Contacts of the helix formed by residues 124 - 135 (chain A) in PDB entry 2HVY
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 PRO 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP 4.4 3.4 - - - +
123A VAL* 1.4 94.4 - - + +
125A GLU* 1.3 65.4 + - - +
126A ASP* 3.2 23.6 - - - +
127A LYS* 3.1 19.5 + - + +
128A ILE* 3.2 10.6 + - - +
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Residues in contact with GLU 125 (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 VAL 3.7 1.2 + - - +
124A PRO* 1.3 71.3 - - - +
126A ASP* 1.3 62.2 + - - +
128A ILE* 3.4 5.5 + - + +
129A ILE* 3.2 35.1 + - + +
166A ILE* 3.7 52.7 + - + +
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Residues in contact with ASP 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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124A PRO* 3.9 16.1 - - - +
125A GLU* 1.3 79.0 + - - +
127A LYS* 1.3 79.1 + - - +
129A ILE* 3.7 8.4 + - - +
130A GLN* 3.2 28.4 + - - +
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Residues in contact with LYS 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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123A VAL* 3.8 12.3 - - + -
124A PRO* 3.1 16.7 + - + +
126A ASP* 1.3 86.1 + - - +
128A ILE* 1.3 65.0 + - - +
130A GLN* 3.9 17.8 - - - +
131A VAL* 3.1 37.4 + - + +
193A ALA 3.4 24.0 + - - -
194A LEU* 3.7 17.2 + - + +
8B LEU* 5.7 3.4 - - - +
9B HIS* 4.1 12.9 - - - -
52B TYR* 5.4 0.6 + - - -
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Residues in contact with ILE 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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117A MET* 4.7 4.0 - - + -
119A LEU* 3.7 22.2 - - + -
123A VAL* 3.5 34.3 - - + +
124A PRO 3.2 10.1 + - - +
125A GLU* 3.6 7.9 - - - +
127A LYS* 1.3 76.3 - - - +
129A ILE* 1.3 62.2 + - + +
131A VAL* 3.5 1.4 + - - +
132A MET* 3.1 50.8 + - + +
163A VAL* 5.2 0.4 - - + -
166A ILE* 4.0 32.5 - - + -
168A GLY 5.0 1.3 - - - +
171A VAL* 3.9 20.4 - - + -
194A LEU* 4.1 11.6 - - + +
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Residues in contact with ILE 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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125A GLU* 3.2 23.9 + - + +
126A ASP* 4.1 7.6 - - - +
128A ILE* 1.3 75.9 - - - +
130A GLN* 1.3 57.8 + - - +
132A MET* 3.5 5.1 + - - +
133A LYS* 3.0 41.4 + - + +
163A VAL* 4.6 21.9 - - + +
166A ILE* 4.5 16.2 - - + -
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Residues in contact with GLN 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 ASP 3.2 18.4 + - - +
127A LYS* 3.9 24.9 + - - +
128A ILE 3.4 0.2 - - - -
129A ILE* 1.3 77.8 - - - +
131A VAL* 1.3 64.0 + - - +
133A LYS* 3.4 12.2 + - + +
134A GLU* 3.4 33.2 + - + +
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Residues in contact with VAL 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 LYS* 3.1 50.2 + - + +
128A ILE 4.1 0.7 - - - +
130A GLN* 1.3 77.8 - - - +
132A MET* 1.3 65.6 + - - +
134A GLU* 3.2 23.6 + - - +
135A PHE* 3.2 24.0 - - + -
190A ILE* 4.4 7.4 - - + +
193A ALA* 3.8 27.6 - - + +
194A LEU* 3.8 19.7 - - + -
52B TYR* 4.0 7.9 - - - +
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Residues in contact with MET 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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117A MET* 3.7 22.0 - - + -
128A ILE* 3.1 34.5 + - + +
129A ILE 4.0 2.9 - - - +
131A VAL* 1.3 73.0 - - - +
133A LYS* 1.3 64.1 + - - +
135A PHE* 3.2 15.7 + - - -
136A GLU 4.0 0.9 + - - -
161A ILE* 3.3 37.7 - - + +
163A VAL* 3.9 16.4 - - + -
171A VAL* 3.9 2.9 - - - -
173A PHE* 3.6 51.6 - - + -
190A ILE* 4.0 27.6 - - + -
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Residues in contact with LYS 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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11A ARG* 5.3 8.7 - - - +
129A ILE* 3.0 29.3 + - + +
130A GLN* 3.5 9.9 - - + +
131A VAL 3.3 0.2 - - - -
132A MET* 1.3 75.6 - - - +
134A GLU* 1.3 61.6 + - + +
135A PHE 3.4 0.3 + - - -
136A GLU* 3.4 34.5 + - - +
161A ILE* 5.7 1.8 - - - -
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Residues in contact with GLU 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 GLN* 3.4 25.7 + - + +
131A VAL* 3.2 20.4 + - - +
133A LYS* 1.3 77.8 - - - +
135A PHE* 1.3 60.0 + - + +
136A GLU 3.2 9.0 + - - +
19B ARG* 2.9 37.0 + - - +
47B PRO* 3.0 28.7 - - + +
52B TYR* 2.6 27.3 + - + -
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Residues in contact with PHE 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 VAL* 3.2 26.7 - - + -
132A MET* 3.2 12.0 + - - +
134A GLU* 1.3 78.2 - - - +
136A GLU* 1.3 60.7 + - - +
139A ILE* 3.5 21.9 - - + +
158A VAL* 3.2 22.0 - - - +
161A ILE* 3.9 13.0 - - + -
186A LEU* 3.7 21.1 - - + -
189A HIS* 3.9 36.8 - - + -
190A ILE* 3.9 19.5 - - + -
193A ALA* 4.0 19.3 - - + -
45B PHE* 4.1 10.3 - + - -
46B GLY* 3.7 29.6 - - - -
47B PRO* 5.4 0.2 - - + -
52B TYR* 4.2 10.8 - + - -
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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