Contacts of the helix formed by residues 121 - 140 (chain B) in PDB entry 5ACY
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 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 3.7 14.6 - - - +
63B LEU* 3.8 5.1 - - - +
119B TYR* 3.5 11.1 - - - +
120B TRP* 1.3 103.8 - - - +
122B ALA* 1.3 63.6 + - - +
123B GLN* 3.7 15.9 - - + +
124B GLU* 3.0 38.5 + - + +
125B CYS 3.7 1.0 + - - -
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Residues in contact with ALA 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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58B ARG* 5.4 0.4 - - - +
60B THR* 5.4 1.2 + - - +
62B GLN* 3.6 38.6 - - + +
63B LEU* 3.8 9.6 - - + +
66B LEU* 3.4 25.6 - - + +
121B ASN* 1.3 72.0 - - - +
123B GLN* 1.3 58.3 + - - +
125B CYS* 3.2 6.1 + - - +
126B ILE* 2.9 35.8 + - + +
164B LEU* 5.0 1.6 - - + -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 3.1 11.2 - - + +
122B ALA* 1.3 76.5 - - - +
124B GLU* 1.3 59.5 + - - +
126B ILE* 3.7 31.3 - - - +
127B GLN* 3.0 35.3 + - + +
130B ASN* 5.3 2.2 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 4.9 8.9 + - - -
119B TYR* 3.3 18.8 - - + -
120B TRP* 2.5 41.0 + - - +
121B ASN* 3.0 27.7 + - + +
123B GLN* 1.3 76.4 - - - +
125B CYS* 1.3 62.4 + - - +
127B GLN* 3.4 8.5 + - - +
128B ASP* 3.2 23.9 + - - +
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Residues in contact with CYS 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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63B LEU* 4.6 1.6 - - + -
66B LEU* 4.1 20.0 - - + -
110B ILE* 4.1 3.1 - - - -
114B LEU* 4.1 16.6 - - - -
119B TYR* 3.5 40.9 - - + -
121B ASN 3.7 1.7 + - - +
122B ALA 3.2 9.5 + - - +
124B GLU* 1.3 77.2 - - - +
126B ILE* 1.3 65.8 + - - +
128B ASP* 2.9 14.9 + - - +
129B PHE* 3.2 35.1 + - - -
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Residues in contact with ILE 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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66B LEU* 4.4 9.0 - - + -
122B ALA* 2.9 24.8 + - + +
123B GLN* 3.7 32.3 - - - +
124B GLU 3.4 0.2 - - - -
125B CYS* 1.3 76.1 - - - +
127B GLN* 1.3 62.6 + - - +
129B PHE* 3.1 6.7 + - - +
130B ASN* 3.0 34.9 + - - +
157B PHE* 4.3 15.4 - - + -
161B ILE* 4.3 37.2 - - + -
164B LEU* 4.5 18.6 - - + -
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Residues in contact with GLN 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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123B GLN* 3.0 24.2 + - - +
124B GLU* 3.6 8.5 - - - +
125B CYS 3.3 0.2 - - - -
126B ILE* 1.3 76.4 - - - +
128B ASP* 1.3 59.5 + - - +
130B ASN* 4.0 15.9 + - - +
131B THR* 2.8 40.1 + - - +
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Residues in contact with ASP 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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105B MET* 3.0 42.6 - - + +
110B ILE* 3.8 7.5 - - + +
113B ARG* 2.8 31.0 + - - -
119B TYR* 2.5 31.5 + - - +
124B GLU 3.2 12.6 + - - +
125B CYS 2.9 11.6 + - - +
127B GLN* 1.3 75.7 - - - +
129B PHE* 1.3 64.8 + - - +
131B THR* 4.0 4.8 + - - -
132B MET* 3.4 9.0 + - - +
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Residues in contact with PHE 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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66B LEU* 4.5 4.9 - - + -
70B VAL* 4.2 8.7 - - + -
71B LEU* 4.2 23.1 - - + -
