Contacts of the helix formed by residues 143 - 161 (chain A) in PDB entry 5IWS
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 VAL 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.2 21.8 - - + +
65A HIS* 3.8 15.0 - - + +
68A PHE* 3.7 38.6 - - + -
142A GLY* 1.3 71.7 - - - -
144A PHE* 1.3 63.8 + - - +
145A VAL 3.3 0.2 - - - -
146A GLY* 3.0 11.1 + - - -
147A ILE* 3.2 11.5 + - + +
237A PHE 4.2 4.3 - - - +
238A GLY 3.4 28.3 - - - +
239A LEU* 4.5 7.7 - - + +
241A HIS* 4.7 7.6 - - + -
242A MSE 5.6 7.2 - - + +
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Residues in contact with PHE 144 (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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141A MSE 3.2 15.2 + - + +
142A GLY 3.1 1.2 - - - -
143A VAL* 1.3 79.2 - - - +
145A VAL* 1.3 61.8 + - - +
147A ILE* 3.2 17.6 + - + +
148A ILE* 3.1 49.7 + - + +
194A LEU* 5.1 2.7 - - + -
198A TRP* 3.4 38.6 - + + -
201A ILE* 5.7 2.7 - - + -
239A LEU* 4.0 33.5 - - + +
242A MSE 5.7 1.1 - - - -
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Residues in contact with VAL 145 (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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65A HIS* 4.7 2.2 - - + -
91A PHE* 3.9 15.5 - - + -
94A THR* 4.2 17.7 - - + -
95A ASN* 3.7 26.5 - - - +
141A MSE 3.7 44.5 + - + +
142A GLY 3.2 19.2 + - - +
144A PHE* 1.3 80.7 - - - +
146A GLY* 1.3 52.1 + - - +
148A ILE* 3.9 5.6 - - + +
149A THR* 2.6 39.1 + - + -
194A LEU* 4.6 3.6 - - + -
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Residues in contact with GLY 146 (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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65A HIS* 3.2 27.4 - - - -
68A PHE* 4.1 4.7 - - - -
69A ALA* 3.3 18.1 + - - -
72A ILE* 4.6 0.3 - - - +
91A PHE* 4.2 2.0 - - - -
142A GLY 4.0 0.6 + - - -
143A VAL 3.0 10.3 + - - -
145A VAL* 1.3 81.6 - - - +
147A ILE* 1.3 59.3 + - - +
149A THR* 3.7 4.9 - - - -
150A GLY* 3.0 21.0 + - - -
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Residues in contact with ILE 147 (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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12A PHE* 4.3 13.5 - - + -
68A PHE* 4.2 8.5 - - + -
72A ILE* 4.1 16.8 - - + -
143A VAL 3.2 13.2 + - - +
144A PHE* 3.2 20.8 + - + +
146A GLY* 1.3 75.9 - - - +
148A ILE* 1.3 67.3 + - + +
150A GLY* 3.3 0.7 + - - -
151A PHE* 3.0 54.3 + - + -
237A PHE* 3.3 39.9 - - + +
239A LEU* 4.9 4.9 - - + -
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Residues in contact with ILE 148 (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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144A PHE* 3.1 49.1 + - + +
145A VAL* 4.1 6.5 - - + +
147A ILE* 1.3 80.0 - - + +
149A THR* 1.3 61.5 + - + +
151A PHE* 3.3 3.6 + - - +
152A LEU* 2.8 33.3 + - + +
190A THR* 3.8 27.4 - - + -
194A LEU* 4.1 24.2 - - + -
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Residues in contact with THR 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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69A ALA* 3.7 3.6 - - - +
87A ALA* 3.5 13.3 - - - -
90A ALA* 3.5 25.3 - - + +
91A PHE* 3.6 31.4 - - - -
94A THR* 3.5 24.0 - - + +
145A VAL* 2.6 25.7 + - + +
146A GLY 3.6 3.8 + - - -
148A ILE* 1.3 78.4 - - + +
150A GLY* 1.3 58.7 + - - +
152A LEU* 3.8 9.1 - - + +
153A GLY 3.0 21.3 + - - -
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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
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69A ALA* 3.5 24.4 - - - +
72A ILE* 3.8 10.5 - - - -
73A GLY* 3.2 14.1 - - - -
87A ALA* 4.0 0.7 - - - -
146A GLY 3.0 19.6 + - - -
147A ILE 3.3 1.1 + - - -
148A ILE 3.1 0.2 - - - -
149A THR* 1.3 75.2 + - - +
151A PHE* 1.3 64.7 + - - +
154A ALA* 3.2 18.4 + - - +
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Residues in contact with PHE 151 (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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8A PHE* 4.4 14.4 - + - -
12A PHE* 3.4 41.3 - + - -
72A ILE* 3.9 14.4 - - + -
76A TRP* 3.4 54.7 - + - -
147A ILE* 3.0 39.2 + - + +
148A ILE* 3.9 3.6 - - - +
150A GLY* 1.3 72.9 - - - +
152A LEU* 1.3 60.1 + - - +
154A ALA* 3.8 3.2 - - - +
155A THR* 2.8 39.5 + - - +
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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
