 49.3 + - - +
138A PHE 3.0 7.2 + - - -
163A LEU* 2.9 49.0 + - + +
166A LYS* 1.3 101.6 - - + +
168A GLY* 1.3 64.5 + - - +
171A GLU* 3.5 39.8 + - + +
172A ALA* 4.2 3.6 - - - +
175A ARG* 3.5 26.6 + - - -
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Residues in contact with GLY 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 2.7 23.7 + - - -
165A GLU 4.3 1.6 + - - -
166A LYS 3.8 0.6 - - - -
167A TYR* 1.3 73.3 - - - +
169A LYS* 1.3 60.9 + - - -
170A GLU 3.4 2.9 + - - -
171A GLU 3.5 0.2 + - - -
172A ALA* 2.9 27.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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