Contacts of the helix formed by residues 116 - 130 (chain A) in PDB entry 3P6Y
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ARG* 5.1 0.2 - - - +
111A LEU* 3.8 1.9 - - - +
114A GLY 3.6 3.6 + - - -
115A GLU* 1.3 77.4 - - - +
117A GLU* 1.3 75.2 + - - +
118A VAL* 3.5 11.6 + - - +
119A GLU* 3.0 35.4 + - + +
120A GLY* 3.0 21.8 + - - -
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Residues in contact with GLU 117 (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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78A ARG* 4.4 15.9 + - - +
80A VAL* 4.0 15.9 - - + +
111A LEU* 4.1 14.1 - - + -
115A GLU 3.7 0.4 + - - -
116A ASP* 1.3 81.1 + - - +
118A VAL* 1.3 64.8 + - + +
120A GLY* 3.9 0.9 - - - -
121A LEU* 3.3 21.5 + - - +
171A HIS* 4.6 8.3 - - - -
173A LYS* 3.3 41.0 + - + +
175A PHE* 4.1 16.1 - - + -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 3.5 10.1 + - - +
117A GLU* 1.3 75.5 - - + +
119A GLU* 1.3 66.7 + - - +
121A LEU* 3.3 16.2 + - - +
122A LYS* 3.3 33.4 + - - +
141A ILE* 4.2 29.2 - - + +
142A ASP* 6.4 0.9 - - - -
175A PHE* 4.3 26.0 - - + -
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 4.6 6.0 - - + +
116A ASP* 3.0 30.5 + - + +
117A GLU 3.4 0.2 - - - -
118A VAL* 1.3 77.9 - - - +
120A GLY* 1.3 61.5 + - - +
122A LYS* 3.6 23.6 + - - +
123A ARG* 3.5 17.7 + - - +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.6 16.6 - - - -
115A GLU* 3.4 28.9 + - - -
116A ASP 3.0 10.1 + - - -
117A GLU 4.0 0.2 - - - -
118A VAL 3.2 0.2 - - - -
119A GLU* 1.3 76.0 - - - +
121A LEU* 1.3 58.2 + - - +
123A ARG* 3.4 5.7 + - - +
124A LEU* 3.1 32.8 + - - +
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Residues in contact with LEU 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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80A VAL* 3.9 22.4 - - + +
81A GLU* 3.9 10.8 - - - +
82A GLY* 3.9 13.2 - - - +
107A PRO 4.4 2.7 - - - +
108A GLY* 4.5 5.2 - - - -
117A GLU 3.3 14.1 + - - +
118A VAL* 3.3 10.5 + - - +
120A GLY* 1.3 75.6 - - - +
122A LYS* 1.3 54.8 + - + +
124A LEU* 3.3 2.2 + - + +
125A MET* 2.7 64.9 + - + +
141A ILE* 4.6 14.8 - - + -
175A PHE* 3.6 42.2 - - + -
177A VAL* 4.8 2.0 - - + -
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Residues in contact with LYS 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 VAL* 3.3 33.9 + - - +
119A GLU* 3.8 25.9 + - - +
121A LEU* 1.3 79.0 - - + +
123A ARG* 1.3 57.5 + - - +
125A MET* 3.8 6.4 - - - +
126A THR* 2.7 32.9 + - - -
139A TRP* 3.7 44.5 + - + +
141A ILE* 5.3 10.1 + - + +
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Residues in contact with ARG 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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110A GLU 3.1 26.7 + - - -
111A LEU* 4.1 0.4 - - - +
112A ASN* 3.8 21.7 + - - +
115A GLU* 3.0 38.5 + - - +
119A GLU 3.5 10.0 + - - +
120A GLY* 3.4 7.0 + - - +
121A LEU 3.2 0.2 - - - -
122A LYS* 1.3 80.0 - - - +
124A LEU* 1.3 80.8 + - - +
126A THR* 3.4 4.3 + - - -
127A GLU* 3.0 39.8 + - + +
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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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80A VAL* 4.1 13.9 - - + +
108A GLY* 3.6 26.9 - - - +