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90A ALA* 4.2 9.6 - - + -
94A THR* 4.7 2.5 - - - +
148A ILE* 2.8 20.6 + - + +
149A THR* 3.9 6.5 - - - +
151A PHE* 1.3 77.0 - - - +
153A GLY* 1.3 62.5 + - - +
155A THR* 4.0 4.7 - - - -
156A LEU* 3.0 45.4 + - + +
186A TRP* 4.0 28.7 - - + +
187A SER* 3.9 23.1 - - - +
190A THR* 3.5 29.6 - - + +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY 3.9 4.8 - - - +
86A ALA* 3.3 24.7 - - - +
87A ALA* 3.7 23.3 - - - -
90A ALA* 4.7 1.9 - - - +
149A THR 3.0 14.0 + - - -
150A GLY 4.0 0.2 - - - -
152A LEU* 1.3 76.5 - - - +
154A ALA* 1.3 60.1 + - - +
156A LEU* 3.8 1.9 + - - -
157A TYR* 3.2 18.9 + - - +
183A VAL* 5.1 2.0 - - - -
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Residues in contact with ALA 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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73A GLY 3.3 23.8 - - - +
76A TRP* 3.6 36.6 - - + -
77A ALA* 4.2 4.5 - - - -
83A GLY* 4.2 1.0 + - - -
150A GLY 3.2 15.2 + - - +
151A PHE 4.0 2.9 - - - +
152A LEU 3.3 0.2 - - - -
153A GLY* 1.3 76.0 - - - +
155A THR* 1.3 59.2 + - - +
157A TYR* 3.5 1.0 + - - +
158A ASN* 3.0 37.1 + - - +
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Residues in contact with THR 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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76A TRP* 4.8 8.9 + - - -
151A PHE* 2.8 28.4 + - - +
152A LEU* 4.0 6.3 - - + -
154A ALA* 1.3 79.0 - - - +
156A LEU* 1.3 69.2 + - + +
158A ASN* 3.4 8.8 + - - +
159A LYS* 3.4 24.7 + - + +
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Residues in contact with LEU 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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152A LEU* 3.0 34.3 + - + +
153A GLY 4.3 2.7 - - - +
155A THR* 1.3 82.4 - - + +
157A TYR* 1.3 61.1 + - - +
159A LYS* 4.9 1.1 - - + -
160A TYR* 3.2 37.7 + - + +
179A VAL* 4.2 5.8 - - + +
182A VAL* 3.5 36.8 - - + +
183A VAL* 3.7 26.2 - - + -
186A TRP* 3.5 38.1 - - + +
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Residues in contact with TYR 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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77A ALA* 4.2 9.4 - - + -
80A ARG* 3.9 41.1 - - + +
82A GLY* 3.5 32.6 + - - +
83A GLY* 3.6 18.2 - - - -
153A GLY 3.2 19.7 + - - +
154A ALA 4.0 2.0 - - - +
155A THR 3.2 0.2 - - - -
156A LEU* 1.3 74.5 - - - +
158A ASN* 1.3 64.8 + - - +
159A LYS 3.1 2.7 + - - -
161A TYR* 3.1 52.2 + - + +
176A LYS* 3.8 33.6 + - + +
179A VAL* 3.7 28.9 - - + +
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Residues in contact with ASN 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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76A TRP* 3.2 28.1 + - - -
77A ALA* 3.4 13.8 - - - +
78A LYS* 4.8 6.9 - - - +
80A ARG* 2.8 27.0 + - - +
154A ALA 3.0 24.6 + - - +
155A THR* 3.4 6.9 + - - +
157A TYR* 1.3 75.2 - - - +
159A LYS* 1.3 58.3 + - - +
161A TYR* 3.7 19.8 - - - -
162A ASN* 5.1 0.2 - - - +
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Residues in contact with LYS 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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155A THR* 3.4 16.0 + - + +
156A LEU* 6.1 0.9 - - + -
157A TYR 3.1 0.4 - - - -
158A ASN* 1.3 80.6 - - - +
160A TYR* 1.3 105.6 + - + +
161A TYR 3.6 1.1 - - - -
162A ASN* 3.5 14.9 - - - +
163A TYR* 4.8 3.3 + - - +
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Residues in contact with TYR 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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156A LEU* 3.2 33.8 + - + +
159A LYS* 1.3 122.9 + - + +
161A TYR* 1.3 62.3 + - - +
162A ASN 3.1 3.4 + - - -
163A TYR* 3.4 35.4 + + - +
175A GLY 2.9 18.9 - - - +
178A PHE* 3.6 34.4 - + + +
179A VAL* 3.7 10.3 - - + +
182A VAL* 3.6 35.1 - - + +
186A TRP* 4.8 7.8 + - - -
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Residues in contact with TYR 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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78A LYS* 5.8 1.7 + - - -
80A ARG* 3.3 32.5 + - - -
157A TYR* 3.1 54.4 + - + +
158A ASN 3.7 17.0 - - - -
160A TYR* 1.3 77.9 - - - +
162A ASN* 1.3 89.8 + - + +
175A GLY* 3.3 19.5 - - - -
176A LYS* 3.4 15.0 + - + +
179A VAL* 3.9 7.4 - - - +
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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