Contacts of the helix formed by residues 125 - 143 (chain A) in PDB entry 2HAS
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS 3.4 3.5 + - - -
124A LEU* 1.3 76.2 - - - +
126A GLU* 1.3 65.2 + - - +
127A GLU* 3.5 9.3 + - - +
128A GLN* 3.0 38.4 + - - +
129A GLN* 3.0 21.9 + - - +
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Residues in contact with GLU 126 (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 SER* 1.3 74.8 - - - +
127A GLU* 1.3 63.2 + - - +
129A GLN* 3.3 19.2 + - - +
130A ARG* 3.0 31.8 + - - +
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Residues in contact with GLU 127 (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 SER* 3.2 8.6 + - - +
126A GLU* 1.3 79.4 - - - +
128A GLN* 1.3 59.7 + - - +
130A ARG* 3.2 23.0 + - - +
131A ILE* 2.9 36.9 + - + +
358A ARG* 4.0 33.1 + - - +
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Residues in contact with GLN 128 (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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123A LYS 4.2 2.0 + - - -
124A LEU* 3.5 24.3 - - + +
125A SER* 3.0 42.0 + - - +
127A GLU* 1.3 77.0 - - + +
129A GLN* 1.3 64.6 + - - +
131A ILE* 3.4 7.3 + - + +
132A ILE* 3.1 30.5 + - - +
358A ARG* 5.1 1.3 - - + +
361A ASN* 3.8 8.8 - - - +
362A THR* 3.4 37.1 + - + +
365A THR* 3.7 20.0 + - - +
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Residues in contact with GLN 129 (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* 3.3 32.4 - - + +
125A SER 3.0 18.8 + - - +
126A GLU* 3.5 18.8 - - - +
127A GLU 3.2 0.2 - - - -
128A GLN* 1.3 75.4 - - - +
130A ARG* 1.3 58.3 + - + +
132A ILE* 3.4 8.4 + - - +
133A ALA* 2.9 30.2 + - - +
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Residues in contact with ARG 130 (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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126A GLU* 3.0 20.8 + - - +
127A GLU* 3.5 28.5 + - - +
129A GLN* 1.3 76.0 - - + +
131A ILE* 1.3 62.3 + - - +
133A ALA* 3.2 6.4 + - - +
134A ILE* 2.8 57.4 + - + +
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Residues in contact with ILE 131 (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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127A GLU* 2.9 30.8 + - + +
128A GLN* 3.6 10.3 - - + +
129A GLN 3.4 0.2 - - - -
130A ARG* 1.3 79.8 - - - +
132A ILE* 1.3 57.1 + - - +
134A ILE* 3.3 2.1 + - - +
135A LEU* 2.9 54.4 + - + +
249A PRO* 4.3 23.8 - - + -
332A LEU* 4.5 6.7 - - + -
358A ARG* 3.8 37.9 - - + +
359A LEU* 3.9 17.5 - - + -
362A THR* 3.9 16.2 - - + +
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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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124A LEU* 4.1 18.6 - - + -
128A GLN 3.1 17.9 + - - +
129A GLN* 3.7 5.4 - - - +
131A ILE* 1.3 74.4 - - - +
133A ALA* 1.3 65.2 + - - +
135A LEU* 3.3 6.2 + - - +
136A LEU* 2.9 32.7 + - + +
328A GLU* 3.6 31.0 - - + +
331A VAL* 5.1 1.3 - - + +
332A LEU* 4.2 11.9 - - + -
362A THR* 3.7 23.3 - - + -
366A TYR* 3.8 28.0 - - + -
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Residues in contact with ALA 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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129A GLN 2.9 18.0 + - - +
130A ARG* 3.6 7.2 - - - +
132A ILE* 1.3 77.9 - - - +
134A ILE* 1.3 63.7 + - + +
136A LEU* 3.4 9.6 + - - +
137A ASP* 3.0 25.8 + - - +
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Residues in contact with ILE 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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130A ARG* 2.8 48.6 + - + +
131A ILE* 3.6 4.3 - - + +
133A ALA* 1.3 78.1 - - + +
135A LEU* 1.3 58.3 + - - +
137A ASP* 3.4 6.2 + - - +
138A ALA* 2.9 27.2 + - - +
247A MET* 3.4 28.9 - - + +
