Contacts of the helix formed by residues 140 - 147 (chain A) in PDB entry 2WEA
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 PHE 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.7 4.9 - - + +
90A VAL* 3.5 35.7 - - + -
92A VAL* 3.6 32.1 - - + -
95A VAL* 3.5 25.1 - - + -
97A ALA* 3.7 21.1 - - + -
100A GLN* 3.3 18.4 + - - +
122A LEU* 4.2 26.0 - - + +
123A GLY 4.5 1.8 + - - -
124A LEU* 4.9 0.2 - - + -
139A THR* 1.3 73.2 - - - +
141A PHE* 1.3 67.4 + - - +
143A THR* 3.3 1.9 + - - -
144A VAL* 3.1 46.4 + - + +
167A PHE* 4.1 27.1 - + - -
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Residues in contact with PHE 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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124A LEU* 3.9 24.8 - - + +
125A ALA 6.0 0.7 - - - -
139A THR* 3.2 6.8 + - - +
140A PHE* 1.3 85.7 - - - +
142A ASP* 1.3 67.1 + - - +
144A VAL* 3.2 2.4 + - - +
145A LYS* 2.7 51.6 + - + +
148A LEU* 3.8 18.4 - - + -
151A PRO 3.5 24.9 - - - -
152A LEU* 3.6 31.4 - - - -
153A PHE* 3.8 26.7 - + + -
167A PHE* 4.3 9.6 - + + -
191A TRP* 4.7 10.5 - + - -
310A PHE 4.6 0.9 - - - -
312A SER* 4.3 10.3 - - - -
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Residues in contact with ASP 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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125A ALA 4.7 0.3 - - - +
126A PHE* 4.4 7.5 - - - +
127A SER* 2.5 45.0 + - - +
138A THR* 3.9 12.7 - - + +
139A THR* 2.9 13.6 + - - +
141A PHE* 1.3 85.6 - - - +
143A THR* 1.3 63.8 + - - +
144A VAL 3.5 0.2 + - - -
145A LYS* 2.9 44.5 + - - +
146A SER 5.0 0.9 + - - -
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Residues in contact with THR 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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97A ALA* 3.9 19.3 - - + -
98A HIS 4.1 15.7 - - - +
99A GLY 5.4 1.3 - - - +
100A GLN* 2.7 32.4 + - - +
138A THR* 2.8 23.9 + - - +
139A THR 2.8 8.4 + - - -
140A PHE 3.5 3.4 - - - -
141A PHE 3.2 0.2 - - - -
142A ASP* 1.3 79.8 - - - +
144A VAL* 1.3 58.1 + - - +
146A SER* 5.0 4.5 + - - -
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Residues in contact with VAL 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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95A VAL* 4.2 12.1 - - + -
96A THR 4.0 7.9 - - - +
97A ALA* 3.6 32.1 - - + -
140A PHE* 3.1 45.1 + - + +
141A PHE* 3.6 8.1 - - + +
143A THR* 1.3 74.9 - - + +
145A LYS* 1.3 68.2 + - - +
146A SER 3.3 2.2 - - - -
147A SER* 2.7 34.0 + - - +
148A LEU* 3.2 23.2 + - + +
167A PHE* 5.4 0.9 - - + -
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Residues in contact with LYS 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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141A PHE* 2.7 30.2 + - + +
142A ASP* 2.9 36.5 + - - +
143A THR 3.5 1.6 - - - -
144A VAL* 1.3 72.1 - - - +
146A SER* 1.3 64.2 + - - +
148A LEU* 3.2 29.2 + - - +
151A PRO* 3.5 26.6 - - + +
312A SER* 3.7 29.0 - - - +
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Residues in contact with SER 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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142A ASP 5.0 1.2 + - - -
143A THR 5.0 4.2 + - - -
144A VAL 3.2 0.6 + - - -
145A LYS* 1.3 82.8 - - - +
147A SER* 1.3 61.7 + - - +
148A LEU 3.4 4.4 - - - +
151A PRO* 5.7 0.9 - - - -
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Residues in contact with SER 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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1A ALA* 3.7 7.5 - - - +
2A ALA* 2.9 29.8 + - - +
95A VAL* 5.2 1.6 - - - +
96A THR 5.7 0.7 + - - -
143A THR 5.8 0.2 - - - -
144A VAL* 2.7 31.5 + - - +
146A SER* 1.3 78.1 + - - +
148A LEU* 1.3 63.6 + - - +
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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