Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 3P3W
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 LEU 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO 3.6 1.6 + - - +
116A ALA* 1.3 71.3 - - - +
118A LYS* 1.3 65.3 + - - +
119A GLY 3.1 2.9 - - - -
120A ALA* 2.8 25.7 + - + -
121A ILE* 3.2 23.0 + - + +
141A ARG* 4.9 11.2 - - - +
145A VAL* 5.3 5.8 - - + -
220A ALA* 4.1 30.1 - - + +
221A ASN* 4.2 3.6 - - - +
222A LEU* 3.7 43.1 - - + +
242A PHE* 3.8 29.6 - - + -
355A ILE* 4.5 7.6 - - + -
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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 ALA* 3.3 12.5 - - + -
117A LEU* 1.3 76.8 - - - +
119A GLY* 1.3 58.8 + - - +
121A ILE* 4.1 5.1 + - - +
122A LEU* 3.9 17.5 + - - +
144A SER* 5.9 4.3 - - - +
145A VAL* 4.5 21.2 - - + +
148A ALA* 4.9 17.9 - - + +
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Residues in contact with GLY 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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116A ALA* 4.5 4.0 + - - +
117A LEU 2.9 1.8 + - - -
118A LYS* 1.3 76.2 - - - +
120A ALA* 1.3 63.7 + - - +
121A ILE 3.3 0.9 - - - -
122A LEU* 3.6 4.3 + - - +
123A SER* 3.0 29.8 + - - -
371A TRP* 3.3 21.0 - - - -
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Residues in contact with ALA 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 ALA 5.0 0.4 + - - -
117A LEU* 2.8 22.8 + - + +
119A GLY* 1.3 73.2 - - - +
121A ILE* 1.3 62.0 + - - +
124A LEU* 3.4 30.9 + - + +
242A PHE* 4.6 10.5 - - + -
355A ILE* 3.9 28.5 - - + -
357A VAL* 6.2 0.4 - - + -
371A TRP* 3.6 27.8 + - + +
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Residues in contact with ILE 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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117A LEU* 3.2 30.9 + - + +
118A LYS* 4.3 6.7 - - - +
120A ALA* 1.3 77.4 - - - +
122A LEU* 1.3 58.3 + - - +
124A LEU* 3.2 5.5 + - - +
125A LEU* 2.8 51.7 + - + +
145A VAL* 5.4 7.0 - - + -
149A ILE* 5.2 7.4 - - + -
190A LEU* 4.2 23.1 - - + -
218A MET* 4.2 5.1 - - - +
220A ALA* 3.9 20.6 - - + -
242A PHE* 3.6 34.3 - - + -
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Residues in contact with LEU 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 LYS 3.9 13.2 + - - +
119A GLY* 3.6 5.7 + - - +
120A ALA 3.5 0.2 - - - -
121A ILE* 1.3 79.7 - - - +
123A SER* 1.3 58.4 + - - +
125A LEU* 3.9 10.7 - - - +
126A SER* 3.1 27.2 + - - -
149A ILE* 6.1 4.7 - - + +
152A ALA* 5.8 7.6 - - + -
158A TRP* 4.9 6.9 - - + -
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Residues in contact with SER 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 GLY 3.0 13.6 + - - -
120A ALA 4.3 0.2 - - - -
121A ILE 3.3 0.4 - - - -
122A LEU* 1.3 77.7 - - - +
124A LEU* 1.3 58.2 + - - +
126A SER* 3.5 7.3 + - - -
127A TYR* 2.9 25.0 + - - +
371A TRP* 3.2 33.6 + - - -
376A ARG* 3.8 19.7 - - - +
377A PHE* 4.3 6.6 - - - +
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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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120A ALA* 3.4 15.8 + - + +
121A ILE* 3.2 3.9 + - - +
123A SER* 1.3 76.9 - - - +
125A LEU* 1.3 55.8 + - - +
126A SER 3.2 1.6 - - - -
127A TYR* 3.5 4.4 - - + +
128A TYR* 2.7 69.7 + - + +
218A MET* 4.3 6.7 - - + -
240A THR* 4.7 3.1 - - + -
242A PHE* 3.4 33.2 - - + -
357A VAL* 3.8 25.8 - - + -
371A TRP* 5.4 1.3 - - + -
377A PHE* 3.7 42.6 - - + -
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Residues in contact with LEU 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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121A ILE* 2.8 39.9 + - + +
122A LEU* 3.9 8.5 - - - +
123A SER 3.4 0.2 - - - -
124A LEU* 1.3 75.5 - - - +
126A SER* 1.3 58.8 + - - +
128A TYR* 4.6 2.0 - - - +
129A LYS* 3.2 17.9 + - - -
130A TRP* 3.2 57.3 + - + +
133A PHE* 4.2 22.0 - - + -
149A ILE* 4.5 11.0 - - + -
158A TRP* 4.2 23.1 - - + -
190A LEU* 4.5 7.9 - - + -
218A MET* 4.4 13.7 - - + -
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Residues in contact with SER 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 LEU 3.1 17.6 + - - -
123A SER* 3.7 7.6 - - - -
124A LEU 3.2 0.2 - - - -
125A LEU* 1.3 76.2 - - - +
127A TYR* 1.3 63.8 + - - +
129A LYS* 3.7 11.7 + - - +
156A ASN* 5.7 3.1 + - - -
158A TRP* 4.6 10.7 - - - -
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Residues in contact with TYR 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 SER 2.9 16.7 + - - +
124A LEU* 3.1 11.2 + - + +
126A SER* 1.3 79.8 - - - +
128A TYR* 1.3 89.4 + + - +
129A LYS* 3.2 3.2 + - - +
359A GLU* 4.6 5.1 + - - -
377A PHE* 3.5 42.0 - + + -
379A PRO* 3.6 26.6 - - + +
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Residues in contact with TYR 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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124A LEU* 2.7 46.3 + - + +
125A LEU* 4.8 0.7 - - - +
127A TYR* 1.3 85.6 - + - +
129A LYS* 1.3 68.9 + - - +
130A TRP* 3.3 32.6 + + + +
188A ARG* 5.5 1.6 + - - -
216A HIS* 4.5 13.5 - + - -
218A MET* 3.7 24.9 - - + -
240A THR* 3.0 31.7 + - + +
357A VAL* 5.2 0.3 - - - +
359A GLU* 2.7 36.9 + - - +
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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