Contacts of the helix formed by residues 117 - 130 (chain A) in PDB entry 4QPL
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 ASP 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.0 7.5 - - + +
45A HIS* 4.0 22.0 - - + -
58A LEU* 3.5 23.1 - - + +
115A GLN 3.7 2.2 + - - -
116A TYR* 1.3 72.9 - - - +
118A GLU* 1.3 58.7 + - - +
119A ARG* 3.0 14.2 + - - +
120A THR* 2.6 43.8 + - - -
121A SER* 2.8 27.9 + - - -
139A ILE* 5.3 1.0 - - - +
177A VAL* 4.3 0.4 - - - -
178A ALA* 3.9 22.2 - - + +
201A V3L 5.1 3.7 + - - -
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Residues in contact with GLU 118 (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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44A VAL* 3.8 26.0 - - + +
45A HIS* 4.5 6.9 + - + +
96A ALA* 5.4 11.6 - - + +
100A ASN* 6.5 0.7 - - - -
116A TYR 3.8 1.3 + - - -
117A ASP* 1.3 73.8 - - - +
119A ARG* 1.3 60.3 + - - +
121A SER* 3.6 8.1 - - - -
122A ARG* 2.9 61.7 + - - +
177A VAL* 5.4 0.4 - - - +
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Residues in contact with ARG 119 (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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39A CYS* 4.5 2.0 - - - -
41A GLN* 3.6 33.2 + - - +
42A THR* 2.7 39.8 + - - +
44A VAL* 3.2 32.0 - - + +
56A CYS* 4.2 10.9 - - - -
117A ASP* 3.0 9.2 + - - +
118A GLU* 1.3 78.8 - - - +
120A THR* 1.3 66.1 + - - +
122A ARG* 3.3 36.7 + - - +
123A GLU* 3.3 11.3 + - - +
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Residues in contact with THR 120 (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 TYR* 3.7 18.6 - - + -
117A ASP* 2.6 33.1 + - - -
119A ARG* 1.3 76.1 - - - +
121A SER* 1.3 63.2 + - - +
123A GLU* 3.1 8.4 + - + +
124A LEU* 2.9 23.0 + - + +
137A MET* 3.4 43.8 - - + +
138A LEU 4.6 4.9 + - - -
139A ILE* 4.2 11.8 - - + +
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Residues in contact with SER 121 (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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100A ASN* 5.3 11.0 + - - -
103A TYR* 5.8 0.2 - - - -
104A ALA* 5.9 0.3 - - - +
105A TRP* 3.8 25.1 + - - +
115A GLN* 5.4 1.2 + - - +
116A TYR* 3.2 23.4 + - - +
117A ASP 2.8 22.2 + - - -
118A GLU* 3.6 10.3 - - - -
119A ARG 3.3 0.2 - - - -
120A THR* 1.3 75.9 - - - +
122A ARG* 1.3 57.4 + - - +
124A LEU* 3.4 7.0 + - - +
125A GLU* 2.9 30.7 + - - +
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Residues in contact with ARG 122 (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 GLU* 2.9 57.3 + - - +
119A ARG* 3.7 40.2 - - - +
120A THR 3.2 0.6 - - - -
121A SER* 1.3 72.8 - - - +
123A GLU* 1.3 60.4 + - - +
125A GLU* 3.5 5.6 + - - +
126A ASP* 2.9 30.3 + - - +
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Residues in contact with GLU 123 (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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119A ARG 3.3 9.3 + - - +
120A THR* 3.1 12.9 + - + +
122A ARG* 1.3 78.9 - - - +
124A LEU* 1.3 62.7 + - + +
126A ASP* 3.2 13.7 + - - +
127A ALA* 3.0 23.9 + - - +
132A LYS* 4.8 6.1 + - - -
135A THR* 2.7 35.3 + - + +
136A GLU 4.4 11.2 - - - +
137A MET* 5.4 6.5 - - + -
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Residues in contact with LEU 124 (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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105A TRP* 3.6 34.4 - - + -
116A TYR* 3.7 47.1 - - + -
120A THR* 2.9 21.6 + - + +
121A SER 3.7 3.8 - - - +
123A GLU* 1.3 74.8 - - + +
125A GLU* 1.3 58.6 + - - +
127A ALA* 3.3 4.5 + - - +
128A PHE* 2.9 32.4 + - - +
135A THR* 4.4 7.4 - - + -
137A MET* 4.0 9.2 - - + -
146A ALA* 3.5 32.1 - - + -
148A LEU* 4.4 11.0 - - + +
165A ILE* 4.8 2.9 - - + -
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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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103A TYR* 3.3 37.6 - - + +
105A TRP* 2.9 18.6 + - - +
121A SER 2.9 17.5 + - - +
122A ARG* 3.8 7.2 - - - +
124A LEU* 1.3 76.4 - - - +
126A ASP* 1.3 57.4 + - - +
128A PHE* 3.8 3.1 - - - +
129A SER* 2.9 41.9 + - - -
167A ARG* 2.8 43.5 + - - -
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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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122A ARG 2.9 19.1 + - - +
123A GLU* 3.2 16.1 + - - +
125A GLU* 1.3 75.5 - - - +
127A ALA* 1.3 63.5 + - - +
129A SER* 3.0 19.3 + - - -
130A LYS* 3.1 52.2 + - - +
132A LYS* 4.2 10.7 + - - -
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Residues in contact with ALA 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 GLU* 3.0 18.6 + - - +
124A LEU 3.8 1.8 - - - +
126A ASP* 1.3 76.9 + - - +
128A PHE* 1.3 63.6 + - - +
130A LYS* 3.3 2.6 + - - -
131A GLY 3.1 4.0 + - - -
132A LYS* 3.0 45.0 + - + +
135A THR* 3.8 24.7 - - + -
148A LEU* 3.7 20.0 - - + -
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Residues in contact with PHE 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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105A TRP* 3.6 24.5 - + + -
124A LEU 2.9 18.2 + - - +
125A GLU* 3.8 4.9 - - - +
127A ALA* 1.3 77.6 - - - +
129A SER* 1.3 61.7 + - - +
131A GLY* 3.0 19.6 + - - -
132A LYS 5.0 0.7 - - - +
148A LEU* 3.7 19.6 - - + +
151A MET* 5.5 8.7 - - + -
167A ARG* 4.0 37.7 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 2.9 25.9 + - - -
126A ASP* 3.0 18.9 + - - -
128A PHE* 1.3 81.6 - - - +
130A LYS* 1.3 63.1 + - - +
131A GLY 3.6 0.3 + - - -
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Residues in contact with LYS 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* 3.1 51.5 + - - +
127A ALA 3.8 3.8 - - - +
128A PHE 3.2 0.4 - - - -
129A SER* 1.3 80.3 + - - +
131A GLY* 1.3 58.6 + - - +
132A LYS* 3.6 24.4 + - + +
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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