Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 1QN9
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ILE* 1.3 69.4 - - - +
130A LEU* 1.3 63.1 + - - +
131A GLU* 3.2 3.8 - - + -
132A GLY* 3.2 20.6 + - - +
133A LEU* 3.2 20.8 + - - +
194A GLU 4.2 1.2 + - - -
195A PHE* 2.8 33.5 + - - +
196A ARG 4.0 9.7 + - - -
197A LYS* 3.6 35.0 - - + +
198A ILE 5.3 1.3 - - - +
190B PRO 3.8 4.6 + - - -
193B SER* 2.9 29.3 + - - -
194B GLU* 3.7 46.3 + - - +
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Residues in contact with LEU 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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128A ILE* 3.1 17.8 + - + +
129A ARG* 1.3 70.9 - - - +
131A GLU* 1.3 59.8 + - - +
133A LEU* 3.4 2.4 + - + -
134A ALA* 3.0 26.3 + - - +
143A TYR* 3.7 29.4 - - + +
149A PRO 3.5 24.7 - - - +
151A LEU* 3.2 23.4 - - + +
164A ILE* 3.5 45.1 - - + +
165A PHE 4.0 4.7 - - - -
166A VAL* 3.6 27.1 - - + +
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Residues in contact with GLU 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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129A ARG* 3.2 1.8 - - + -
130A LEU* 1.3 78.8 - - - +
132A GLY* 1.3 63.1 + - - +
134A ALA* 3.4 2.4 + - - +
135A TYR* 3.0 24.7 + - + +
143A TYR* 3.9 19.5 - - + -
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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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129A ARG* 3.2 29.2 + - - +
131A GLU* 1.3 80.8 - - - +
133A LEU* 1.3 52.0 + - - +
135A TYR* 3.5 7.1 + - - +
136A SER* 2.7 33.3 + - - -
195A PHE* 3.5 12.6 - - - -
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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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128A ILE* 4.1 13.9 - - + -
129A ARG 3.2 12.2 + - - +
130A LEU* 3.7 8.1 - - - +
131A GLU 3.3 0.2 - - - -
132A GLY* 1.3 74.1 - - - +
134A ALA* 1.3 63.5 + - - +
136A SER* 3.0 16.3 + - - -
137A HIS* 3.0 23.4 + - + +
141A SER* 4.5 1.6 - - - +
151A LEU* 3.9 13.5 - - + -
153A TYR* 4.2 16.2 - - + -
164A ILE* 4.6 10.1 - - + -
188A ILE* 5.6 0.7 - - + -
191A VAL* 3.7 29.8 - - + -
192A LEU* 3.9 30.5 - - + -
195A PHE* 3.7 14.8 - - + -
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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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130A LEU 3.0 16.8 + - - +
131A GLU* 3.8 4.5 - - - +
133A LEU* 1.3 77.8 - - - +
135A TYR* 1.3 62.4 + - - +
137A HIS 3.1 2.4 - - - +
138A ALA* 3.1 26.0 + - - -
141A SER* 3.6 21.2 - - - -
143A TYR* 3.9 19.1 - - + +
151A LEU* 3.7 11.6 - - + +
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Residues in contact with TYR 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 GLU* 3.0 17.7 + - + +
132A GLY* 3.7 7.9 - - - +
133A LEU 3.3 0.2 - - - -
134A ALA* 1.3 79.0 - - - +
136A SER* 1.3 62.5 + - - +
137A HIS 3.3 0.2 + - - -
138A ALA* 3.7 14.6 + - + +
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Residues in contact with SER 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 2.7 17.3 + - - -
133A LEU 3.0 8.1 + - - -
135A TYR* 1.3 79.6 - - - +
137A HIS* 1.3 72.0 + - - +
138A ALA 3.7 1.2 + - - -
195A PHE* 2.9 26.9 - - - -
196B ARG* 5.8 8.7 - - - -
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Residues in contact with HIS 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* 3.0 21.1 + - + +
134A ALA 3.1 3.8 - - - -
136A SER* 1.3 94.4 + - - +
138A ALA* 1.3 58.8 + - - +
139A ALA 3.3 2.9 - - - -
140A PHE* 3.2 23.2 + + + -
141A SER* 2.7 40.6 + - - +
153A TYR* 3.2 32.1 + + + -
191A VAL* 3.6 31.5 - - + +
194A GLU* 4.9 4.7 - - - -
195A PHE* 4.4 4.5 - + - -
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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