Contacts of the helix formed by residues 131 - 138 (chain A) in PDB entry 2H07
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 ALA 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP* 3.2 27.8 - - - +
129A LEU* 3.7 8.1 - - - +
130A HIS* 1.3 82.8 - - + +
132A ALA* 1.3 66.1 + - - +
133A GLN* 3.8 14.6 - - - +
134A ILE* 3.0 26.9 + - + +
133B GLN* 3.8 12.6 - - + +
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Residues in contact with ALA 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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129A LEU* 4.4 9.3 + - - -
131A ALA* 1.3 70.7 - - - +
133A GLN* 1.3 65.8 + - - +
134A ILE 3.1 1.0 + - - -
135A GLN* 3.1 22.9 + - - +
144A ASN* 5.0 2.0 - - - +
1006A SO4 3.0 42.7 + - - +
99B LYS* 3.8 25.5 - - + +
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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 ALA* 3.0 9.9 - - - +
132A ALA* 1.3 82.7 + - - +
134A ILE* 1.3 52.8 + - - +
135A GLN 3.0 0.2 - - - -
136A GLY 2.7 23.2 + - - -
137A PHE* 3.8 1.9 + - - -
98B ASP* 3.0 51.9 + - + +
99B LYS* 4.1 23.1 + - - +
130B HIS* 6.0 0.8 - - - -
131B ALA* 3.6 12.9 - - + +
133B GLN* 3.5 35.2 + - + -
134B ILE* 5.7 0.4 - - + -
137B PHE* 3.2 21.0 - - + -
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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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92A PHE* 4.3 19.7 - - + -
95A ALA* 3.5 43.3 - - + +
98A ASP* 4.2 13.2 - - + +
109A ALA* 4.3 2.5 - - + -
129A LEU* 4.1 21.3 - - + -
130A HIS 4.6 2.2 - - - +
131A ALA* 3.0 28.1 + - + +
133A GLN* 1.3 74.7 - - - +
135A GLN* 1.3 65.9 + - - +
137A PHE* 2.8 47.0 + - + +
138A PHE* 3.8 9.1 - - + -
133B GLN* 5.5 0.2 - - + -
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Residues in contact with GLN 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 LEU* 3.5 21.2 - - + +
132A ALA 3.1 12.3 + - - +
133A GLN 3.0 0.4 - - - -
134A ILE* 1.3 78.8 - - - +
136A GLY* 1.3 60.3 + - - +
137A PHE 3.3 0.9 + - - -
138A PHE* 3.4 20.5 + - - +
140A ILE 5.0 0.7 - - - +
142A VAL* 3.1 36.5 - - + +
144A ASN* 3.3 20.7 - - - +
146A TYR* 5.1 0.2 + - - -
1006A SO4 2.7 31.8 + - - -
100B LYS* 3.0 36.0 - - - +
107B ILE* 4.0 13.6 - - + +
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Residues in contact with GLY 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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133A GLN 2.7 12.5 + - - -
135A GLN* 1.3 76.6 - - - +
137A PHE* 1.3 53.9 + - - +
138A PHE 3.1 8.3 - - - -
107B ILE* 3.8 19.7 - - - +
110B LYS* 2.8 37.2 + - - +
137B PHE* 3.6 19.1 - - - -
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Residues in contact with PHE 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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98A ASP* 3.8 22.9 - - + -
107A ILE* 4.1 3.8 - - + -
109A ALA* 3.8 24.2 - - + -
110A LYS* 3.4 54.4 + - + +
113A ALA* 3.5 18.7 - - + +
114A ASN* 4.3 2.3 - - - +
133A GLN 4.0 4.5 - - - -
134A ILE* 2.8 33.9 + - + +
136A GLY* 1.3 76.8 - - - +
138A PHE* 1.3 58.7 + - - +
110B LYS* 4.1 2.8 + - - -
133B GLN* 3.2 33.4 - - + -
136B GLY* 3.5 24.5 - - - -
137B PHE* 3.7 13.5 - + - -
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Residues in contact with PHE 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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92A PHE* 3.7 28.7 - + - -
113A ALA* 3.4 40.6 - - + -
116A LEU* 4.1 5.6 - - + -
117A SER* 3.7 13.5 - - - -
124A ILE* 3.7 27.4 - - + -
129A LEU* 6.4 0.4 - - + -
134A ILE* 3.8 18.8 - - + -
135A GLN* 3.4 9.3 + - - +
136A GLY* 3.1 4.4 - - - +
137A PHE* 1.3 81.0 - - - +
139A ASP* 1.3 61.0 + - - +
140A ILE* 3.5 35.4 - - + +
142A VAL* 3.6 22.2 - - + -
110B LYS* 2.9 19.2 + - - +
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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