Contacts of the helix formed by residues 128 - 147 (chain B) in PDB entry 1YTB
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 SER 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LEU* 5.0 4.5 - - - -
70B ILE* 3.5 9.6 - - - +
126B ALA* 3.5 2.6 - - - +
127B LYS* 1.3 81.9 - - - +
129B GLU* 1.3 53.0 + - - +
130B ASP* 3.8 7.8 + - - +
131B ASP* 3.0 32.3 + - - +
132B SER* 2.8 34.3 + - - -
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Residues in contact with GLU 129 (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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67B LEU* 5.8 1.2 - - - +
70B ILE* 4.5 4.5 - - + +
128B SER* 1.3 72.6 - - - +
130B ASP* 1.3 61.3 + - - +
132B SER* 3.3 4.4 + - - -
133B LYS* 2.9 34.8 + - + +
155B PHE* 3.8 15.0 - - + -
157B ILE* 3.4 35.5 - - + +
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Residues in contact with ASP 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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128B SER* 3.2 7.0 + - - +
129B GLU* 1.3 81.0 - - - +
131B ASP* 1.3 60.9 + - - +
133B LYS* 3.5 10.8 + - - +
134B LEU* 2.9 31.2 + - - +
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Residues in contact with ASP 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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109B PRO* 3.7 33.4 - - + +
126B ALA* 4.0 12.3 - - + -
127B LYS* 4.7 4.9 + - - +
128B SER* 3.0 27.9 + - - +
130B ASP* 1.3 77.2 - - - +
132B SER* 1.3 57.9 + - - +
134B LEU* 4.4 5.6 - - - +
135B ALA* 2.9 32.7 + - - +
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Residues in contact with SER 132 (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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70B ILE* 3.8 22.3 + - - +
72B ALA* 3.5 14.2 + - - +
123B VAL* 4.2 7.7 - - - +
126B ALA* 3.6 13.4 - - - +
128B SER 2.8 16.1 + - - -
129B GLU 3.3 5.6 + - - -
131B ASP* 1.3 77.8 - - - +
133B LYS* 1.3 52.0 + - - +
135B ALA* 3.5 4.9 + - - +
136B SER* 2.8 37.5 + - - -
155B PHE* 3.3 20.7 - - - -
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Residues in contact with LYS 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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151A LYS* 4.7 15.0 - - - +
129B GLU* 2.9 21.9 + - + +
130B ASP* 3.8 12.6 - - - +
132B SER* 1.3 76.0 - - - +
134B LEU* 1.3 64.3 + - - +
136B SER* 3.5 2.8 + - - -
137B ARG* 3.2 35.7 + - - +
152B PHE* 3.5 35.0 - - + -
155B PHE* 3.8 29.1 - - + -
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Residues in contact with LEU 134 (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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109B PRO* 4.0 23.1 - - + -
130B ASP 2.9 18.6 + - - +
131B ASP* 3.8 8.7 - - - +
133B LYS* 1.3 73.8 - - - +
135B ALA* 1.3 65.6 + - - +
137B ARG* 3.1 34.2 + - + +
138B LYS* 3.0 49.3 + - + +
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Residues in contact with ALA 135 (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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106B ILE* 4.1 12.1 - - + -
109B PRO* 4.2 6.7 - - + +
111B THR* 3.4 37.2 - - + +
123B VAL* 4.2 2.9 - - + -
131B ASP 2.9 17.9 + - - +
132B SER 3.6 4.7 - - - +
134B LEU* 1.3 75.8 - - - +
136B SER* 1.3 64.3 + - - +
138B LYS* 2.9 5.2 + - - +
139B TYR* 2.9 31.3 + - + -
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Residues in contact with SER 136 (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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74B VAL* 3.6 18.4 - - - +
121B MET* 3.7 9.1 - - - +
123B VAL* 3.4 18.2 - - - +
132B SER 2.8 21.4 + - - -
133B LYS 3.7 1.1 - - - -
134B LEU 3.3 0.2 - - - -
135B ALA* 1.3 75.3 - - - +
137B ARG* 1.3 57.0 + - - +
139B TYR* 3.2 13.0 + - - +
140B ALA* 3.0 26.0 + - - +
152B PHE* 3.5 26.3 - - - -
155B PHE* 3.7 7.7 - - - -
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Residues in contact with ARG 137 (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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133B LYS* 3.2 23.7 + - - +
134B LEU* 3.1 34.2 + - + +
136B SER* 1.3 73.4 - - - +
138B LYS* 1.3 61.9 + - + +
140B ALA* 3.3 7.0 + - - +
141B ARG* 3.0 27.8 + - - +
152B PHE* 3.7 37.2 - - + -
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Residues in contact with LYS 138 (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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106B ILE* 4.0 17.7 - - + -
