Contacts of the helix formed by residues 116 - 127 (chain B) in PDB entry 4Y2H
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 ILE 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A PHE* 3.6 37.5 - - + -
51B TYR 3.5 20.2 - - - +
52B SER* 4.4 5.2 + - - +
57B HIS* 3.5 35.9 - - + +
92B GLY 3.6 14.2 - - - +
93B THR* 4.1 9.6 - - + -
112B GLU* 3.7 24.7 - - + -
114B SER* 2.9 8.9 + - - +
115B ALA* 1.3 71.1 - - - +
117B TRP* 1.3 67.3 + - - +
118B GLN 3.0 2.9 - - - -
119B GLN* 2.9 29.1 + - + +
120B ALA 3.1 8.5 + - - -
401B SAH 4.3 0.7 - - - +
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Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 3.7 30.5 - - + +
113B ALA 5.1 0.9 - - - -
114B SER 3.0 25.9 + - - -
115B ALA* 3.0 13.3 + - - +
116B ILE* 1.3 78.2 - - - +
118B GLN* 1.3 83.4 + - + +
120B ALA* 3.2 9.5 + - - +
121B ARG* 2.9 69.9 + - - -
135B VAL* 3.6 21.5 - - + +
137B PRO* 3.5 40.7 - - + +
138B GLY 5.0 0.7 - - - -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA* 3.1 29.7 + - - +
116B ILE 3.0 0.4 - - - -
117B TRP* 1.3 115.5 - - + +
119B GLN* 1.3 72.2 + - - +
121B ARG* 3.5 10.2 + - - +
122B GLU* 3.0 34.2 + - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.6 30.5 - - + +
225A PHE* 3.6 47.7 - - + +
228A ARG* 3.9 13.3 - - - +
93B THR* 4.6 1.1 - - + -
115B ALA 3.9 5.5 - - - +
116B ILE* 2.9 33.3 + - + +
118B GLN* 1.3 85.0 + - - +
120B ALA* 1.3 60.5 + - - +
122B GLU* 3.2 17.7 + - - +
123B VAL* 2.8 34.9 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 5.2 5.4 - - + -
92B GLY 3.0 26.3 + - - +
93B THR* 3.4 20.9 + - - +
94B GLY* 3.8 5.8 - - - +
112B GLU* 5.8 0.2 - - + -
116B ILE 3.1 4.8 + - - +
117B TRP* 3.4 11.7 - - - +
119B GLN* 1.3 77.9 - - - +
121B ARG* 1.3 61.6 + - - +
123B VAL* 3.3 1.9 + - - +
124B VAL* 3.1 27.7 + - - +
135B VAL* 3.9 14.1 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 2.9 54.4 + - + +
118B GLN* 3.7 11.9 - - - +
119B GLN 3.2 0.2 - - - -
120B ALA* 1.3 76.3 - - - +
122B GLU* 1.3 63.7 + - - +
124B VAL* 3.2 5.2 + - + +
125B ARG* 3.0 44.4 + - + +
135B VAL* 3.8 25.2 + - + +
137B PRO* 5.8 1.0 - - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A CYS* 4.3 15.3 - - + +
222A LEU* 5.0 6.5 - - + +
225A PHE* 6.0 0.9 - - - +
228A ARG* 5.6 1.9 + - - -
118B GLN* 3.0 28.2 + - - +
119B GLN* 3.4 22.3 + - - +
121B ARG* 1.3 80.4 - - - +
123B VAL* 1.3 62.4 + - - +
125B ARG* 3.3 29.9 + - - +
126B PHE* 2.9 26.9 + - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.2 3.4 - - + -
218A ASP 3.9 8.5 - - - +
219A MET* 3.8 26.2 - - + -
221A CYS* 4.0 11.2 - - - -
222A LEU* 4.0 20.2 - - + -
93B THR 3.6 19.7 - - - +
98B ILE* 3.7 17.9 - - + -
119B GLN 2.8 23.6 + - - +
120B ALA 3.3 1.5 + - - +
122B GLU* 1.3 71.3 - - - +
124B VAL* 1.3 58.4 + - - +
126B PHE* 3.3 0.3 + - - +
127B ASN* 2.7 50.8 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLY* 5.4 5.6 - - - -
98B ILE* 4.5 19.3 - - + -
120B ALA 3.1 15.6 + - - +
121B ARG* 3.5 9.2 - - - +
123B VAL* 1.3 75.5 - - - +
125B ARG* 1.3 60.9 + - - +
127B ASN* 3.2 5.4 + - - -
129B LEU* 3.0 49.3 + - + +
130B GLU* 3.6 6.5 - - + +
133B VAL* 3.5 47.3 - - + +
135B VAL* 3.9 10.5 - - + -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 3.0 42.4 + - + +
122B GLU* 3.4 34.8 + - - +
124B VAL* 1.3 75.6 - - - +
126B PHE* 1.3 59.3 + - - +
128B GLY* 3.0 19.9 + - - -
130B GLU* 3.7 27.1 - - + +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 3.4 51.0 - - + +
220A SER* 3.5 16.4 - - - -
221A CYS* 3.7 32.1 - - + -
122B GLU 2.9 18.2 + - - +
123B VAL 3.6 3.6 - - - +
125B ARG* 1.3 78.8 - - - +
127B ASN* 1.3 60.5 + - - +
128B GLY 3.2 1.1 + - - -
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLY 5.1 0.5 - - - +
217A VAL* 3.7 11.8 - - - +
218A ASP* 2.8 53.4 + - - +
98B ILE* 4.5 3.5 - - + +
102B GLN* 5.5 1.4 + - - -
123B VAL* 2.7 38.5 + - - +
124B VAL 3.2 3.6 + - - +
125B ARG 3.2 0.4 - - - -
126B PHE* 1.3 79.1 - - - +
128B GLY* 1.3 61.9 + - - +
129B LEU* 3.2 25.8 + - + +
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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