Contacts of the helix formed by residues 138 - 160 (chain A) in PDB entry 1IT8
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 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP 3.7 1.3 - - - +
137A ALA* 1.3 85.4 - - + +
139A ARG* 1.3 65.7 + - - +
140A GLU* 4.4 4.0 - - + +
141A GLN* 3.1 35.0 + - + +
142A ALA* 3.1 18.5 + - - +
173A TYR* 4.2 0.9 - - - +
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Residues in contact with ARG 139 (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 PRO* 1.3 71.0 - - - +
140A GLU* 1.3 63.1 + - - +
142A ALA* 3.2 2.4 + - - +
143A VAL* 3.0 46.6 + - + +
173A TYR* 3.1 45.0 + - + +
175A ASP* 2.5 40.6 + - - -
176A LEU* 3.8 13.3 - - + +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.2 5.0 - - + +
139A ARG* 1.3 79.0 - - - +
141A GLN* 1.3 58.1 + - - +
143A VAL* 3.1 7.8 + - + +
144A LYS* 2.8 42.1 + - + +
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 5.0 0.7 - - - -
134A PRO* 4.4 9.0 - - - +
137A ALA* 3.6 13.6 - - + +
138A PRO* 3.1 39.6 + - + +
140A GLU* 1.3 78.9 - - - +
142A ALA* 1.3 57.6 + - - +
144A LYS* 4.5 10.8 - - + +
145A GLU* 2.8 68.6 + - + +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 3.8 28.3 + - + +
138A PRO 3.1 12.3 + - - +
139A ARG 3.5 8.1 - - - +
141A GLN* 1.3 75.5 - - - +
143A VAL* 1.3 58.2 + - - +
145A GLU* 3.8 1.0 - - - +
146A LEU* 2.9 30.7 + - - +
170A GLY* 4.4 4.4 - - - +
171A SER* 4.3 2.9 - - - -
173A TYR* 3.9 17.3 - - + -
176A LEU* 3.7 20.4 - - + +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.0 41.5 + - + +
140A GLU* 3.5 8.1 - - + +
142A ALA* 1.3 75.0 - - - +
144A LYS* 1.3 69.8 + - - +
146A LEU* 3.0 16.7 + - + +
147A GLU* 3.1 22.9 + - + +
176A LEU* 4.1 17.7 - - + -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 2.8 32.5 + - + +
141A GLN* 3.9 8.7 - - + +
143A VAL* 1.3 75.9 - - - +
145A GLU* 1.3 68.2 + - + +
147A GLU* 3.1 14.0 + - - +
148A ILE* 3.2 29.6 + - + +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 3.5 37.5 - - + +
133A THR* 2.6 43.5 + - - +
134A PRO* 4.4 1.8 - - - +
141A GLN* 2.8 53.8 + - + +
144A LYS* 1.3 82.8 - - + +
146A LEU* 1.3 59.7 + - - +
148A ILE* 3.5 4.2 + - + -
149A THR* 3.0 27.4 + - - -
169A GLN* 6.3 0.2 - - - -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 4.9 0.6 + - - -
142A ALA 2.9 19.6 + - - +
143A VAL* 3.0 7.8 + - + +
145A GLU* 1.3 77.4 - - - +
147A GLU* 1.3 60.8 + - + +
149A THR* 3.2 10.4 - - + -
150A LEU* 2.8 40.0 + - + +
169A GLN* 4.5 20.2 - - + +
170A GLY* 4.8 5.4 - - - +
176A LEU* 3.8 42.2 - - + +
179A TYR* 4.0 20.9 - - + -
180A ALA* 3.8 21.1 - - + -
184A LEU* 6.4 0.2 - - + -
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Residues in contact with GLU 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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143A VAL* 3.1 23.3 + - + +
144A LYS* 3.1 8.9 + - - +
146A LEU* 1.3 75.9 - - + +
148A ILE* 1.3 56.5 + - + +
149A THR 3.1 1.6 - - - -
150A LEU* 3.6 16.5 - - - +
151A SER* 2.7 35.7 + - - -
154A ARG* 3.8 17.0 + - - -
179A TYR* 3.8 27.3 + - - -
183A ARG* 5.2 0.2 + - - -
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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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131A ILE* 3.4 24.7 - - + -
144A LYS* 3.2 33.6 + - + +
145A GLU* 3.8 4.3 - - + +
147A GLU* 1.3 76.1 - - + +
149A THR* 1.3 57.7 + - - +
151A SER* 3.3 7.0 - - - -
152A ARG* 3.0 57.4 + - + +
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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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128A PHE* 3.7 6.8 - - + -
130A ASP* 4.0 24.2 - - + +
131A ILE* 2.9 32.6 + - - +
145A GLU 3.0 17.1 + - - -
146A LEU* 3.2 20.2 - - + +
148A ILE* 1.3 77.3 - - - +
150A LEU* 1.3 60.7 + - + +
152A ARG* 3.1 7.4 + - - +
153A ALA* 2.9 26.4 + - + +
167A THR 4.4 12.8 - - - +
169A GLN* 4.3 7.9 - - + +
184A LEU* 5.5 2.9 - - + -
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 2.8 34.2 + - + +
147A GLU* 3.8 21.8 - - - +
149A THR* 1.3 73.5 - - + +
151A SER* 1.3 62.0 + - - +
153A ALA* 3.3 5.2 - - - +
154A ARG* 3.2 34.2 + - - +
179A TYR* 3.6 36.3 - - + +
180A ALA* 4.7 3.8 - - - +
183A ARG* 4.2 25.6 - - + +
184A LEU* 3.2 35.0 - - + -
187A MET* 4.4 5.5 - - + +
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Residues in contact with SER 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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147A GLU 2.7 21.7 + - - -
