Contacts of the helix formed by residues 117 - 135 (chain B) in PDB entry 4AY1
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 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B VAL 3.2 1.0 + - - -
116B ASP* 1.3 80.6 - - - +
118B SER* 1.3 64.8 + - - +
119B THR* 3.0 22.7 + - - -
120B SER* 3.2 14.2 + - - -
121B ARG* 3.0 33.5 + - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 1.3 74.6 - - - +
119B THR* 1.3 64.5 + - - +
121B ARG* 3.5 26.0 - - - +
122B LEU* 2.9 29.6 + - - +
161B GLU* 5.0 5.2 - - - +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.0 15.4 + - - -
118B SER* 1.3 82.1 + - - +
120B SER* 1.3 64.2 + - - +
122B LEU* 3.3 10.8 + - + +
123B GLU* 3.0 22.9 + - - +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASN* 3.7 28.2 - - - +
113B PRO 3.4 10.9 + - - -
114B MET* 2.7 24.5 + - - +
116B ASP* 4.5 0.7 - - - +
117B SER* 3.2 23.6 + - - -
119B THR* 1.3 82.2 + - - +
121B ARG* 1.3 59.1 + - - +
123B GLU* 3.4 7.7 + - - +
124B PHE* 3.0 22.3 + - - +
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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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114B MET* 3.3 28.4 + - - +
115B VAL* 3.0 34.0 + - - +
116B ASP 4.5 0.4 - - - -
117B SER* 3.0 29.1 + - - +
118B SER* 3.5 21.8 - - - +
120B SER* 1.3 76.2 - - - +
122B LEU* 1.3 56.8 + - - +
124B PHE* 3.2 1.7 + - - +
125B ILE* 2.8 39.9 + - + +
154B HIS 5.6 0.7 - - - -
157B VAL* 3.7 16.1 - - - +
158B LEU* 4.6 21.8 - - + +
161B GLU* 2.7 46.4 + - - +
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Residues in contact with LEU 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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118B SER 2.9 18.8 + - - +
119B THR* 3.6 10.1 - - + +
121B ARG* 1.3 72.2 - - - +
123B GLU* 1.3 68.3 + - - +
125B ILE* 4.5 9.4 - - + +
126B ASN* 2.9 56.1 + - - +
161B GLU* 5.2 0.6 + - - -
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Residues in contact with GLU 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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68B ASN 3.8 7.4 - - - +
69B ASN* 3.4 35.1 + - + +
70B LYS* 3.1 30.7 + - + +
119B THR 3.0 12.9 + - - +
120B SER* 3.4 10.3 - - - +
122B LEU* 1.3 76.5 - - - +
124B PHE* 1.3 63.5 + - - +
126B ASN* 3.5 6.1 + - - +
127B SER* 3.0 24.1 + - - -
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Residues in contact with PHE 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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66B ILE* 3.7 25.8 - - + -
69B ASN 3.0 20.8 + - - +
71B VAL* 4.2 12.1 - - + -
101B ILE* 3.7 17.7 - - + -
111B PHE* 6.1 1.3 - + - -
114B MET* 3.3 51.4 - - + -
120B SER 3.0 6.2 + - - +
121B ARG 3.5 6.1 - - - +
123B GLU* 1.3 74.6 - - - +
125B ILE* 1.3 71.5 + - + +
127B SER* 2.7 21.5 + - - -
128B ILE* 2.9 43.3 + - + +
140B LEU* 4.8 3.6 - - + -
142B VAL* 6.2 0.9 - - + -
158B LEU* 4.3 11.7 - - + -
162B LEU* 4.5 11.4 - - + -
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Residues in contact with ILE 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* 2.8 28.6 + - + +
122B LEU* 3.9 9.4 - - + +
124B PHE* 1.3 75.8 - - + +
126B ASN* 1.3 69.3 + - - +
128B ILE* 3.1 8.2 + - - +
129B ILE* 3.1 28.6 + - + +
158B LEU* 4.8 4.5 - - + +
161B GLU* 3.6 45.5 - - + +
162B LEU* 3.7 26.5 - - + +
165B ALA* 3.4 30.1 - - + -
166B PHE* 5.3 0.2 - - + -
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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
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122B LEU* 2.9 50.4 + - - +
123B GLU* 3.8 5.8 - - - +
125B ILE* 1.3 75.6 - - - +
127B SER* 1.3 62.6 + - - +
129B ILE* 3.5 10.1 + - - +
130B LEU* 3.2 28.3 + - + +
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Residues in contact with SER 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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70B LYS* 3.6 28.6 - - - -
