Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 5SWW
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.3 42.4 - - + +
103A SER* 3.4 20.0 - - - +
133A ASP* 3.0 6.9 + - - +
134A PRO* 1.3 90.6 - - + +
136A TYR* 1.3 64.0 + - - +
137A LYS 3.3 2.2 - - - +
138A GLU* 3.2 27.5 + - + +
139A ALA 3.1 16.1 + - - -
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Residues in contact with TYR 136 (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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99A SER* 5.0 4.7 - - - +
100A PRO 5.0 2.9 - - - +
101A CYS* 5.8 0.7 - - - +
129A ILE* 3.5 27.1 - - + -
130A TYR* 3.2 22.0 - - + +
131A ASP* 3.6 23.5 - - + +
133A ASP* 3.1 27.1 + - + +
134A PRO* 4.3 7.9 - - + -
135A LEU* 1.3 74.5 - - - +
137A LYS* 1.3 108.9 + - + +
139A ALA* 3.0 10.9 + - - +
140A LEU* 2.9 29.3 + - + +
189A ARG* 3.8 12.4 + - - -
193A ILE* 3.6 17.3 - - + +
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Residues in contact with LYS 137 (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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134A PRO 4.7 9.3 + - - -
135A LEU 3.3 0.6 - - - -
136A TYR* 1.3 112.5 - - + +
138A GLU* 1.3 73.3 + - - +
140A LEU* 3.3 2.2 + - - +
141A GLN* 2.9 44.6 + - - +
193A ILE* 3.9 35.7 - - + -
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Residues in contact with GLU 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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102A PHE* 4.4 17.9 - - + -
134A PRO 4.5 0.4 - - - +
135A LEU* 3.2 44.7 + - + +
137A LYS* 1.3 92.0 + - - +
139A ALA* 1.3 58.4 + - - +
141A GLN* 4.1 13.1 - - - +
142A MET* 2.9 32.0 + - + +
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Residues in contact with ALA 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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100A PRO 3.3 25.6 - - - +
101A CYS 3.7 8.1 - - - +
102A PHE* 3.6 22.8 - - + +
107A ALA* 4.0 10.5 - - + +
135A LEU 3.1 5.5 + - - +
136A TYR* 3.0 11.8 + - - +
138A GLU* 1.3 75.4 - - - +
140A LEU* 1.3 60.9 + - - +
142A MET* 3.3 2.8 + - - +
143A LEU* 2.9 35.3 + - - +
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Residues in contact with LEU 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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99A SER* 3.8 27.4 - - - +
100A PRO* 5.1 3.4 - - + +
129A ILE* 4.6 11.4 - - + -
136A TYR* 2.9 29.4 + - + +
137A LYS 3.9 3.1 - - - +
139A ALA* 1.3 75.9 - - + +
141A GLN* 1.3 58.5 + - - +
143A LEU* 3.3 15.3 + - + +
144A ARG* 2.9 27.4 + - - +
150A VAL* 3.7 26.7 - - + +
152A ILE* 6.5 0.9 - - + -
190A LEU* 3.7 21.3 - - + -
193A ILE* 3.8 25.4 - - + -
194A LEU* 3.9 14.2 - - + +
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Residues in contact with GLN 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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137A LYS* 2.9 29.5 + - - +
138A GLU* 4.1 15.1 - - - +
140A LEU* 1.3 75.4 - - - +
142A MET* 1.3 58.7 + - - +
144A ARG* 3.2 22.5 + - - +
145A ASP* 2.8 40.2 + - - +
193A ILE* 3.1 33.6 + - + +
194A LEU* 4.0 11.9 - - + -
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Residues in contact with MET 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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102A PHE* 3.6 30.1 - - + -
107A ALA* 4.0 9.2 - - + +
108A GLY* 3.9 25.4 - - - -
111A ARG* 3.5 54.3 - - + +
138A GLU* 2.9 21.8 + - + +
139A ALA* 3.7 3.8 - - - +
141A GLN* 1.3 76.3 - - - +
143A LEU* 1.3 63.5 + - - +
145A ASP* 3.4 7.3 + - - +
146A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 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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100A PRO* 3.7 36.8 - - + +
107A ALA* 4.2 17.9 - - + +
110A VAL* 3.8 34.8 - - + -
111A ARG* 5.1 2.0 - - - +
114A LEU* 5.7 0.7 - - + -
124A ILE* 3.8 16.4 - - + -
139A ALA 2.9 25.2 + - - +
140A LEU* 3.3 11.9 + - + +
142A MET* 1.3 76.4 - - - +
144A ARG* 1.3 61.9 + - - +
146A ALA* 3.3 8.9 + - + +
148A ALA* 3.2 31.5 + - + +
150A VAL* 3.8 13.5 - - + -
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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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140A LEU 2.9 16.0 + - - +
141A GLN* 3.2 26.2 + - - +
143A LEU* 1.3 77.1 - - - +
145A ASP* 1.3 83.6 + - - +
146A ALA 3.0 1.8 + - - -
147A GLY* 3.1 14.0 + - - -
148A ALA 3.5 11.8 + - - +
150A VAL* 3.9 7.1 - - + +
194A LEU* 3.2 61.0 + - + +
195A GLN 3.7 10.1 - - - +
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Residues in contact with ASP 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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111A ARG* 5.8 4.0 - - - +
141A GLN* 2.8 30.0 + - - +
142A MET* 3.4 7.0 + - - +
143A LEU 3.4 0.2 - - - -
144A ARG* 1.3 100.8 + - - +
146A ALA* 1.3 58.0 + - - +
147A GLY 3.3 0.8 + - - -
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Residues in contact with ALA 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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111A ARG* 3.7 32.8 - - + +
114A LEU* 3.9 29.0 - - + +
115A GLN* 6.0 2.9 - - + +
142A MET 3.1 15.7 + - - +
143A LEU* 3.7 7.9 - - - +
144A ARG 3.0 1.6 - - - -
145A ASP* 1.3 76.5 - - - +
147A GLY* 1.3 59.7 + - - +
148A ALA 3.4 1.1 + - - -
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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