Contacts of the helix formed by residues 142 - 153 (chain B) in PDB entry 2ADM
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 LEU 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.5 12.3 - - + -
107B PRO* 3.7 24.7 - - + +
108B TYR 5.6 0.2 - - - -
109B GLY* 2.7 25.3 + - - +
110B ILE* 4.9 0.6 - - - +
111B VAL* 4.6 11.7 - - - +
112B GLY* 4.1 27.6 - - - +
129B TYR* 4.1 25.8 - - + -
136B TRP* 4.3 15.3 - - + -
141B ASN* 1.3 70.5 + - - +
143B TYR* 1.3 61.6 + - - +
145B ALA* 3.1 7.1 + - - +
146B PHE* 3.1 33.8 + - + -
500B SAM 5.3 9.9 - - - +
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Residues in contact with TYR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PRO* 4.1 17.8 - - + +
107B PRO 3.4 14.6 + - - +
108B TYR* 4.1 8.3 - + + -
141B ASN* 2.9 42.7 + - + -
142B LEU* 1.3 78.1 - - - +
144B GLY* 1.3 65.0 + - - +
146B PHE* 3.5 8.9 + - - +
147B LEU* 3.1 28.3 + - + +
164B VAL* 3.9 16.8 - - + -
165B PRO* 3.7 29.7 + - + -
167B THR* 2.6 28.5 + - - -
168B TRP* 3.1 42.4 + + + +
174B PHE* 3.6 13.4 - + - -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 3.5 26.8 + - - -
141B ASN* 3.0 9.8 + - - +
143B TYR* 1.3 83.4 - - - +
145B ALA* 1.3 64.8 + - - +
147B LEU* 3.2 5.8 + - - +
148B GLU* 3.1 20.3 + - - +
174B PHE* 4.7 1.3 - - - -
177B LEU* 3.9 17.5 - - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.7 13.4 - - + +
133B PHE* 3.8 36.7 - - + -
136B TRP* 3.9 19.7 - - + -
140B TYR* 3.6 9.5 - - + -
141B ASN 3.6 0.8 + - - -
142B LEU* 3.1 10.7 + - - +
144B GLY* 1.3 73.7 - - - +
146B PHE* 1.3 59.6 + - - +
148B GLU* 3.3 3.7 + - - +
149B LYS* 2.9 31.0 + - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 4.3 9.2 - - + -
47B ALA* 4.0 13.7 - - + -
90B PHE* 3.5 36.6 - + + -
91B LEU* 3.7 29.4 - - + -
106B PRO* 3.7 24.2 - - + -
107B PRO* 3.5 29.4 - - + -
142B LEU* 3.1 31.0 + - + +
143B TYR 3.6 8.3 - - - +
145B ALA* 1.3 76.4 - - - +
147B LEU* 1.3 58.0 + - - +
149B LYS* 3.8 0.9 - - - +
150B ALA* 2.9 32.2 + - - +
162B PHE* 3.9 5.6 - + + -
500B SAM 3.8 29.6 - + - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TYR* 3.1 26.5 + - + +
144B GLY 3.2 9.1 + - - +
146B PHE* 1.3 78.0 - - - +
148B GLU* 1.3 57.2 + - - +
150B ALA* 3.2 3.3 + - - +
151B VAL* 2.9 34.4 + - - +
160B LEU* 4.0 13.9 - - + -
162B PHE* 3.9 25.8 - - + -
164B VAL* 4.6 9.4 - - + -
168B TRP* 5.3 4.7 - - + -
177B LEU* 4.0 29.6 - - + -
181B LEU* 4.8 9.6 - - + -
206B ILE* 3.8 36.1 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA 4.3 2.1 - - - +
133B PHE* 3.4 24.6 - - + +
134B SER* 3.1 29.1 + - - -
135B THR* 2.9 35.7 + - + +
144B GLY 3.1 12.0 + - - +
145B ALA* 3.3 6.9 + - - +
147B LEU* 1.3 75.2 - - - +
149B LYS* 1.3 62.6 + - - +
151B VAL* 3.4 2.4 + - - +
152B ARG* 3.0 56.8 + - - +
177B LEU* 4.7 1.9 - - + +
180B PHE* 3.7 23.6 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.1 49.6 - - + +
91B LEU* 4.0 19.5 + - + +
92B LEU* 4.5 0.6 - - - +
93B TRP 2.9 15.0 + - - +
94B GLU* 2.8 29.3 + - - -
133B PHE* 4.0 15.0 - - + -
145B ALA 2.9 17.5 + - - +
146B PHE 3.8 3.8 - - - +
148B GLU* 1.3 75.7 - - - +
150B ALA* 1.3 62.8 + - - +
152B ARG* 3.1 20.8 + - + +
153B LEU* 3.1 33.0 + - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 4.0 8.3 - - + -
102B ILE* 3.5 26.5 - - + +
146B PHE 2.9 19.7 + - - +
147B LEU 3.4 5.2 - - - +
149B LYS* 1.3 76.7 - - - +
151B VAL* 1.3 61.6 + - - +
153B LEU* 3.1 10.9 + - - +
154B LEU* 3.3 10.9 + - - +
160B LEU* 3.7 18.8 - - + -
162B PHE* 3.9 19.3 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 2.9 20.0 + - + +
148B GLU 3.8 0.2 - - - +
149B LYS 3.3 0.2 - - - -
150B ALA* 1.3 75.8 - - - +
152B ARG* 1.3 61.3 + - + +
154B LEU* 3.3 15.5 - - - +
160B LEU* 3.8 15.3 - - + -
180B PHE* 3.6 27.6 - - + -
181B LEU* 4.0 22.0 - - + -
184B GLU* 4.1 6.5 - - + +
208B PHE* 3.8 33.2 - - + -
210B LYS* 2.8 34.5 + - - -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA 5.5 2.0 + - - -
133B PHE* 6.1 2.2 - - - -
134B SER* 3.2 27.7 + - - -
148B GLU* 3.0 34.0 + - - +
149B LYS* 3.1 15.5 + - + +
151B VAL* 1.3 79.2 - - + +
153B LEU* 1.3 61.9 + - + +
154B LEU 3.3 2.5 + - - +
180B PHE* 3.4 27.4 - - + -
184B GLU* 5.8 2.2 + - - -
210B LYS* 4.1 10.9 + - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.8 3.1 - - + -
90B PHE* 3.7 22.0 - - + -
93B TRP* 3.7 26.7 - - + +
94B GLU* 5.8 0.2 - - - +
95B PRO* 3.3 33.0 - - + -
97B GLU 4.8 3.1 - - - +
98B ALA* 3.3 9.9 - - - +
99B PHE* 2.8 42.5 + - + -
102B ILE* 4.2 9.2 - - + -
149B LYS* 3.1 31.6 + - + +
150B ALA 3.1 5.3 + - - +
152B ARG* 1.3 79.9 - - + +
154B LEU* 1.3 53.9 + - - +
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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
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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