71B VAL* 3.2 25.4 + - - +
123B GLU 3.0 14.9 + - - -
124B PHE 2.7 18.5 + - - -
126B ASN* 1.3 76.3 - - - +
128B ILE* 1.3 56.0 + - - +
130B LEU* 3.6 6.6 - - - +
131B PHE* 3.0 31.2 + - - +
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Residues in contact with ILE 128 (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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71B VAL* 3.7 28.3 - - + -
99B LEU* 5.3 1.6 - - + -
101B ILE* 4.1 0.2 - - + -
124B PHE* 2.9 47.9 + - + +
125B ILE* 3.1 9.6 + - - +
127B SER* 1.3 78.8 + - - +
129B ILE* 1.3 68.1 + - - +
131B PHE* 3.2 1.2 + - - +
132B LEU* 2.9 50.4 + - + +
140B LEU* 4.0 26.0 - - + -
162B LEU* 4.5 2.2 - - + -
166B PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 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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125B ILE* 3.1 17.5 + - + +
126B ASN* 4.0 8.7 - - - +
128B ILE* 1.3 77.3 - - - +
130B LEU* 1.3 69.1 + - + +
132B LEU* 4.1 0.7 - - - +
133B ARG* 3.2 29.3 + - + +
165B ALA* 3.8 41.7 - - + +
166B PHE* 3.8 21.1 - - + -
169B ASP* 3.6 30.3 - - + +
178B LEU* 4.2 12.5 - - + +
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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* 3.2 15.3 + - + +
127B SER* 3.6 11.4 - - - +
128B ILE 3.2 0.2 - - - -
129B ILE* 1.3 83.8 - - + +
131B PHE* 1.3 57.4 + - - +
133B ARG* 3.9 2.6 - - - +
134B ASN* 2.9 63.7 + - - +
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Residues in contact with PHE 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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71B VAL* 3.6 30.3 - - + -
72B ILE* 5.0 1.8 - - - -
73B ILE* 3.4 35.2 - - + -
78B GLU* 5.0 2.7 - - - -
82B TYR* 3.2 24.5 - - - -
99B LEU* 3.9 23.6 - - + -
127B SER 3.0 19.1 + - - +
128B ILE* 3.2 2.0 + - + +
130B LEU* 1.3 76.4 - - - +
132B LEU* 1.3 67.2 + - + +
134B ASN* 3.3 3.0 + - - +
135B HIS* 3.0 54.0 + + - +
137B PHE* 4.2 8.3 - + - -
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Residues in contact with LEU 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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99B LEU* 4.0 24.9 - - + -
128B ILE* 2.9 41.4 + - + +
129B ILE 4.1 1.6 - - - +
131B PHE* 1.3 77.5 - - + +
133B ARG* 1.3 62.5 + - - +
135B HIS 3.4 0.2 + - - -
136B ASN 3.1 3.3 + - - -
137B PHE* 2.8 56.9 + - + +
139B GLY 3.6 30.7 - - - +
140B LEU* 4.1 5.4 - - + +
166B PHE* 4.1 11.2 - - + -
178B LEU* 4.0 23.8 - - + -
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Residues in contact with ARG 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 ILE* 3.2 26.5 + - + +
130B LEU* 3.9 4.5 - - - +
132B LEU* 1.3 78.3 - - - +
134B ASN* 1.3 64.4 + - - +
135B HIS 3.3 0.9 + - - -
136B ASN* 3.5 8.4 + - - +
137B PHE 4.9 5.1 + - - -
138B ASP* 5.9 0.6 - - - +
169B ASP* 3.0 29.7 + - - +
170B PHE* 5.2 1.0 - - - +
173B SER* 3.9 14.5 + - - -
175B LYS* 3.8 48.7 + - - +
176B GLU* 2.9 31.7 + - - +
177B ARG* 4.4 1.4 - - - +
178B LEU* 3.7 30.2 - - + +
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Residues in contact with ASN 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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130B LEU* 2.9 43.1 + - - +
131B PHE* 3.3 5.1 + - - +
133B ARG* 1.3 80.6 - - - +
135B HIS* 1.3 74.1 + - + +
136B ASN 3.5 0.4 - - - -
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Residues in contact with HIS 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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78B GLU* 5.5 0.2 + - - -
82B TYR* 3.3 54.9 - + + +
85B ILE* 3.9 11.6 - - - +
86B ASN* 4.6 2.4 - - - +
131B PHE* 3.0 58.8 + + - +
134B ASN* 1.3 90.1 + - + +
136B ASN* 1.3 71.8 + - - +
137B PHE* 3.3 18.1 + - + -
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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