Contacts of the helix formed by residues 118 - 133 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D MET* 4.8 2.0 - - - +
116D LEU* 3.7 2.2 - - - +
117D ASP* 1.3 87.4 - - - +
119D ARG* 1.3 65.5 + - - +
120D ALA* 3.0 14.2 + - - +
121D ALA* 2.7 36.4 + - + +
122D ARG* 3.0 27.1 + - - +
801D ATP 4.1 16.4 - - - +
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP 4.2 1.6 + - - -
118D ASN* 1.3 72.3 + - - +
120D ALA* 1.3 65.3 + - - +
122D ARG* 3.1 11.5 + - - +
123D ASN* 2.9 37.6 + - - +
159D TYR* 3.7 30.4 + - - -
163D PRO* 4.5 10.0 - - - +
164D LYS* 2.9 52.0 + - - +
165D PRO 3.4 13.3 + - - -
166D THR* 5.0 5.6 - - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET* 4.2 19.3 - - + +
118D ASN* 3.0 13.0 + - - +
119D ARG* 1.3 79.5 - - - +
121D ALA* 1.3 57.0 + - - +
123D ASN* 3.5 10.5 + - - +
124D HIS* 3.0 26.2 + - - +
474D ALA* 4.9 10.6 - - + +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ILE* 3.7 20.9 - - + -
97D MET* 3.9 11.4 - - - -
116D LEU* 3.7 12.8 - - + -
118D ASN* 2.7 27.8 + - + +
120D ALA* 1.3 71.1 - - - +
122D ARG* 1.3 61.7 + - - +
124D HIS* 3.2 4.1 + - - +
125D VAL* 2.8 34.1 + - - +
801D ATP 3.7 13.9 - - - +
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASN* 3.9 16.8 + - - +
116D LEU* 3.5 31.3 + - + +
117D ASP* 4.6 11.5 + - - +
118D ASN 3.0 20.4 + - - +
119D ARG* 3.1 8.3 + - - +
121D ALA* 1.3 74.1 - - - +
123D ASN* 1.3 55.9 + - - +
125D VAL* 3.2 2.3 + - - +
126D ASN* 2.7 36.9 + - - +
138D GLU* 2.9 23.3 + - - +
139D SER 2.9 26.5 + - - -
140D GLY* 3.8 11.1 - - - -
159D TYR* 3.1 42.0 + - + -
164D LYS* 6.2 0.2 - - - +
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Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ARG* 2.9 36.9 + - - +
120D ALA* 3.7 5.9 - - - +
122D ARG* 1.3 75.4 - - - +
124D HIS* 1.3 62.8 + - - +
126D ASN* 3.4 4.4 - - - +
127D ARG* 3.0 31.6 + - - +
159D TYR* 3.4 14.6 - - - -
160D GLU* 3.1 41.9 + - - +
163D PRO* 6.1 0.2 - - - +
472D LYS 5.9 0.2 + - - -
474D ALA* 3.8 24.7 - - + +
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Residues in contact with HIS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ILE* 3.5 31.5 + - + -
97D MET* 3.9 22.4 - - + -
98D ASN 5.5 0.2 + - - -
101D TYR 4.7 2.0 + - - -
106D PHE* 5.5 1.1 - + - -
120D ALA 3.0 14.1 + - - +
121D ALA* 3.4 11.4 - - - +
122D ARG 3.1 0.2 - - - -
123D ASN* 1.3 75.1 - - - +
125D VAL* 1.3 67.1 + - + +
127D ARG* 3.2 4.0 + - - +
128D MET* 2.9 61.6 + - + +
474D ALA 5.4 1.1 + - - +
476D VAL* 3.5 11.8 - - + +
523D LEU* 3.8 24.8 - - + +
524D GLN* 3.0 32.1 + - + +
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 4.2 6.3 - - + -
96D ILE* 3.8 29.6 - - + -
106D PHE* 4.4 8.5 - - + -
112D VAL* 4.3 6.7 - - + -
114D ASN* 3.1 33.4 - - - +
116D LEU* 4.1 6.1 - - + -
121D ALA 2.8 23.7 + - - +
122D ARG 3.8 2.9 - - - +
124D HIS* 1.3 73.4 - - + +
126D ASN* 1.3 63.8 + - - +
128D MET* 3.3 8.2 + - - +
129D CYS* 2.9 30.4 + - - -
136D LEU* 4.0 15.5 - - + -
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Residues in contact with ASN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ARG 2.7 17.3 + - - +
