Contacts of the helix formed by residues 117 - 132 (chain A) in PDB entry 1PVI
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 PRO 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG 3.5 20.9 - - - +
96A GLN* 3.6 22.9 - - - +
97A VAL 4.0 12.6 - - - +
98A PRO* 4.4 9.1 - - + -
115A LEU 4.0 0.4 - - - -
116A GLU* 1.4 92.6 - - + +
118A LYS* 1.3 58.1 + - + +
120A LEU* 2.7 34.9 + - + +
121A GLU* 3.1 14.5 + - - +
124A TYR* 4.7 3.2 - - + +
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Residues in contact with LYS 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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116A GLU* 4.4 21.2 - - + +
117A PRO* 1.3 83.1 - - + +
119A ASP* 1.3 68.5 + - - +
121A GLU* 3.4 30.9 + - - +
122A PHE 4.8 0.3 + - - -
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Residues in contact with ASP 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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115A LEU* 3.1 35.0 - - + +
116A GLU* 2.7 26.9 + - - +
118A LYS* 1.3 83.2 + - - +
120A LEU* 1.3 58.9 + - - +
121A GLU 3.2 1.6 + - - -
122A PHE* 4.1 3.3 + - - +
148A TYR* 2.8 27.3 + - - +
152A HIS* 3.6 29.6 + - + +
154A THR* 5.9 1.7 - - - +
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Residues in contact with LEU 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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99A TRP* 3.3 44.9 - - + -
101A PHE* 4.2 11.0 - - + -
115A LEU* 3.5 33.2 - - + +
116A GLU 3.9 10.3 - - - +
117A PRO* 2.7 20.0 + - + +
119A ASP* 1.3 72.7 - - - +
121A GLU* 1.3 60.2 + - - -
122A PHE 3.4 0.7 - - - -
123A TYR* 3.3 18.0 + - + +
124A TYR* 3.3 39.5 + - + +
144A ILE* 4.8 13.5 - - + -
148A TYR* 4.9 7.6 - - + -
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Residues in contact with GLU 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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95A ARG* 5.9 5.8 + - - +
117A PRO* 3.1 8.2 + - - +
118A LYS* 3.5 27.4 - - - +
119A ASP 3.2 1.4 - - - -
120A LEU* 1.3 73.3 - - - +
122A PHE* 1.3 68.2 + - - +
123A TYR 2.9 2.6 + - - -
124A TYR* 3.2 11.8 + - + -
125A ASP* 3.1 38.3 + - - +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS 4.8 0.6 + - - -
119A ASP 4.1 1.8 + - - +
120A LEU 3.4 0.4 - - - -
121A GLU* 1.3 77.3 - - - +
123A TYR* 1.3 91.8 + + - +
125A ASP* 3.7 8.1 - - - +
126A LYS* 3.6 33.4 + - + +
148A TYR* 3.7 26.5 - + + +
3C G 5.6 2.9 - - - -
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Residues in contact with TYR 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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120A LEU* 3.3 14.6 + - + +
121A GLU 2.9 2.0 + - - -
122A PHE* 1.3 98.1 - + - +
124A TYR* 1.3 66.3 + - + +
125A ASP 3.1 2.5 + - - -
126A LYS* 3.3 18.5 + - + +
127A TRP* 3.2 61.4 + + + -
143A LYS 4.5 9.9 - - - -
144A ILE* 4.6 12.8 - - + -
145A PRO* 3.3 28.9 - - + +
148A TYR* 3.7 41.3 - + - -
3C G 3.5 20.1 + - - -
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Residues in contact with TYR 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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91A ILE* 3.7 31.8 - - + +
94A TYR* 4.0 5.7 + - + +
95A ARG* 3.8 47.7 + - + +
97A VAL 5.1 0.2 + - - -
99A TRP* 3.0 44.6 + + - -
117A PRO* 4.7 4.0 - - + +
120A LEU* 3.3 40.0 + - + +
121A GLU* 3.2 12.8 + - + +
123A TYR* 1.3 77.9 - - + +
125A ASP* 1.3 63.6 + - - +
127A TRP* 3.5 31.2 + + - +
128A GLU* 3.1 26.4 + - - +
