Contacts of the helix formed by residues 118 - 133 (chain B) in PDB entry 1Y8Q
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 ASN 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B MET* 5.4 1.7 - - - +
116B LEU* 3.8 1.4 - - - +
117B ASP* 1.3 96.9 + - - +
119B ARG* 1.3 64.8 + - - +
120B ALA* 3.7 10.9 - - - +
121B ALA* 3.2 26.9 + - - +
122B ARG* 3.2 28.0 + - - +
802B ATP 3.2 23.3 + - - -
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Residues in contact with ARG 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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118B ASN* 1.3 71.6 - - - +
120B ALA* 1.3 66.2 + - - +
122B ARG* 3.1 9.2 + - - +
123B ASN* 2.8 61.5 + - - +
159B TYR* 4.9 9.0 - - + +
164B LYS* 5.8 7.7 + - + -
166B THR* 5.8 8.8 + - - +
167B GLN* 6.0 3.1 - - - +
442B TYR* 5.0 3.8 + - - -
471B GLU* 3.5 17.2 + - - +
472B LYS* 3.1 30.9 + - - +
474B ALA* 4.4 10.7 - - - +
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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
----------------------------------------------------------
97B MET* 4.2 18.1 - - + +
118B ASN* 3.4 10.1 + - - +
119B ARG* 1.3 88.2 - - - +
121B ALA* 1.3 61.9 + - - +
123B ASN* 3.5 6.2 + - - +
124B HIS* 3.1 22.9 + - - +
474B ALA* 5.0 8.3 - - + +
476B VAL* 6.0 0.2 - - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 4.3 3.1 - - + +
97B MET* 3.8 13.9 - - - -
116B LEU* 3.4 20.2 - - + -
118B ASN* 3.2 20.5 + - - +
119B ARG 3.3 0.2 - - - -
120B ALA* 1.3 76.8 - - - +
122B ARG* 1.3 61.6 + - - +
124B HIS* 3.3 1.7 + - - +
125B VAL* 2.8 34.1 + - - +
802B ATP 3.6 26.0 - - + +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 4.3 5.0 + - - +
116B LEU* 3.7 39.6 + - + -
117B ASP* 4.7 5.1 - - - +
118B ASN 3.2 26.9 + - - +
119B ARG 3.1 6.1 + - - +
121B ALA* 1.3 75.0 - - - +
123B ASN* 1.3 59.5 + - - +
125B VAL* 3.9 1.0 - - - +
126B ASN* 2.9 28.6 + - - +
138B GLU* 2.6 45.8 + - - +
139B SER 3.4 17.8 + - - -
140B GLY* 4.4 6.9 - - - -
147B GLN* 6.2 0.8 - - - +
159B TYR* 3.3 37.6 + - + -
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Residues in contact with ASN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 2.8 51.1 + - - +
120B ALA 3.8 4.3 - - - +
122B ARG* 1.3 72.1 - - - +
124B HIS* 1.3 66.9 + - - +
126B ASN* 3.1 5.2 + - - +
127B ARG* 3.0 30.2 + - - +
159B TYR* 3.2 21.8 - - - -
160B GLU* 3.1 43.8 - - - +
474B ALA* 3.9 16.1 - - + +
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Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.7 30.9 + - + -
97B MET* 3.9 16.6 - - + -
101B TYR 4.9 2.0 + - - -
120B ALA 3.1 11.1 + - - +
121B ALA* 3.5 10.3 - - - +
123B ASN* 1.3 79.0 - - - +
125B VAL* 1.3 66.7 + - - +
127B ARG* 3.0 5.8 + - - +
128B MET* 2.9 46.4 + - + +
474B ALA 5.3 0.6 + - - +
476B VAL* 3.7 14.1 - - + +
523B LEU* 3.7 25.4 - - + +
524B GLN* 2.8 48.8 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 4.4 4.5 - - + -
96B ILE* 4.0 32.8 - - + -
106B PHE* 4.4 8.5 - - + -
112B VAL* 4.4 2.9 - - + -
114B ASN* 3.2 40.2 - - - +
116B LEU* 4.2 4.7 - - + -
121B ALA 2.8 21.9 + - - +
122B ARG 3.9 0.2 - - - +
124B HIS* 1.3 75.6 - - + +
126B ASN* 1.3 65.5 + - - +
128B MET* 3.2 7.0 + - - +
129B CYS* 3.0 31.2 + - - +
136B LEU* 4.1 13.2 - - + -
