Contacts of the helix formed by residues 140 - 148 (chain B) in PDB entry 3ANX
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 ASP 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ILE* 3.5 29.5 - - + +
139B ASP* 1.3 85.6 + - - +
141B ALA* 1.3 56.3 + - - +
142B ARG* 2.7 53.1 + - - +
143B ALA* 3.0 20.3 + - + +
144B TYR* 3.1 10.2 + - - +
168B PRO* 4.3 19.2 - - - +
172B LEU* 3.9 6.5 - - - +
315B MTA 4.0 11.0 + - - -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.0 21.1 - - + -
107B VAL* 3.4 38.6 - - + -
139B ASP 3.3 3.8 + - - -
140B ASP* 1.3 71.8 + - - +
142B ARG* 1.3 49.4 - - - +
144B TYR* 3.9 2.7 - - - -
145B LEU* 2.0 42.0 + - + +
172B LEU* 4.2 5.6 - - + -
177B PHE* 4.7 2.2 - - + -
315B MTA 3.6 18.8 + - + +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP* 2.7 19.2 + - - +
141B ALA* 1.3 79.9 - - - +
143B ALA* 1.3 59.0 + - - +
145B LEU* 3.2 4.1 - - - +
146B GLU* 3.0 49.1 + - - +
171B LEU* 3.1 48.0 + - - +
172B LEU* 4.4 10.2 - - + +
176B GLU* 3.8 5.7 + - - +
177B PHE* 3.5 38.0 - - + +
180B LEU* 3.9 9.6 - - + +
295B ASP* 2.5 45.2 + - - -
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Residues in contact with ALA 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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139B ASP* 3.3 23.3 - - - +
140B ASP* 3.0 11.8 + - + +
142B ARG* 1.3 73.9 - - - +
144B TYR* 1.3 53.9 + - - +
146B GLU* 3.3 7.8 + - - +
147B ARG* 2.6 43.0 + - + +
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Residues in contact with TYR 144 (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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82B LEU* 4.9 5.2 - - + -
105B VAL* 3.7 16.6 - - + +
107B VAL* 4.0 27.8 - - + -
137B VAL* 3.9 28.0 - - + -
139B ASP* 3.5 9.5 + - - +
140B ASP 3.1 9.5 + - - +
141B ALA 4.2 2.0 - - - +
142B ARG 3.4 0.4 - - - -
143B ALA* 1.3 74.1 - - - +
145B LEU* 1.3 79.7 + - + +
147B ARG* 2.8 51.9 + - - +
148B THR* 2.9 36.9 + - + +
150B GLU* 3.4 17.3 + - - -
152B TYR* 2.9 31.1 + + - -
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Residues in contact with LEU 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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82B LEU* 4.0 27.4 - - + -
84B VAL* 5.2 2.2 - - + -
107B VAL* 5.8 0.2 - - + -
141B ALA* 2.0 37.2 - - + +
142B ARG* 3.2 16.4 - - + +
144B TYR* 1.3 85.0 - - + +
146B GLU* 1.3 54.9 + - - -
148B THR* 3.2 9.5 - - - +
152B TYR* 5.6 0.4 - - + -
177B PHE* 4.3 18.2 - - + -
180B LEU* 3.8 19.0 - - + +
181B VAL* 4.5 22.0 - - + +
184B HIS* 2.6 49.3 + - + -
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Residues in contact with GLU 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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142B ARG* 3.0 41.0 + - - +
143B ALA* 3.4 6.7 + - - +
145B LEU* 1.3 76.0 - - - +
147B ARG* 1.3 56.7 + - - +
148B THR 3.2 12.7 + - - +
180B LEU* 3.7 27.0 - - + +
184B HIS* 5.3 0.2 - - - -
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Residues in contact with ARG 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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137B VAL* 4.2 7.3 - - - +
139B ASP* 3.0 38.8 + - - +
143B ALA* 2.6 23.2 + - + +
144B TYR* 2.8 37.1 + - - +
146B GLU* 1.3 68.9 - - - +
148B THR* 1.4 56.9 + - - -
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Residues in contact with THR 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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144B TYR* 2.9 49.2 + - + +
145B LEU* 3.2 12.0 - - - +
146B GLU 3.2 5.0 - - - +
147B ARG* 1.4 82.3 - - - +
149B GLU* 1.3 64.9 + - - +
150B GLU* 3.0 29.3 + - + +
184B HIS* 2.9 25.5 + - + +
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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