123D ASN* 3.4 6.1 - - - +
124D HIS 3.1 0.2 - - - -
125D VAL* 1.3 78.7 - - - +
127D ARG* 1.3 62.0 + - - +
129D CYS* 3.4 2.4 + - - +
130D LEU* 3.1 31.8 + - - +
136D LEU* 4.0 10.7 - - + +
138D GLU* 5.9 0.2 - - - +
151D ILE* 3.9 11.8 - - - +
158D CYS* 3.3 33.4 - - - +
159D TYR* 3.0 34.8 + - + +
160D GLU* 3.0 24.4 + - - +
443D VAL* 4.2 1.6 - - - +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN 3.0 12.8 + - - +
124D HIS 3.7 4.5 - - - +
126D ASN* 1.3 71.3 - - - +
128D MET* 1.3 61.4 + - - +
130D LEU* 3.1 9.8 + - - +
131D ALA* 2.9 31.9 + - - +
160D GLU* 2.8 35.8 + - - +
442D TYR* 4.5 4.9 + - - -
443D VAL* 4.0 21.5 - - + +
473D PHE 2.7 32.3 + - - -
474D ALA* 3.0 20.9 + - - +
475D MET* 3.9 1.6 - - - +
524D GLN* 2.9 50.7 + - + +
526D TYR* 3.5 29.4 - - + -
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Residues in contact with MET 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR 3.3 24.9 - - - +
102D ASN* 3.4 24.2 - - - -
103D VAL* 3.4 9.3 - - + +
106D PHE* 3.7 28.2 - - + +
124D HIS* 2.9 52.6 + - + +
125D VAL 3.7 4.7 - - - +
127D ARG* 1.3 76.1 - - - +
129D CYS* 1.3 58.0 + - - +
131D ALA* 3.4 4.3 + - - +
132D ALA* 2.9 31.2 + - - +
523D LEU* 3.5 25.4 - - + +
524D GLN* 3.8 11.4 - - - -
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Residues in contact with CYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 4.1 7.6 - - - -
112D VAL* 3.8 39.7 - - - -
125D VAL* 2.9 22.8 + - - +
126D ASN 3.8 4.0 - - - +
127D ARG 3.2 0.2 - - - -
128D MET* 1.3 73.8 - - - +
130D LEU* 1.3 62.5 + - + +
132D ALA* 4.4 4.3 - - - +
133D ASP* 2.7 24.8 + - - -
134D VAL* 3.0 28.5 + - - +
136D LEU* 3.9 24.0 - - + -
151D ILE* 6.1 1.3 - - + -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ASN* 3.1 27.5 + - - +
127D ARG* 3.1 7.4 + - - +
129D CYS* 1.3 75.0 - - + +
131D ALA* 1.3 62.1 + - - +
133D ASP 3.2 5.9 + - - -
151D ILE* 4.4 11.0 - - + -
152D LYS* 5.4 0.2 - - - -
153D LYS* 3.0 69.4 + - + +
156D THR 6.1 0.7 - - - +
158D CYS* 3.8 31.4 - - + -
443D VAL* 4.4 9.0 - - + +
444D CYS* 3.8 23.1 - - + -
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 3.9 14.3 - - + +
107D ARG* 3.8 15.4 + - - -
127D ARG 2.9 16.0 + - - +
128D MET* 3.7 4.9 - - - +
130D LEU* 1.3 80.1 - - - +
132D ALA* 1.3 59.2 + - - +
133D ASP* 3.2 1.8 + - - +
153D LYS* 4.4 8.3 + - - +
524D GLN 3.7 18.8 - - - +
525D ASP* 3.8 25.8 - - + +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D VAL* 3.9 19.5 - - + +
106D PHE* 3.7 23.6 - - + -
107D ARG* 3.8 21.9 + - + +
128D MET 2.9 17.9 + - - +
129D CYS* 4.2 1.3 - - - +
131D ALA* 1.3 75.8 - - - +
133D ASP* 1.3 71.5 + - - +
134D VAL* 3.4 18.7 + - + +
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Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D CYS 2.7 10.0 + - - -
130D LEU* 3.2 8.2 + - - +
131D ALA 3.2 5.4 - - - +
132D ALA* 1.3 82.4 - - - +
134D VAL* 1.3 56.9 + - - +
135D PRO* 4.4 3.3 - - - +
152D LYS* 4.9 13.9 + - - +
153D LYS* 3.6 33.9 + - + +
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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