Contacts of the helix formed by residues 128 - 147 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 5.2 0.2 - - - -
70A ILE* 3.9 8.2 - - - +
126A ALA* 3.5 3.6 - - - +
127A LYS* 1.3 79.6 - - - +
129A GLU* 1.3 65.7 + - - +
130A ASP* 3.6 9.7 + - - +
131A ASP* 3.0 33.1 + - - +
132A SER* 3.0 26.9 + - - -
220A ARG* 4.7 7.9 - - - +
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Residues in contact with GLU 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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67A LEU* 4.2 6.5 - - - +
70A ILE* 3.8 10.1 - - + +
128A SER* 1.3 70.6 - - - +
130A ASP* 1.3 65.6 + - - +
132A SER* 3.4 4.7 + - - -
133A LYS* 3.2 22.9 + - - +
155A PHE* 4.5 4.2 - - - -
157A ILE* 3.6 31.4 - - + +
160A ILE* 4.6 4.8 - - + +
220A ARG* 2.7 62.3 + - - +
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Residues in contact with ASP 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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128A SER* 3.7 8.5 - - - +
129A GLU* 1.3 76.4 + - - +
131A ASP* 1.3 79.2 + - - +
133A LYS* 3.4 7.6 + - - +
134A LEU* 3.0 32.8 + - - +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.7 32.0 - - + +
126A ALA* 4.2 10.3 - - + -
127A LYS* 4.7 7.1 + - - +
128A SER* 3.0 26.5 + - - +
130A ASP* 1.3 92.3 + - - +
132A SER* 1.3 56.8 + - - +
134A LEU* 3.6 3.2 - - - +
135A ALA* 2.9 33.4 + - - +
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Residues in contact with SER 132 (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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70A ILE* 4.0 21.8 + - - +
72A ALA* 3.5 28.2 + - - +
123A VAL* 4.7 7.7 + - - +
126A ALA* 3.8 12.0 - - - +
128A SER 3.0 13.2 + - - -
129A GLU* 3.5 9.9 - - - -
130A ASP 3.2 0.4 - - - -
131A ASP* 1.3 77.6 - - - +
133A LYS* 1.3 57.6 + - - +
135A ALA* 3.9 2.9 - - - +
136A SER* 2.8 33.6 + - - -
155A PHE* 3.6 6.6 - - - -
157A ILE* 4.9 0.2 - - - -
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Residues in contact with LYS 133 (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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129A GLU 3.2 10.8 + - - +
130A ASP* 4.0 6.7 - - - +
132A SER* 1.3 78.2 - - - +
134A LEU* 1.3 57.7 + - - +
136A SER* 3.3 2.3 + - - -
137A ARG* 2.9 76.1 + - - +
152A PHE* 4.0 12.3 - - + -
155A PHE* 3.5 32.5 - - + -
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Residues in contact with LEU 134 (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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109A PRO* 3.9 23.6 - - + -
130A ASP* 3.0 28.2 + - - +
131A ASP* 3.6 7.0 - - - +
132A SER 3.3 0.2 - - - -
133A LYS* 1.3 77.5 - - - +
135A ALA* 1.3 62.5 + - - +
137A ARG* 3.3 15.9 + - + +
138A LYS* 3.0 49.2 + - + +
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Residues in contact with ALA 135 (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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106A ILE* 3.7 14.8 - - + -
109A PRO* 3.9 9.1 - - + +
111A THR* 3.5 36.8 - - + +
123A VAL* 4.6 1.6 - - + -
131A ASP 2.9 19.6 + - - +
132A SER 4.0 2.7 - - - +
134A LEU* 1.3 76.2 - - - +
136A SER* 1.3 57.3 + - - +
138A LYS* 3.2 2.9 + - - +
139A TYR* 2.9 36.1 + - + -
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Residues in contact with SER 136 (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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74A VAL* 3.8 11.5 - - - +
121A MET* 3.8 6.3 - - - +
123A VAL* 3.6 22.5 - - - +
132A SER 2.8 20.5 + - - -
133A LYS 3.5 5.4 - - - -
135A ALA* 1.3 74.1 - - - +
137A ARG* 1.3 65.8 + - - +
139A TYR* 3.2 8.4 + - - -
140A ALA* 3.1 22.9 + - - +
152A PHE* 3.8 18.8 - - - -
155A PHE* 3.4 15.9 - - - -
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Residues in contact with ARG 137 (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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133A LYS* 2.9 63.3 + - - +
134A LEU* 3.7 14.1 - - + +
136A SER* 1.3 74.7 - - - +
138A LYS* 1.3 64.3 + - + +
140A ALA* 3.1 6.4 + - - +
141A ARG* 3.0 22.8 + - - +
152A PHE* 3.4 45.3 - - + -
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Residues in contact with LYS 138 (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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106A ILE* 4.0 17.5 - - + -
108A GLU* 2.8 36.0 + - - +
109A PRO* 4.0 6.2 - - + +
