Contacts of the helix formed by residues 129 - 143 (chain A) in PDB entry 3QPV
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 THR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ASN 3.5 0.6 - - - -
128A THR* 1.3 84.0 - - - +
130A ARG* 1.3 64.5 + - - +
131A GLU* 3.8 14.4 + - - +
132A ARG* 3.0 26.5 + - - +
133A ARG* 3.1 29.7 + - - +
196A SER* 3.5 33.9 - - - +
198A GLN* 3.8 8.1 - - - +
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Residues in contact with ARG 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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129A THR* 1.3 68.6 - - - +
131A GLU* 1.3 56.8 + - - +
133A ARG* 3.2 22.2 + - - +
134A HIS* 2.7 39.5 + - + +
198A GLN* 3.0 44.3 + - - +
199A PRO* 5.0 5.5 + - - +
201A ASP* 4.7 13.1 + - - +
205A CYS* 3.5 40.2 - - - +
206A ASP* 5.4 4.1 + - - +
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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
----------------------------------------------------------
129A THR* 3.2 12.6 + - - +
130A ARG* 1.3 77.0 - - - +
132A ARG* 1.3 63.6 + - - +
134A HIS* 3.4 5.3 + - - +
135A MET* 3.2 22.3 + - - +
198A GLN* 4.6 1.0 + - - -
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Residues in contact with ARG 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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98A ARG* 4.8 14.1 + - - +
99A LYS* 5.1 3.0 - - - +
102A ALA* 3.9 22.3 - - - +
123A PHE* 4.5 2.1 - - - -
125A ALA* 4.2 4.6 - - - +
127A ASN* 2.8 48.3 + - - +
129A THR* 3.0 26.2 + - - +
131A GLU* 1.3 78.4 + - - +
133A ARG* 1.3 62.7 + - - +
135A MET* 3.2 30.9 + - - +
136A ILE* 3.1 24.0 + - + +
524A FDP 3.0 38.8 + - - -
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Residues in contact with ARG 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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38A VAL* 5.0 0.7 - - + -
40A VAL* 3.8 14.7 - - - +
127A ASN* 2.7 44.5 + - + +
128A THR* 3.3 14.6 + - - +
129A THR 3.1 11.7 + - - +
130A ARG* 3.8 28.7 - - - +
132A ARG* 1.3 76.3 - - - +
134A HIS* 1.3 53.3 + - - +
136A ILE* 3.0 9.7 + - - +
137A LEU* 2.8 42.0 + - + +
149A PHE* 3.8 26.5 - - + -
198A GLN 2.6 30.2 + - - -
199A PRO 3.9 7.3 + - - -
200A LEU* 3.5 30.2 - - - +
206A ASP* 4.7 7.3 + - - -
209A LEU* 5.5 2.9 - - + +
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 2.7 24.2 + - + +
131A GLU* 3.8 5.6 - - - +
133A ARG* 1.3 73.3 - - - +
135A MET* 1.3 58.2 + - - +
137A LEU* 3.3 18.3 - - + +
138A HIS* 2.9 30.9 + - + +
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Residues in contact with MET 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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99A LYS* 5.0 16.4 - - + +
102A ALA* 4.5 10.3 - - + -
103A LEU* 3.8 25.4 - - + -
106A LEU* 3.7 29.2 - - + -
123A PHE* 5.8 0.2 - - + -
131A GLU 3.2 13.2 + - - +
132A ARG* 3.5 35.2 - - - +
134A HIS* 1.3 76.9 - - - +
136A ILE* 1.4 66.4 + - + +
138A HIS* 3.0 11.4 + - + +
139A PHE* 3.0 22.7 + - + +
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Residues in contact with ILE 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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36A VAL* 4.5 11.7 - - + -
38A VAL* 3.7 32.3 - - + -
106A LEU* 4.4 19.3 - - + -
123A PHE* 3.4 26.2 - - + -
127A ASN* 3.4 31.0 - - + +
132A ARG* 3.1 21.4 + - + +
133A ARG* 3.0 9.5 + - - +
135A MET* 1.4 74.6 - - + +
137A LEU* 1.3 65.4 + - + +
139A PHE* 3.1 10.5 + - + +
140A ALA* 2.9 23.0 + - + +
147A ALA* 5.9 1.3 - - + -
149A PHE* 5.3 2.5 - - + -
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Residues in contact with LEU 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 ARG* 2.8 15.8 + - + +
134A HIS* 3.3 20.9 - - + +
136A ILE* 1.3 77.3 - - - +
138A HIS* 1.3 63.6 + - - +
140A ALA* 3.2 5.2 + - + +
141A LYS* 2.9 27.0 + - - +
147A ALA* 4.0 16.8 - - + -
149A PHE* 3.5 32.5 - - + -
209A LEU* 3.8 31.2 - - + -
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Residues in contact with HIS 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 HIS* 2.9 21.7 + - + +
135A MET* 3.0 14.7 + - + +
137A LEU* 1.3 75.1 - - - +
139A PHE* 1.3 59.5 + - - +
141A LYS* 3.3 9.8 - - + +
142A GLU* 3.0 55.0 + - + +
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Residues in contact with PHE 139 (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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36A VAL* 4.4 5.4 - - + -
106A LEU* 3.2 68.0 - - + -
107A ARG* 5.1 1.3 - - - -
109A VAL* 3.9 18.8 - - + -
110A LYS* 4.1 15.0 - - + -
135A MET* 3.0 12.3 + - + +
136A ILE* 3.3 14.6 - - + +
138A HIS* 1.3 76.0 - - + +
140A ALA* 1.3 68.0 + - + +
142A GLU* 3.8 15.9 - - - +
143A ASN* 2.7 50.5 + - - +
145A PHE* 4.0 15.9 - + - -
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Residues in contact with ALA 140 (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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36A VAL* 5.2 5.4 - - + -
136A ILE* 2.9 17.0 + - + +
137A LEU* 3.2 8.3 + - + +
139A PHE* 1.3 76.0 - - + +
141A LYS* 1.3 54.8 + - - +
143A ASN* 2.8 5.2 + - - -
144A ASP 2.8 31.7 + - - -
145A PHE* 3.0 39.2 + - + +
146A LYS 4.5 0.7 - - - +
147A ALA* 4.1 22.0 - - + -
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Residues in contact with LYS 141 (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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137A LEU 2.9 17.9 + - - +
138A HIS* 3.3 11.0 - - + +
140A ALA* 1.3 74.6 - - - +
142A GLU* 1.3 64.6 + - + +
143A ASN 3.1 1.0 + - - -
144A ASP* 3.2 15.3 + - - +
145A PHE 4.2 2.6 + - - -
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Residues in contact with GLU 142 (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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110A LYS* 6.1 0.2 - - - +
138A HIS* 3.0 46.0 + - + +
139A PHE* 3.8 13.6 - - - +
140A ALA 3.2 0.2 - - - -
141A LYS* 1.3 77.8 - - + +
143A ASN* 1.3 82.0 + - - +
144A ASP* 3.4 1.0 - - - +
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Residues in contact with ASN 143 (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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110A LYS* 3.3 35.2 + - - +
139A PHE* 2.7 48.6 + - - +
140A ALA 2.8 3.0 + - - -
142A GLU* 1.3 92.2 + - - +
144A ASP* 1.3 70.4 + - - +
145A PHE* 3.5 37.6 - - + -
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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