Contacts of the helix formed by residues 139 - 150 (chain A) in PDB entry 4IRV
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 ASN 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LYS* 4.1 20.9 - - - +
136A SER 4.0 11.1 + - - +
137A LYS* 3.8 11.1 + - - +
138A ILE* 1.3 76.6 - - - +
140A THR* 1.3 65.7 + - - +
141A ARG* 2.8 38.6 + - - +
142A SER* 2.7 38.4 + - - -
143A ILE* 3.1 25.7 + - - +
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Residues in contact with THR 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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36A LYS* 4.8 9.7 + - - +
39A ASN* 4.7 13.0 - - + +
40A VAL* 4.0 21.4 - - + +
43A SER* 5.8 2.2 - - - +
139A ASN* 1.3 75.7 - - - +
141A ARG* 1.3 54.1 + - - +
143A ILE* 3.9 0.3 - - - +
144A ARG* 2.5 62.9 + - + +
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Residues in contact with ARG 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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139A ASN* 2.8 31.7 + - - +
140A THR* 1.3 75.1 - - - +
142A SER* 1.3 63.6 + - - +
144A ARG* 3.7 6.3 - - - +
145A ASN* 3.0 30.2 + - + +
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Residues in contact with SER 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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128A TRP* 3.5 22.9 - - - -
132A GLN* 5.8 0.7 - - - -
137A LYS 2.7 27.6 + - - -
138A ILE* 3.6 2.8 - - - -
139A ASN* 2.7 28.2 + - - -
141A ARG* 1.3 80.8 - - - +
143A ILE* 1.3 55.7 + - - +
145A ASN* 3.7 8.5 + - - +
146A PHE* 2.9 25.6 + - - +
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Residues in contact with ILE 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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33A ALA* 4.9 2.7 - - + +
36A LYS* 3.7 37.0 - - + +
37A VAL* 4.3 10.1 - - + +
40A VAL* 4.0 22.2 - - + -
125A PHE* 4.6 8.7 - - + -
128A TRP* 4.2 19.5 - - + -
138A ILE* 3.9 14.4 - - + -
139A ASN 3.1 21.8 + - - +
140A THR 4.0 1.8 - - - +
142A SER* 1.3 74.7 - - - +
144A ARG* 1.3 67.6 + - - +
146A PHE* 3.3 6.2 + - - +
147A MSE 3.0 23.5 + - + +
165A LEU* 4.1 23.3 - - + -
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Residues in contact with ARG 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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40A VAL* 4.4 10.8 - - + -
43A SER* 3.9 23.0 + - - -
44A PHE* 3.7 40.4 - - + -
140A THR* 2.5 56.9 + - + +
141A ARG* 3.7 5.8 - - - +
143A ILE* 1.3 78.1 - - - +
145A ASN* 1.3 56.5 + - - +
147A MSE 3.2 3.5 + - - +
148A GLU* 3.0 44.0 + - + +
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Residues in contact with ASN 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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128A TRP* 6.3 0.2 - - - -
141A ARG* 3.0 19.7 + - + +
142A SER* 3.7 8.5 + - - +
144A ARG* 1.3 74.6 - - - +
146A PHE* 1.3 60.9 + - - +
148A GLU* 4.6 3.6 - - - -
149A ASN* 2.8 55.5 + - - +
150A ILE* 3.4 24.3 - - - +
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Residues in contact with PHE 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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124A ILE* 4.1 6.3 - - + -
125A PHE* 3.4 52.0 - + + -
128A TRP* 3.6 42.8 - + + -
142A SER 2.9 15.7 + - - +
143A ILE* 3.3 12.6 - - - +
145A ASN* 1.3 76.6 - - - +
147A MSE 1.3 75.1 + - + +
150A ILE* 2.9 42.7 + - + -
151A ILE* 2.9 55.4 + - + -
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Residues in contact with MSE 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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44A PHE* 4.0 15.5 - - + -
143A ILE 3.0 15.0 + - - +
144A ARG 3.2 6.3 + - - +
146A PHE* 1.3 96.5 - - + +
148A GLU* 1.3 59.9 + - - +
151A ILE* 3.6 19.9 - - + +
154A PRO* 5.9 0.3 - - - +
155A ILE* 3.9 20.6 + - + +
161A LYS* 3.4 50.9 - - + +
164A PHE* 3.5 37.5 - - + -
165A LEU* 3.9 27.8 - - + -
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Residues in contact with GLU 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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44A PHE* 3.9 19.2 - - + -
144A ARG* 3.0 27.9 + - + +
145A ASN* 3.9 3.4 - - - +
147A MSE 1.3 78.1 - - - +
149A ASN* 1.3 78.8 + - - +
150A ILE 3.9 0.2 - - - -
151A ILE* 5.6 1.3 - - - -
154A PRO* 5.6 6.5 - - - +
158A ASP* 4.5 5.1 - - - +
161A LYS* 3.7 21.4 + - - +
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Residues in contact with ASN 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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145A ASN* 2.8 35.2 + - - +
148A GLU* 1.3 93.6 + - - +
150A ILE* 1.3 68.1 + - + +
151A ILE 4.0 1.3 - - - -
152A GLN* 4.8 7.2 + - - -
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Residues in contact with ILE 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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124A ILE* 4.7 9.6 - - + +
128A TRP* 4.9 13.2 - - + +
145A ASN* 3.4 37.2 - - - +
146A PHE* 2.9 37.5 + - + +
149A ASN* 1.3 89.7 - - + +
151A ILE* 1.3 74.6 + - - +
152A GLN* 3.3 14.5 + - - +
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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