108B GLU* 2.8 35.7 + - - +
109B PRO* 4.2 6.6 - - + +
134B LEU* 3.0 36.8 + - + +
135B ALA 2.9 8.5 + - - +
137B ARG* 1.3 74.8 - - + +
139B TYR* 1.3 63.5 + - - +
141B ARG* 3.2 10.6 + - - +
142B ILE* 3.1 29.7 + - + +
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Residues in contact with TYR 139 (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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104B MET* 3.6 36.5 + - + -
106B ILE* 3.4 30.0 + - + -
111B THR* 2.8 49.9 + - - -
112B THR 3.5 1.2 + - - -
113B ALA* 3.7 31.6 - - + -
115B ILE* 4.6 2.0 - - + -
121B MET* 3.8 17.0 - - - -
123B VAL* 4.2 10.3 - - + -
135B ALA* 2.9 33.8 + - + -
136B SER* 3.2 10.5 + - - +
138B LYS* 1.3 77.3 - - - +
140B ALA* 1.3 61.2 + - - +
142B ILE* 3.4 7.0 + - + +
143B ILE* 3.1 29.6 + - - +
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Residues in contact with ALA 140 (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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76B LEU* 3.9 27.1 - - + -
121B MET* 4.8 0.8 - - - +
136B SER 3.0 13.6 + - - +
137B ARG* 3.3 9.6 + - - +
139B TYR* 1.3 75.4 - - - +
141B ARG* 1.3 57.7 + - - +
143B ILE* 3.4 5.5 + - - +
144B GLN* 2.9 40.7 + - - +
150B ALA* 4.3 2.7 - - + +
151B LYS 4.6 1.3 - - - -
152B PHE* 4.3 24.0 - - + +
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Residues in contact with ARG 141 (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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137B ARG 3.0 13.3 + - - +
138B LYS* 3.2 14.8 + - - +
140B ALA* 1.3 75.9 - - - +
142B ILE* 1.3 65.2 + - + +
144B GLN* 3.2 23.1 + - - +
145B LYS* 2.9 70.6 + - - +
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Residues in contact with ILE 142 (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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88B HIS 5.6 0.2 - - - +
89B ALA* 4.5 18.8 - - + -
90B ARG 5.6 0.4 - - - +
104B MET* 4.2 24.5 - - + -
106B ILE* 3.8 29.2 - - + -
138B LYS* 3.1 18.2 + - + +
139B TYR* 3.4 12.5 + - - +
141B ARG* 1.3 77.5 - - + +
143B ILE* 1.3 61.7 + - + +
145B LYS* 3.4 18.5 + - + +
146B ILE* 3.3 21.2 - - + +
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Residues in contact with ILE 143 (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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76B LEU* 4.3 14.8 - - + -
80B LEU* 3.8 16.4 - - + -
85B VAL* 3.8 17.3 - - + -
104B MET* 3.7 30.3 - - + -
115B ILE* 4.3 11.4 - - + -
139B TYR 3.1 17.6 + - - +
140B ALA 3.6 5.8 - - - +
142B ILE* 1.3 73.2 - - + +
144B GLN* 1.3 65.2 + - - +
146B ILE* 3.1 24.9 + - + +
148B PHE* 3.6 26.5 + - + -
150B ALA* 3.6 22.2 - - + -
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Residues in contact with GLN 144 (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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140B ALA* 2.9 23.6 + - - +
141B ARG* 3.2 29.1 + - - +
143B ILE* 1.3 77.5 - - - +
145B LYS* 1.3 57.6 + - - +
147B GLY* 2.9 21.7 + - - -
148B PHE 3.6 14.4 + - - +
149B ALA* 5.7 0.2 - - - -
150B ALA* 2.7 32.4 + - + +
151B LYS* 4.2 6.7 - - - +
152B PHE 5.0 0.8 - - - +
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Residues in contact with LYS 145 (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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90B ARG* 4.1 23.0 - - - +
141B ARG* 2.9 41.5 + - - +
142B ILE* 3.4 16.6 - - + +
143B ILE 3.3 0.2 - - - -
144B GLN* 1.3 75.7 - - - +
146B ILE* 1.3 61.9 + - + +
147B GLY* 3.6 0.3 + - - -
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Residues in contact with ILE 146 (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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84B THR* 3.8 8.3 - - + -
85B VAL* 4.1 24.0 - - + +
88B HIS* 3.7 46.9 - - + -
89B ALA 4.8 1.6 - - - +
142B ILE* 3.3 25.6 - - + +
143B ILE* 3.4 24.2 - - + +
144B GLN 3.1 0.8 - - - -
145B LYS* 1.3 80.0 - - + +
147B GLY* 1.3 57.3 + - - +
148B PHE* 3.6 22.4 - - + -
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Residues in contact with GLY 147 (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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144B GLN 2.9 9.7 + - - -
145B LYS 3.3 1.2 - - - -
146B ILE* 1.3 82.4 - - - +
148B PHE* 1.3 67.4 + - - +
149B ALA 3.9 0.7 + - - -
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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