Contacts of the helix formed by residues 131 - 140 (chain A) in PDB entry 2HW6
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 SER 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLY* 1.3 75.7 - - - +
132A ILE* 1.3 64.4 + - - +
133A LEU* 3.6 8.0 + - - +
134A ALA* 3.4 24.9 + - - +
135A HIS* 3.2 14.8 - - - -
173A PRO 3.6 14.8 - - - -
174A GLU* 4.1 18.1 - - - +
176A ILE 3.3 8.7 - - - -
177A LEU* 3.9 9.3 - - - +
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Residues in contact with ILE 132 (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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130A GLY 3.8 0.2 + - - -
131A SER* 1.3 69.6 - - - +
133A LEU* 1.3 68.0 + - - +
135A HIS* 3.0 6.1 + - - +
136A ILE* 3.0 33.7 + - + +
142A PHE* 3.8 22.2 - - + -
150A VAL* 4.1 17.9 - - + -
173A PRO* 3.5 26.6 + - + -
176A ILE* 2.8 35.0 + - + +
178A CYS* 3.5 26.4 - - - -
184A VAL* 4.3 2.2 - - + -
187A VAL* 3.6 23.3 - - + -
249A VAL* 5.0 3.1 - - + -
253A MET* 4.7 7.4 - - - -
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Residues in contact with LEU 133 (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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131A SER* 3.1 10.5 - - - +
132A ILE* 1.3 81.1 - - - +
134A ALA* 1.3 64.4 + - - +
136A ILE* 3.1 21.3 + - + +
137A GLN* 3.2 38.9 + - - +
173A PRO* 3.5 30.3 + - + -
174A GLU* 3.5 31.4 - - + +
252A ILE* 6.5 0.9 - - + -
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Residues in contact with ALA 134 (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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129A GLY 5.7 0.4 - - - +
130A GLY* 5.3 1.3 - - - -
131A SER* 3.4 20.5 + - - +
132A ILE 3.3 0.4 - - - -
133A LEU* 1.3 81.1 - - - +
135A HIS* 1.3 67.3 + - + +
136A ILE 3.0 1.7 + - - -
137A GLN* 3.2 27.0 + - - +
138A LYS* 3.2 16.9 + - - +
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Residues in contact with HIS 135 (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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129A GLY 2.9 24.1 + - - -
131A SER 3.2 22.9 - - - -
132A ILE* 3.0 10.1 + - - +
134A ALA* 1.3 83.0 - - + +
136A ILE* 1.3 60.1 + - - +
138A LYS* 4.0 17.9 + - - +
139A GLN* 3.0 44.2 + - - +
142A PHE* 3.5 17.3 - - + -
178A CYS* 3.7 19.5 - - - -
180A SER 3.8 11.9 - - - -
181A PRO* 3.7 24.7 + - + +
184A VAL* 3.9 17.4 - - + +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.0 26.6 + - + +
133A LEU* 3.3 15.9 - - + +
134A ALA 3.0 0.4 - - - -
135A HIS* 1.3 74.4 - - - +
137A GLN* 1.3 57.4 + - + +
138A LYS 2.8 5.1 + - - -
139A GLN 3.1 0.9 + - - -
140A LYS* 2.8 52.4 + - - +
141A HIS* 5.0 1.6 - - - -
142A PHE* 3.5 26.9 - - + -
173A PRO* 5.4 1.8 - - + -
252A ILE* 4.3 20.9 - - + +
253A MET* 3.8 33.7 - - + +
256A GLY* 4.6 8.5 - - - +
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Residues in contact with GLN 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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133A LEU* 3.4 40.2 + - - +
134A ALA* 3.3 22.3 - - - +
136A ILE* 1.3 78.7 - - + +
138A LYS* 1.3 56.6 + - - +
140A LYS* 4.5 4.3 - - - +
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Residues in contact with LYS 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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134A ALA* 3.2 14.1 + - - +
135A HIS* 4.0 27.3 + - - +
136A ILE 2.8 0.8 + - - -
137A GLN* 1.3 80.6 - - - +
139A GLN* 1.3 83.9 + - + +
140A LYS 3.5 0.7 - - - -
181A PRO 4.6 9.7 + - - -
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Residues in contact with GLN 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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135A HIS* 3.0 32.9 + - - +
136A ILE 3.1 1.8 + - - -
138A LYS* 1.3 100.2 + - + +
140A LYS* 1.3 60.7 + - - +
141A HIS* 2.9 30.2 + - - +
142A PHE* 3.9 14.6 - - - -
146A GLU* 3.8 26.9 + - - -
184A VAL* 5.1 3.6 - - - +
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Residues in contact with LYS 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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136A ILE* 2.8 23.3 + - - +
137A GLN* 4.5 2.8 - - - +
138A LYS 3.5 2.8 - - - +
139A GLN* 1.3 77.3 - - - +
141A HIS* 1.3 81.2 + - + +
255A SER 3.7 17.3 + - - +
256A GLY* 3.3 33.5 - - - +
257A TYR* 5.1 5.6 - - - -
298A ASP* 4.9 8.5 + - - -
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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