Contacts of the helix formed by residues 137 - 151 (chain A) in PDB entry 2AG1
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 HIS 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.3 1.1 - - + -
133A MSE 4.7 1.2 + - - -
134A ALA* 3.4 37.3 + - + +
135A THR 3.0 1.6 + - - -
136A GLU* 1.3 85.6 + - + +
138A ILE* 1.3 66.4 + - - +
139A PRO* 3.5 0.7 - - - -
140A ARG* 3.4 34.6 + - - +
141A LEU* 3.0 43.9 + - + +
104C LEU 3.3 26.4 + - - -
105C ARG* 3.8 3.3 - - - +
106C ASP* 3.3 21.3 + - - -
107C ASP* 3.9 13.4 + - - +
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Residues in contact with ILE 138 (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 GLY* 3.8 28.7 - - - +
9A LEU* 3.9 4.5 - - + -
10A VAL* 3.5 39.0 - - + +
132A VAL* 4.0 20.6 - - + -
135A THR* 2.9 21.0 + - - +
137A HIS* 1.3 76.9 - - - +
139A PRO* 1.4 62.4 - - + +
141A LEU* 3.7 1.4 - - - +
142A VAL* 2.8 42.7 + - + +
161A LEU* 4.2 13.5 - - + -
165A ILE* 3.6 23.3 - - + +
166A LEU* 4.5 4.3 - - + -
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Residues in contact with PRO 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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9A LEU* 3.9 20.9 - - + -
13A THR* 3.4 27.6 - - + +
135A THR 4.1 0.7 - - - +
136A GLU 3.6 13.2 - - - +
138A ILE* 1.4 93.4 - - + +
140A ARG* 1.3 62.4 + - - +
142A VAL 3.3 0.2 + - - -
143A MSE 3.0 25.5 + - - +
175A VAL* 3.7 18.8 - - + -
176A ILE 3.7 7.4 - - - +
177A ILE* 4.2 9.6 - - + -
178A PRO* 3.7 21.8 - - + -
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Residues in contact with ARG 140 (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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136A GLU 5.2 1.5 + - - +
137A HIS* 3.4 44.2 + - - +
139A PRO* 1.3 79.4 - - - +
141A LEU* 1.3 81.9 + - - +
143A MSE 3.6 2.4 + - - +
144A GLN* 2.9 33.8 + - - +
147A ARG* 4.8 2.8 + - - -
178A PRO* 4.4 15.6 - - + +
106C ASP* 4.3 1.2 - - - +
107C ASP 2.8 23.0 + - - -
108C GLU 3.1 24.2 + - - -
109C THR* 3.5 17.7 - - - +
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Residues in contact with LEU 141 (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 TRP* 4.1 14.7 - - + -
130A HIS* 4.5 7.0 - - + -
132A VAL* 4.2 29.4 - - + -
137A HIS* 3.0 35.4 + - + +
138A ILE 3.9 1.6 - - - +
140A ARG* 1.3 110.4 - - + +
142A VAL* 1.3 64.7 + - - +
144A GLN* 3.7 15.4 - - - +
145A ALA* 2.9 24.6 + - - +
159A LEU* 4.3 8.0 - - + +
107C ASP* 4.1 19.5 - - - +
108C GLU* 4.2 9.0 - - + -
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Residues in contact with VAL 142 (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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10A VAL* 4.5 16.4 - - + +
13A THR* 3.8 20.4 - - + -
14A LEU* 3.9 20.2 - - + -
96A LEU* 4.5 5.8 - - + -
98A LEU* 4.9 2.9 - - + -
138A ILE* 2.8 41.0 + - + +
141A LEU* 1.3 71.4 - - - +
143A MSE 1.3 59.9 + - - +
145A ALA* 3.2 5.9 + - - +
146A ILE* 2.9 49.4 + - + +
159A LEU* 3.7 22.4 - - + -
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Residues in contact with MSE 143 (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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13A THR* 4.0 17.7 - - + +
17A ALA* 3.7 21.5 - - + -
139A PRO 3.0 17.1 + - - +
140A ARG* 3.9 5.2 - - - +
142A VAL* 1.3 75.7 - - - +
144A GLN* 1.3 64.0 + - - +
146A ILE* 3.4 40.2 + - + -
147A ARG* 3.0 42.6 + - - +
178A PRO* 4.5 13.9 - - + +
179A ASP 3.7 20.2 - - - +
180A LEU* 3.2 43.5 - - + -
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Residues in contact with GLN 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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128A TRP* 3.5 23.3 - - + -