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Residues in contact with ASP 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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95A ARG* 4.8 7.4 + - - -
121A GLU* 3.1 23.3 + - - +
122A PHE* 3.7 11.7 - - + +
123A TYR 3.1 0.4 - - - -
124A TYR* 1.3 74.2 - - - +
126A LYS* 1.3 60.3 + - - +
127A TRP 3.1 0.3 + - - -
128A GLU* 3.2 7.9 + - - +
129A ARG* 2.8 39.3 + - + +
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Residues in contact with LYS 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 PHE* 3.6 26.6 + - + +
123A TYR* 3.3 25.3 + - + +
125A ASP* 1.3 78.2 - - - +
127A TRP* 1.3 67.9 + - + +
129A ARG* 3.9 8.7 + - - +
130A LYS* 2.9 32.5 + - + +
3C G 2.8 42.5 + - - +
4C A 3.8 23.3 - - - +
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Residues in contact with TRP 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A THR* 4.2 20.9 - - + -
86A MET* 4.2 25.4 - - + -
91A ILE* 4.0 11.9 - - + -
99A TRP* 5.6 3.1 - + - -
123A TYR* 3.2 44.5 + + + +
124A TYR* 3.7 35.7 - + - +
125A ASP 3.1 0.6 - - - -
126A LYS* 1.3 82.9 - - + +
128A GLU* 1.3 67.2 + - - +
130A LYS* 3.0 7.8 + - + +
131A TRP* 2.8 24.8 + - - +
139A ILE* 3.8 23.0 - - + +
142A PRO* 3.3 41.9 - - + +
143A LYS 5.1 1.3 + - - -
144A ILE* 4.2 19.3 - - + -
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Residues in contact with GLU 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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88A PRO* 4.4 23.5 - - + +
91A ILE* 4.2 10.4 - - + +
95A ARG* 3.5 26.4 + - - -
124A TYR 3.1 14.0 + - - +
125A ASP* 3.8 7.6 - - - +
127A TRP* 1.3 77.0 - - - +
129A ARG* 1.3 63.1 - - - +
131A TRP* 3.1 23.9 + - - +
132A TYR* 3.3 36.0 + - + -
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Residues in contact with ARG 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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125A ASP* 2.8 22.6 + - - +
126A LYS* 3.9 7.9 + - - +
128A GLU* 1.3 78.9 - - - +
130A LYS* 1.3 63.1 + - - +
132A TYR* 3.4 9.9 + - - +
133A SER* 3.0 38.5 + - - +
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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 LYS* 2.9 22.5 + - + +
127A TRP* 3.0 9.4 + - + +
129A ARG* 1.3 74.9 - - - +
131A TRP* 1.3 67.3 + - - +
132A TYR 3.1 1.0 + - - -
133A SER* 3.1 13.1 + - - +
134A ASP* 3.0 39.0 - - + +
139A ILE* 3.6 42.2 - - + +
142A PRO* 5.8 0.8 - - - +
3C G 5.6 0.4 - - - +
4C A 3.8 59.3 + - - +
5C C 4.4 7.0 + - - -
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Residues in contact with TRP 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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86A MET 4.3 9.0 - - - -
87A ASN* 3.8 20.6 - - + +
88A PRO* 3.4 31.9 - - + -
127A TRP 2.8 12.2 + - - +
128A GLU* 3.1 15.3 - - - +
130A LYS* 1.3 77.5 - - - +
132A TYR* 1.3 75.8 + + - +
134A ASP* 3.7 3.9 - - - +
135A GLY 3.6 2.6 + - - -
136A HIS* 3.0 73.5 + + + -
137A LYS 3.0 40.1 + - - -
138A ASP* 3.6 13.1 + - - -
139A ILE* 4.7 8.7 - - + +
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Residues in contact with TYR 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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88A PRO* 4.9 6.3 - - + +
128A GLU* 3.3 43.4 + - + -
129A ARG* 3.7 8.1 - - - +
130A LYS 3.2 0.2 - - - -
131A TRP* 1.3 90.0 - + - +
133A SER* 1.3 56.0 + - - +
134A ASP 2.6 18.9 + - - -
135A GLY* 3.1 12.6 + - - -
136A HIS* 3.7 37.8 + + - +
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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