109A GLY* 3.5 35.7 - - - +
110A GLU 3.7 15.3 - - - +
111A LEU* 4.8 0.4 - - + +
120A GLY 3.1 18.8 + - - +
121A LEU* 3.8 3.8 - - - +
123A ARG* 1.3 97.4 - - - +
125A MET* 1.3 65.8 + - - +
127A GLU* 3.2 19.8 + - - +
128A ILE* 3.0 31.6 + - + +
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Residues in contact with MET 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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82A GLY* 3.1 40.4 - - - +
84A LEU* 3.7 21.1 - - + -
107A PRO* 3.7 27.6 - - + +
108A GLY* 5.5 0.2 - - - -
121A LEU* 2.7 38.6 + - + +
122A LYS* 3.8 2.9 - - - +
124A LEU* 1.3 73.1 - - - +
126A THR* 1.3 53.2 + - - +
128A ILE* 3.3 2.9 + - - +
129A LEU* 2.7 41.1 + - - +
130A GLY 3.6 0.3 + - - -
139A TRP* 3.5 40.2 - - + +
177A VAL* 3.8 10.1 - - + -
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Residues in contact with THR 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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50A LYS* 3.4 5.4 + - - -
122A LYS 2.7 22.1 + - - -
123A ARG* 3.9 3.8 - - - -
125A MET* 1.3 74.0 - - - +
127A GLU* 1.3 62.9 + - - +
130A GLY* 2.9 37.2 + - - +
131A ARG 5.9 0.9 - - - +
137A GLN* 5.0 5.5 + - + +
139A TRP* 3.0 19.7 + - - +
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Residues in contact with GLU 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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50A LYS* 3.0 20.1 + - - +
123A ARG* 3.0 26.1 + - + +
124A LEU* 3.2 25.5 + - - +
126A THR* 1.3 77.7 - - - +
128A ILE* 1.3 74.3 + - - +
188A PRO* 5.0 2.1 - - - +
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Residues in contact with ILE 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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50A LYS* 3.4 3.3 - - - -
53A LEU* 5.7 8.5 - - + -
97A LEU* 3.5 33.0 - - + -
105A LYS* 4.8 11.0 - - - +
107A PRO* 4.5 6.1 - - + -
108A GLY 4.3 24.7 - - - +
124A LEU* 3.0 18.7 + - + +
125A MET 4.0 1.6 - - - +
127A GLU* 1.3 96.7 - - - +
129A LEU* 1.3 65.6 + - + +
130A GLY 3.7 0.4 - - - -
186A ALA 3.0 13.3 - - - +
188A PRO* 3.1 30.5 - - + +
191A TYR* 5.4 9.0 - - + +
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Residues in contact with LEU 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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84A LEU* 3.9 27.8 - - + -
95A LEU* 6.2 0.7 - - + -
97A LEU* 4.6 9.4 - - + -
107A PRO* 4.1 23.1 - - + -
125A MET* 2.7 18.4 + - - +
128A ILE* 1.3 84.1 - - + +
130A GLY* 1.3 62.8 + - - +
131A ARG 3.5 0.3 + - - -
137A GLN* 4.1 1.2 - - - +
139A TRP* 4.2 15.0 - - + -
185A PHE* 3.4 30.5 - - + +
186A ALA 3.1 18.3 + - - +
187A VAL* 4.3 13.7 - - + -
193A LEU* 3.8 29.4 - - + -
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Residues in contact with GLY 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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50A LYS* 3.0 17.7 + - - +
125A MET 3.6 0.6 + - - -
126A THR* 2.9 40.1 + - - -
129A LEU* 1.3 77.3 - - - +
131A ARG* 1.3 64.7 + - - -
132A GLN* 3.9 3.4 + - - -
137A GLN* 4.5 5.4 - - - -
139A TRP* 5.1 2.0 - - - -
186A ALA* 3.2 12.1 - - - +
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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