134A LEU* 3.0 40.7 + - + +
135A ALA 3.4 7.9 - - - +
136A SER 3.1 0.2 - - - -
137A ARG* 1.3 77.6 - - + +
139A TYR* 1.3 62.0 + - - +
141A ARG* 3.3 9.4 + - - +
142A ILE* 3.2 27.2 + - + +
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Residues in contact with TYR 139 (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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104A MET* 3.8 33.3 - - + +
105A ARG* 3.4 3.6 - - - -
106A ILE* 3.2 30.5 + - + -
111A THR* 2.9 49.8 + - - -
112A THR* 3.4 1.6 + - - -
113A ALA* 3.7 31.0 - - + -
115A ILE* 4.9 1.6 - - + -
121A MET* 3.7 19.5 - - - -
123A VAL* 3.9 19.5 - - + -
135A ALA 2.9 30.1 + - - -
136A SER 3.2 3.5 + - - +
138A LYS* 1.3 75.3 - - - +
140A ALA* 1.3 63.5 + - - +
142A ILE* 3.2 9.1 + - + +
143A ILE* 3.1 26.4 + - - +
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Residues in contact with ALA 140 (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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76A LEU* 3.9 28.5 - - + -
121A MET* 4.4 1.0 - - + +
136A SER 3.1 12.2 + - - +
137A ARG* 3.1 10.8 + - - +
139A TYR* 1.3 76.8 - - - +
141A ARG* 1.3 62.1 + - - +
143A ILE* 3.2 6.4 + - - +
144A GLN* 3.0 31.8 + - - +
150A ALA* 4.6 1.5 - - + +
151A LYS 5.2 0.7 - - - -
152A PHE* 4.2 26.5 - - + +
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Residues in contact with ARG 141 (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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137A ARG 3.0 12.0 + - - +
138A LYS* 3.6 11.7 - - - +
140A ALA* 1.3 75.7 - - - +
142A ILE* 1.3 52.1 + - + +
144A GLN* 2.7 47.6 + - - +
145A LYS* 2.8 41.9 + - + +
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Residues in contact with ILE 142 (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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89A ALA* 4.7 7.9 - - + -
90A ARG 5.9 0.9 - - - +
104A MET* 3.9 30.1 - - + -
105A ARG 5.5 0.4 - - - +
106A ILE* 3.7 30.5 - - + -
138A LYS* 3.2 15.8 + - + +
139A TYR* 3.2 9.8 + - - +
141A ARG* 1.3 75.9 - - + +
143A ILE* 1.3 62.9 + - - +
145A LYS* 3.2 9.3 + - - +
146A ILE* 3.0 43.4 + - + +
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Residues in contact with ILE 143 (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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76A LEU* 3.9 20.4 - - + -
80A LEU* 3.9 24.0 - - + -
85A VAL* 4.0 19.7 - - + -
104A MET* 3.9 27.6 - - + -
115A ILE* 4.0 15.0 - - + -
121A MET* 5.5 0.2 - - - -
139A TYR 3.1 15.4 + - - +
140A ALA 3.2 7.4 + - - +
142A ILE* 1.3 74.4 - - - +
144A GLN* 1.3 63.8 + - - +
146A ILE* 3.1 17.8 + - + +
147A GLY 3.2 8.1 + - - -
148A PHE* 3.4 13.7 + - + -
150A ALA* 3.8 21.1 - - + -
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Residues in contact with GLN 144 (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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140A ALA* 3.0 20.7 + - - +
141A ARG* 2.7 54.0 + - - +
143A ILE* 1.3 75.9 - - - +
145A LYS* 1.3 53.1 + - - +
147A GLY* 2.7 27.2 + - - -
148A PHE 3.8 13.0 - - - +
150A ALA* 3.0 34.7 + - + +
151A LYS* 4.4 5.5 - - - +
152A PHE* 5.0 4.0 - - - +
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Residues in contact with LYS 145 (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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90A ARG* 3.4 28.6 - - - +
141A ARG* 2.8 28.0 + - + +
142A ILE* 3.2 9.8 + - - +
144A GLN* 1.3 72.1 - - - +
146A ILE* 1.3 61.2 + - + +
147A GLY* 3.3 0.9 + - - -
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Residues in contact with ILE 146 (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 THR* 4.2 16.5 - - + +
85A VAL* 3.9 30.5 - - + +
88A HIS* 3.8 27.7 - - + +
89A ALA* 3.9 13.9 - - + +
142A ILE* 3.0 35.1 + - + +
143A ILE* 3.5 11.9 - - + +
144A GLN 3.1 0.2 - - - -
145A LYS* 1.3 77.8 - - + +
147A GLY* 1.3 57.1 + - - +
148A PHE* 3.8 21.8 - - + -
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Residues in contact with GLY 147 (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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143A ILE 3.2 0.6 + - - -
144A GLN 2.7 15.0 + - - -
145A LYS 3.1 1.7 - - - -
146A ILE* 1.3 80.8 - - - +
148A PHE* 1.3 65.1 + - - +
149A ALA 4.1 0.3 + - - -
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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