Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 2HE7
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 ARG 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG 3.5 3.6 + - - +
130A SER* 1.3 77.0 - - - +
132A GLY* 1.3 65.3 + - - +
133A GLN* 3.1 7.4 + - + +
134A VAL* 3.1 24.1 + - + +
167A PRO 3.5 11.7 - - - +
168A ALA* 3.2 31.4 + - - +
169A LYS* 3.4 13.4 - - - +
170A GLU* 3.9 8.5 - - + +
171A ILE* 3.9 4.3 - - - +
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Residues in contact with GLY 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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131A ARG* 1.3 71.6 - - - +
133A GLN* 1.3 61.6 + - - +
134A VAL 3.1 0.3 + - - -
135A LEU* 3.2 5.2 + - - +
136A PHE* 3.0 22.1 + - - +
165A LEU* 3.8 19.4 - - - +
166A ASP 4.0 3.1 - - - -
167A PRO* 3.5 14.8 + - - -
169A LYS 3.0 12.9 + - - -
171A ILE* 3.8 17.3 - - - +
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Residues in contact with GLN 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 ARG* 3.1 5.8 - - + -
132A GLY* 1.3 78.1 - - - +
134A VAL* 1.3 58.1 + - + +
136A PHE* 3.7 18.2 - - - -
137A ASP* 2.8 68.9 + - - +
148A LYS* 4.6 5.5 - - - +
167A PRO* 3.0 39.4 + - - +
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Residues in contact with VAL 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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126A VAL* 4.2 14.6 - - + -
127A GLU 5.6 0.2 - - - +
130A SER* 4.0 25.8 - - - +
131A ARG* 3.1 22.6 + - + +
132A GLY 3.1 0.2 + - - -
133A GLN* 1.3 78.2 - - + +
135A LEU* 1.3 61.1 + - - +
137A ASP* 3.8 5.3 - - - +
138A LYS* 3.2 30.9 + - + +
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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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112A CYS* 3.9 18.2 - - + -
114A VAL* 4.3 5.8 - - + -
124A CYS* 3.5 31.6 - - - -
126A VAL* 4.4 7.4 - - + -
131A ARG 4.1 0.8 + - - -
132A GLY 3.2 8.3 + - - +
134A VAL* 1.3 81.9 - - - +
136A PHE* 1.3 64.1 + - - +
138A LYS* 3.1 3.4 + - + +
139A VAL* 3.0 37.1 + - + +
153A LEU* 3.7 18.2 - - + -
165A LEU* 4.4 3.1 - - + -
171A ILE* 4.1 14.6 - - + +
182A PHE* 3.4 42.4 - - + -
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Residues in contact with PHE 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 GLY 3.0 17.0 + - - +
133A GLN* 3.8 25.6 - - - +
135A LEU* 1.3 76.9 - - - +
137A ASP* 1.3 66.0 + - - +
139A VAL* 3.3 2.7 + - + +
140A CYS* 3.0 46.2 + - - -
148A LYS* 3.1 37.0 - - + -
149A ASP* 5.6 2.0 - - - -
151A PHE* 3.5 22.9 - - + -
152A GLY* 3.7 13.9 - - - -
153A LEU* 4.0 28.7 - - + +
167A PRO* 5.5 5.4 - - + -
184A PHE* 4.2 10.5 - + - -
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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 GLN* 2.8 52.5 + - - +
134A VAL* 3.8 6.3 - - - +
136A PHE* 1.3 79.6 - - - +
138A LYS* 1.3 57.6 + - + +
140A CYS* 3.4 1.4 + - - +
141A GLU* 3.1 31.3 + - - +
148A LYS* 2.5 35.5 + - - +
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Residues in contact with LYS 138 (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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122A TYR* 3.6 25.4 + - + +
124A CYS* 3.7 19.2 - - - +
125A ASP 3.6 21.8 - - - -
126A VAL* 4.2 14.4 - - + -
134A VAL* 3.2 21.0 + - + +
135A LEU* 3.1 8.4 + - - +
137A ASP* 1.3 76.1 - - + +
139A VAL* 1.3 60.0 + - - +
141A GLU* 3.5 12.6 + - - +
142A HIS* 2.9 29.1 + - - +
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Residues in contact with VAL 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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114A VAL* 4.0 22.4 - - + -
116A LEU* 4.1 21.1 - - + -
122A TYR* 3.8 25.1 - - + -
135A LEU* 3.0 20.7 + - + +
136A PHE* 3.6 8.3 - - - +
138A LYS* 1.3 76.2 - - - +
140A CYS* 1.3 62.0 + - - +
142A HIS* 3.2 6.9 + - + +
143A LEU* 3.1 23.1 + - + +
153A LEU* 4.5 5.6 - - + -
184A PHE* 3.7 30.7 - - + -
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Residues in contact with CYS 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 PHE* 3.0 44.1 + - - +
137A ASP 4.0 3.6 - - - +
138A LYS 3.4 0.2 - - - -
139A VAL* 1.3 72.8 - - - +
141A GLU* 1.3 63.6 + - - +
143A LEU* 3.3 3.1 + - - -
144A ASN 3.1 3.3 + - - -
145A LEU* 2.9 59.8 + - + +
148A LYS* 3.5 36.1 - - + +
184A PHE* 4.3 5.6 - - - -
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Residues in contact with GLU 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 ASP 3.1 18.5 + - - +
138A LYS* 3.5 12.6 - - - +
140A CYS* 1.3 73.2 - - - +
142A HIS* 1.3 66.9 + - - +
144A ASN* 3.1 19.8 + - - +
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Residues in contact with HIS 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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116A LEU* 3.6 30.4 - - + +
121A GLU 5.7 0.8 + - - -
122A TYR* 3.5 41.1 - + + +
138A LYS 2.9 14.5 + - - +
139A VAL 3.2 8.7 + - - +
141A GLU* 1.3 77.5 - - - +
143A LEU* 1.3 69.7 + - + +
144A ASN* 3.5 5.9 + - - -
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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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116A LEU* 4.2 17.9 - - + -
139A VAL* 3.1 24.6 + - + +
140A CYS 3.7 4.9 - - - +
141A GLU 3.1 0.4 - - - -
142A HIS* 1.3 92.9 - - + +
144A ASN* 1.3 69.3 + - - +
145A LEU* 3.2 6.1 + - + -
184A PHE* 3.7 43.5 - - + -
200A ILE* 4.5 2.9 - - - +
204A TYR* 2.5 54.9 + - + +
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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