140A ARG* 2.9 21.3 + - - +
141A LEU* 3.7 19.7 - - - +
142A VAL 3.3 0.2 - - - -
143A MSE 1.3 75.8 - - - +
145A ALA* 1.3 63.9 + - - +
147A ARG* 3.2 29.1 + - - +
148A ALA* 3.0 22.5 + - + +
108C GLU* 3.3 34.3 + - - +
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Residues in contact with ALA 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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96A LEU* 4.3 10.8 - - + -
128A TRP* 3.9 17.8 - - + -
141A LEU 2.9 14.1 + - - +
142A VAL* 3.3 10.1 - - - +
144A GLN* 1.3 76.5 - - - +
146A ILE* 1.3 56.7 + - - +
148A ALA* 3.2 4.8 + - - +
149A ALA* 2.9 25.6 + - - +
157A VAL* 3.6 28.6 - - + +
159A LEU* 4.2 13.7 - - + -
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Residues in contact with ILE 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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13A THR 5.2 0.2 - - - +
14A LEU* 4.2 8.1 - - + -
17A ALA* 3.9 16.6 - - + -
19A VAL* 5.0 0.2 - - + -
67A LEU* 3.9 21.5 - - + -
96A LEU* 3.9 21.5 - - + -
142A VAL* 2.9 35.2 + - + +
143A MSE 3.4 35.4 - - + -
144A GLN 3.2 0.2 - - - -
145A ALA* 1.3 73.5 - - - +
147A ARG* 1.3 65.6 + - - +
149A ALA* 3.2 6.9 + - - +
150A LEU* 3.0 44.5 + - + +
180A LEU* 4.4 3.6 - - + -
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Residues in contact with ARG 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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140A ARG 4.8 1.8 + - - -
143A MSE 3.0 44.8 + - - +
144A GLN* 3.6 38.9 - - - +
146A ILE* 1.3 75.0 - - - +
148A ALA* 1.3 63.1 + - - +
150A LEU* 3.3 0.9 + - - +
151A SER* 3.0 29.1 + - - -
178A PRO* 6.0 1.0 - - - +
179A ASP 5.3 2.0 + - - -
180A LEU* 3.9 18.4 - - + -
181A VAL 4.3 19.9 - - - +
182A LEU* 4.0 25.4 - - + +
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Residues in contact with ALA 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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127A LYS* 2.9 35.8 + - + +
128A TRP* 4.6 15.5 - - + -
144A GLN* 3.0 13.9 + - + +
145A ALA* 3.5 9.6 - - - +
147A ARG* 1.3 78.1 - - - +
149A ALA* 1.3 60.1 + - - +
151A SER* 3.7 5.7 + - - -
157A VAL* 3.9 13.2 - - + -
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Residues in contact with ALA 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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67A LEU* 4.0 23.3 - - + -
94A PRO* 3.5 10.8 - - + +
95A VAL 4.4 7.4 - - - +
96A LEU* 4.9 1.6 - - - +
145A ALA 2.9 13.4 + - - +
146A ILE* 3.2 9.1 + - - +
148A ALA* 1.3 77.7 - - - +
150A LEU* 1.3 59.9 + - - +
154A ARG* 3.5 3.6 - - - -
155A GLY 3.3 40.9 + - - +
157A VAL* 3.7 10.2 - - + +
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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
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66A LYS 4.8 1.8 - - - -
67A LEU* 4.0 35.9 - - + +
94A PRO* 4.3 11.9 - - + -
146A ILE* 3.0 38.5 + - + +
147A ARG 3.3 2.2 + - - +
148A ALA 3.3 0.2 - - - -
149A ALA* 1.3 77.6 - - - +
151A SER* 1.3 60.3 + - - +
154A ARG* 2.9 33.0 + - + +
180A LEU* 4.3 18.2 - - + -
182A LEU* 4.4 15.3 - - + -
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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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127A LYS* 2.9 23.5 + - - -
147A ARG 3.0 17.9 + - - -
148A ALA* 3.7 7.4 + - - -
149A ALA 3.4 0.4 - - - -
150A LEU* 1.3 79.5 - - - +
152A ALA* 1.3 61.5 + - - +
153A PRO 3.0 7.8 - - - +
154A ARG* 3.4 6.9 + - - +
182A LEU* 5.1 14.6 - - - -
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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