148A ILE* 3.3 12.1 - - - -
149A THR 3.1 0.2 - - - -
150A LEU* 1.3 73.1 - - - +
152A ARG* 1.3 65.5 + - - +
154A ARG* 3.0 36.3 + - - +
155A GLU* 3.3 10.4 + - - +
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Residues in contact with ARG 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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101A LEU* 4.2 6.3 - - - +
111A ASN* 3.4 42.4 - - + +
128A PHE* 4.0 7.0 - - + -
129A LEU* 2.7 60.7 + - - +
131A ILE* 4.0 14.5 - - - +
148A ILE* 3.0 41.7 + - + +
149A THR* 3.6 4.7 - - - +
151A SER* 1.3 74.2 - - - +
153A ALA* 1.3 60.4 + - - +
155A GLU* 3.3 8.3 + - - +
156A ALA* 2.8 31.4 + - - +
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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
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128A PHE* 3.6 27.8 - - + -
149A THR 2.9 13.7 + - - +
150A LEU* 3.3 16.2 - - - +
151A SER 3.1 0.2 - - - -
152A ARG* 1.3 79.0 - - - +
154A ARG* 1.3 62.7 + - - +
156A ALA* 3.2 0.5 + - - +
157A GLU* 2.9 17.8 + - - +
184A LEU* 4.0 19.1 - - + -
187A MET* 4.3 7.2 - - - -
189A PHE* 3.2 15.0 - - + -
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Residues in contact with ARG 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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147A GLU* 3.8 18.6 + - - -
150A LEU* 3.3 19.6 + - - +
151A SER* 3.0 33.5 + - - +
153A ALA* 1.3 76.0 - - - +
155A GLU* 1.3 65.1 + - - +
157A GLU* 2.9 28.4 + - - +
158A GLU* 3.2 15.9 + - - +
183A ARG* 3.4 29.5 - - - +
187A MET* 4.5 11.9 - - + -
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Residues in contact with GLU 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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111A ASN* 3.2 25.6 - - - +
112A ARG* 3.3 40.8 + - - +
151A SER 3.3 8.7 + - - +
152A ARG* 3.3 11.5 + - - +
154A ARG* 1.3 76.3 - - - +
156A ALA* 1.3 55.2 + - - +
158A GLU* 2.7 32.8 + - - +
159A ILE* 3.2 28.5 + - + +
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Residues in contact with ALA 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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111A ASN* 4.4 0.4 + - - -
115A ILE* 3.5 30.3 - - + -
128A PHE* 3.8 22.0 - - + -
152A ARG 2.8 20.4 + - - +
153A ALA 3.5 4.7 - - - +
155A GLU* 1.3 71.9 - - - +
157A GLU* 1.3 56.8 + - - +
159A ILE* 4.0 3.4 - - - -
160A LYS* 3.0 38.0 + - - +
164A MET* 4.2 7.4 - - - -
189A PHE* 4.3 3.4 - - + -
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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
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153A ALA 2.9 11.6 + - - +
154A ARG* 2.9 17.7 + - - +
156A ALA* 1.3 78.8 - - - +
158A GLU* 1.3 63.0 + - + +
160A LYS* 4.0 18.7 - - - +
187A MET* 3.2 27.0 - - - +
188A ASN* 2.6 45.6 + - + +
189A PHE* 3.9 8.0 - - + -
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Residues in contact with GLU 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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154A ARG* 3.2 14.8 + - - +
155A GLU* 2.7 18.4 + - - +
157A GLU* 1.3 79.5 - - + +
159A ILE* 1.3 64.5 + - + +
160A LYS 3.6 1.6 - - - +
161A GLU* 5.2 2.6 - - - +
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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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112A ARG* 3.5 51.1 - - + +
115A ILE* 4.0 28.7 - - + -
116A GLU* 5.3 4.3 - - + +
119A HIS* 4.1 6.3 + - - -
155A GLU* 3.5 33.2 - - + +
156A ALA* 4.0 5.6 - - - +
158A GLU* 1.3 84.0 - - + +
160A LYS* 1.3 67.8 + - - +
161A GLU* 3.5 14.4 + - - +
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Residues in contact with LYS 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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7A MET* 4.4 6.6 - - + +
115A ILE* 5.0 0.7 - - + -
119A HIS* 3.9 8.3 - - + -
156A ALA 3.0 21.0 + - - +
157A GLU* 4.0 17.6 - - - +
158A GLU 3.6 1.6 - - - +
159A ILE* 1.3 80.4 - - - +
161A GLU* 1.3 68.0 + - - +
162A ILE 3.0 25.6 + - - +
164A MET* 3.9 21.2 - - + +
188A ASN* 2.9 36.7 + - - +
189A PHE* 4.1 14.1 - - + -
190A GLU* 3.0 27.8 + - - -
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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
------------------------------------------------------------
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