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG 2.9 15.4 + - - +
123B ASN* 3.1 9.8 + - - +
125B VAL* 1.3 77.8 - - - +
127B ARG* 1.3 56.0 + - - +
129B CYS* 3.5 2.4 + - - +
130B LEU* 3.1 40.5 + - - +
136B LEU* 3.9 12.0 - - + +
151B ILE* 3.8 12.5 - - - +
158B CYS* 3.5 27.6 - - - +
159B TYR* 2.9 36.7 + - + +
160B GLU* 3.1 22.6 + - - -
443B VAL* 4.1 0.8 - - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 3.0 11.7 + - - +
124B HIS 3.0 5.8 + - - +
126B ASN* 1.3 74.0 - - - +
128B MET* 1.3 65.5 + - - +
130B LEU* 3.2 8.2 + - - +
131B ALA* 2.9 24.9 + - - +
160B GLU* 2.6 40.0 + - - +
442B TYR* 3.3 11.5 + - - -
443B VAL* 3.9 18.9 - - + +
473B PHE 2.8 29.7 + - - -
474B ALA* 3.1 19.2 + - - +
475B MET 4.0 0.8 - - - +
524B GLN* 2.9 50.9 + - + +
526B TYR* 3.4 29.9 - - + -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR 3.5 11.0 - - - +
102B ASN* 3.4 10.1 - - - +
103B VAL* 3.4 32.6 - - + +
106B PHE* 3.7 30.9 - - + +
124B HIS* 2.9 45.4 + - + +
125B VAL 3.7 5.6 - - - +
127B ARG* 1.3 75.6 - - - +
129B CYS* 1.3 58.9 + - - +
131B ALA* 3.2 4.9 + - - +
132B ALA* 2.9 29.6 + - - +
523B LEU* 3.3 29.8 - - + +
524B GLN* 3.6 16.2 - - - -
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Residues in contact with CYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.9 7.6 - - - -
112B VAL* 3.6 43.7 - - - -
125B VAL* 3.0 22.4 + - - +
126B ASN 3.9 3.6 - - - +
128B MET* 1.3 75.4 - - - +
130B LEU* 1.3 60.7 + - - +
133B ASP* 2.8 23.6 + - - -
134B VAL* 3.0 34.2 + - - +
136B LEU* 3.9 20.2 - - + -
151B ILE* 6.1 1.3 - - + -
153B LYS* 5.2 0.7 - - - +
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Residues in contact with LEU 130 (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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126B ASN* 3.1 44.5 + - - +
127B ARG* 3.2 8.0 + - - +
129B CYS* 1.3 75.4 - - - +
131B ALA* 1.3 64.3 + - - +
133B ASP 3.1 8.7 + - - -
151B ILE* 4.6 9.0 - - + -
152B LYS 5.2 0.2 - - - -
153B LYS* 3.1 57.1 + - + +
158B CYS* 4.0 15.9 - - + -
443B VAL* 4.0 13.5 - - + +
444B CYS* 3.9 28.0 - - + -
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Residues in contact with ALA 131 (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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103B VAL* 3.7 29.6 - - + +
107B ARG* 5.0 2.9 + - - -
127B ARG 2.9 16.6 + - - +
128B MET 3.5 5.2 - - - +
130B LEU* 1.3 80.1 - - - +
132B ALA* 1.3 58.9 + - - +
133B ASP* 3.4 2.3 + - - +
153B LYS* 4.6 7.9 + - - +
524B GLN 3.9 3.6 - - - +
525B ASP* 3.9 28.5 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 3.8 15.7 - - + +
106B PHE* 3.9 8.3 - - + -
107B ARG* 3.5 52.8 + - - +
128B MET 2.9 20.2 + - - +
131B ALA* 1.3 70.4 - - - +
133B ASP* 1.3 72.4 + - - +
134B VAL* 3.5 9.2 + - + +
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Residues in contact with ASP 133 (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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129B CYS 2.8 11.1 + - - -
130B LEU 3.5 8.7 - - - +
131B ALA 3.1 5.6 - - - +
132B ALA* 1.3 82.8 - - - +
134B VAL* 1.3 56.1 + - - +
135B PRO* 4.3 3.1 - - - +
152B LYS* 3.2 30.0 + - - -
153B LYS* 3.3 31.5 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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