Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 2QNU
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 GLU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLU 3.4 9.2 + - - +
127A ALA* 1.3 78.9 - - - +
129A VAL* 1.3 66.5 + - - +
130A GLU* 4.5 3.1 - - + +
131A ALA* 3.2 29.9 + - + +
132A PHE* 3.2 12.3 + - - +
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Residues in contact with VAL 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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10A LEU* 4.0 35.7 - - + -
12A GLY* 4.2 23.1 - - - +
13A ARG* 3.0 49.6 - - - +
17A VAL* 5.7 1.8 - - + -
127A ALA* 3.9 5.3 + - + +
128A GLU* 1.3 72.6 - - - +
130A GLU* 1.3 57.2 + - - +
132A PHE* 3.2 9.1 + - + +
133A GLU* 2.9 35.8 + - + +
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Residues in contact with GLU 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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13A ARG* 3.1 34.8 + - - +
19A ARG* 5.1 1.7 + - - -
128A GLU* 3.3 3.9 - - + +
129A VAL* 1.3 77.7 - - - +
131A ALA* 1.3 57.3 + - - +
133A GLU* 3.3 27.4 + - - +
134A GLN* 3.1 34.0 + - + +
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Residues in contact with ALA 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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128A GLU* 3.2 26.9 + - + +
130A GLU* 1.3 73.8 - - - +
132A PHE* 1.3 66.0 + - - +
134A GLN* 3.9 4.5 - - - +
135A ALA* 3.2 23.4 + - - +
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Residues in contact with PHE 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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6A PHE* 3.7 33.7 - + + -
10A LEU* 4.1 22.9 - - + -
89A LEU* 4.0 15.3 - - + -
91A VAL* 4.0 14.8 - - + -
118A LEU* 3.5 29.4 - - + -
119A LEU* 4.2 3.8 - - - -
121A SER* 4.7 3.1 - - - +
122A THR* 3.2 29.4 - - + -
128A GLU 3.2 9.4 + - - +
129A VAL* 3.2 10.5 + - - +
131A ALA* 1.3 79.4 - - - +
133A GLU* 1.3 66.9 + - + +
134A GLN 3.1 1.2 + - - -
135A ALA* 3.2 5.5 + - - +
136A VAL* 3.2 42.0 + - + +
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Residues in contact with GLU 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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6A PHE* 3.6 32.9 - - + -
13A ARG* 3.9 9.5 + - - -
17A VAL* 5.6 3.3 - - - +
19A ARG* 3.2 48.9 + - + +
129A VAL* 2.9 24.8 + - + +
130A GLU* 3.3 34.1 + - - +
131A ALA 3.3 0.2 - - - -
132A PHE* 1.3 76.6 - - + +
134A GLN* 1.3 58.5 + - + +
136A VAL* 4.1 2.5 - - - +
137A ALA* 3.2 25.3 + - - +
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Residues in contact with GLN 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 GLU* 3.1 19.6 + - + +
131A ALA* 3.9 6.1 - - - +
132A PHE 3.1 0.6 - - - -
133A GLU* 1.3 78.3 - - + +
135A ALA* 1.3 56.2 + - - +
136A VAL 3.2 0.2 - - - -
137A ALA* 3.1 8.9 + - - +
138A GLN* 2.7 59.7 + - - +
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Residues in contact with ALA 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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118A LEU* 3.4 35.7 - - + +
131A ALA 3.2 15.4 + - - +
132A PHE* 3.2 4.7 + - - +
134A GLN* 1.3 77.8 - - - +
136A VAL* 1.3 58.4 + - - +
138A GLN* 3.1 11.4 + - - +
139A LEU* 3.0 27.7 + - - +
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Residues in contact with VAL 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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4A VAL* 3.7 17.7 - - + +
5A GLY* 3.8 39.3 - - - +
6A PHE* 3.9 9.4 - - + -
19A ARG* 6.2 0.2 - - + -
91A VAL* 4.1 12.3 - - + -
118A LEU* 4.2 11.0 - - + -
132A PHE* 3.2 47.8 + - + +
133A GLU 4.1 3.6 - - - +
135A ALA* 1.3 75.5 - - - +
137A ALA* 1.3 62.9 + - - +
139A LEU* 3.2 21.0 + - - +
229A PGE 5.3 0.3 - - - +
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Residues in contact with ALA 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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4A VAL 4.7 1.6 - - - -
133A GLU 3.2 17.1 + - - +
134A GLN* 3.1 15.3 + - - +
136A VAL* 1.3 80.5 - - - +
138A GLN* 1.3 59.4 + - + +
139A LEU 3.3 1.1 + - - +
229A PGE 3.1 40.4 - - - +
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Residues in contact with GLN 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 GLN* 2.7 46.7 + - - +
135A ALA* 3.4 9.0 + - - +
137A ALA* 1.3 74.1 - - + +
139A LEU* 1.3 60.1 + - - +
140A PRO* 3.6 7.6 - - - +
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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