249A PRO* 3.9 24.0 - - + -
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Residues in contact with LEU 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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131A ILE* 2.9 29.9 + - + +
132A ILE* 3.8 2.7 - - - +
134A ILE* 1.3 74.4 - - - +
136A LEU* 1.3 65.4 + - - +
138A ALA* 3.3 4.1 + - + +
139A HIS* 2.9 24.9 + - - +
244A PHE* 3.8 12.5 - - + -
247A MET 4.8 1.8 - - - +
248A ILE* 4.0 24.2 - - + +
249A PRO* 3.8 21.8 - - + -
331A VAL* 3.8 17.0 - - + +
332A LEU* 3.5 37.7 - - + -
335A ALA* 4.2 17.5 - - + -
359A LEU* 4.3 3.4 - - + -
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Residues in contact with LEU 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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132A ILE* 2.9 38.7 + - + +
133A ALA* 3.7 8.5 - - - +
135A LEU* 1.3 75.8 - - - +
137A ASP* 1.3 59.2 + - - +
139A HIS* 3.3 2.0 + - - +
140A HIS* 2.9 46.4 + - + +
327A GLU* 3.6 39.9 - - + +
328A GLU* 4.0 32.5 - - + +
331A VAL* 4.1 7.2 - - + -
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Residues in contact with ASP 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 ALA 3.0 17.9 + - - +
134A ILE* 3.7 6.1 - - - +
136A LEU* 1.3 75.1 - - - +
138A ALA* 1.3 65.5 + - - +
140A HIS* 3.2 10.8 + - - +
141A LYS* 2.8 70.3 + - - +
247A MET* 5.6 1.2 - - - +
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Residues in contact with ALA 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 ILE 2.9 18.7 + - - +
135A LEU* 3.3 7.6 + - + +
137A ASP* 1.3 76.3 + - - +
139A HIS* 1.3 61.0 + - - +
141A LYS* 3.3 2.4 + - - +
142A THR* 2.8 32.3 + - - +
244A PHE* 3.8 17.0 - - + +
247A MET* 3.7 44.0 - - + +
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Residues in contact with HIS 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 LEU 2.9 9.8 + - - +
136A LEU 3.6 3.1 - - - +
138A ALA* 1.3 78.0 - - - +
140A HIS* 1.3 58.2 + + - +
142A THR* 3.1 6.8 + - - -
143A TYR* 2.9 65.3 + + + +
244A PHE* 3.8 8.6 - - + -
274A ARG* 4.8 6.0 + - + -
277A GLU* 3.1 22.1 + - - -
327A GLU* 3.5 25.4 - - + -
330A HIS* 4.2 8.8 - + - -
331A VAL* 3.5 30.3 - - + -
334A MET* 3.6 24.7 - - + +
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Residues in contact with HIS 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 LEU* 2.9 35.4 + - + +
137A ASP* 3.7 11.4 + - - +
139A HIS* 1.3 80.2 - + - +
141A LYS* 1.3 61.8 + - + +
142A THR 3.7 0.2 + - - -
143A TYR 3.9 13.7 - - - +
144A ASP* 5.6 0.2 - - - -
145A PRO* 5.6 1.2 - - - +
327A GLU* 2.6 42.4 + - - -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASP* 2.8 51.8 + - - +
138A ALA* 3.3 4.9 + - - +
139A HIS 3.1 0.2 - - - -
140A HIS* 1.3 79.4 - - + +
142A THR* 1.3 64.2 + - + +
143A TYR 3.7 0.4 - - - -
240A LYS* 5.4 4.3 + - - -
247A MET* 4.7 16.3 - - + -
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Residues in contact with THR 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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138A ALA 2.8 21.4 + - - +
139A HIS* 3.1 9.4 + - - -
141A LYS* 1.3 84.0 - - + +
143A TYR* 1.3 57.0 + - - +
144A ASP 4.1 1.7 + - - -
240A LYS* 3.3 50.1 - - + +
243A GLY* 4.2 4.5 - - - -
244A PHE* 3.8 15.1 - - - +
247A MET* 3.6 21.3 - - + -
274A ARG* 2.9 19.2 + - - -
1001A C3O 5.3 0.5 - - - +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A HIS* 2.9 40.0 + + + +
140A HIS* 3.9 13.6 - - - +
141A LYS 3.7 0.6 - - - -
142A THR* 1.3 79.5 - - - +
144A ASP* 1.3 63.6 + - - +
145A PRO* 3.1 18.5 - - + +
147A TYR* 3.1 24.9 + + - -
274A ARG* 3.5 43.1 - - + +
277A GLU* 3.4 41.0 - - + +
278A SER 3.6 0.7 + - - -
1001A C3O 2.8 50.3 + - + -
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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