74B LEU* 3.6 30.3 - - + -
107B MET* 4.3 13.7 - - + -
110B ILE* 3.7 32.8 - - + -
125B CYS* 3.2 44.3 + - - -
126B ILE* 3.1 3.9 + - - +
128B ASP* 1.3 75.3 - - - +
130B ASN* 1.3 64.6 + - - +
132B MET* 3.2 16.7 + - + +
133B PHE* 3.1 30.5 + + + -
157B PHE* 3.4 37.5 - + + -
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLN* 5.3 2.2 - - - +
126B ILE* 3.0 32.9 + - - +
127B GLN* 3.6 22.6 + - - +
129B PHE* 1.3 76.9 - - - +
131B THR* 1.3 53.2 + - - +
133B PHE* 3.4 10.0 + - - +
134B THR* 2.6 39.7 + - - +
154B GLU* 4.9 7.8 - - - +
157B PHE* 4.1 15.1 - - - -
158B LEU* 5.4 4.5 - - - +
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Residues in contact with THR 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 THR* 3.2 43.2 - - + +
105B MET* 4.0 9.2 - - + -
127B GLN* 2.8 38.9 + - - +
128B ASP* 4.0 9.9 + - - +
130B ASN* 1.3 74.1 - - - +
132B MET* 1.3 58.7 + - - +
134B THR* 3.2 6.0 + - - -
135B ASN* 2.8 40.7 + - - +
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Residues in contact with MET 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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83B PHE* 4.0 28.6 - - + -
105B MET* 3.5 24.6 - - + +
106B ASP* 3.7 17.7 - - - -
107B MET* 3.6 38.8 - - + -
110B ILE* 4.8 1.6 - - - -
128B ASP 3.4 11.3 + - - +
129B PHE* 3.2 22.1 + - + +
131B THR* 1.3 79.7 - - - +
133B PHE* 1.3 95.0 + - + +
135B ASN* 3.7 7.3 - - - +
136B CYS* 3.4 19.9 + - - +
153B LEU* 5.3 0.9 - - + -
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Residues in contact with PHE 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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74B LEU* 4.5 6.5 - - + -
83B PHE* 5.2 2.9 - + - -
129B PHE* 3.1 26.9 + - + -
130B ASN* 3.8 9.6 - - - +
132B MET* 1.3 98.2 - - + +
134B THR* 1.3 64.2 + - - +
136B CYS* 3.3 7.3 + - - +
137B TYR* 3.1 42.6 + - + +
150B ALA* 3.7 23.1 - - + -
153B LEU* 3.7 32.1 - - + -
154B GLU* 3.6 38.4 - - + -
157B PHE* 4.0 23.8 - + + -
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Residues in contact with THR 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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115A GLU* 3.2 37.1 + - - +
116A ASN* 5.3 0.2 - - - -
117A ASN* 5.9 0.7 - - - +
130B ASN* 2.6 24.7 + - - +
131B THR* 3.6 8.0 - - - -
133B PHE* 1.3 76.4 - - - +
135B ASN* 1.3 52.2 + - - +
137B TYR* 3.0 11.9 + - - +
138B ILE* 2.8 53.0 + - + +
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Residues in contact with ASN 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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97B TYR* 4.0 12.0 + - - +
101B ILE* 3.6 30.8 - - + +
103B THR* 2.8 30.5 + - - +
104B PRO* 3.5 4.0 - - - +
105B MET 3.5 20.3 + - - +
131B THR* 2.8 33.0 + - - +
132B MET* 3.7 7.6 - - - +
134B THR* 1.3 71.3 - - - +
136B CYS* 1.3 63.8 + - - +
138B ILE* 3.2 6.3 + - - +
139B TYR* 3.0 28.7 + - - +
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Residues in contact with CYS 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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83B PHE* 3.9 14.6 - - + -
97B TYR* 5.6 0.2 - - - -
132B MET 3.4 9.9 + - - +
133B PHE 3.3 10.7 + - - +
134B THR 3.2 0.2 - - - -
135B ASN* 1.3 80.1 - - - +
137B TYR* 1.3 57.4 + - - +
140B ASN* 2.9 55.5 + - - +
146B ILE* 3.7 25.4 - - - -
147B VAL* 4.5 4.0 - - - -
150B ALA* 3.6 26.0 - - + -
1169B 9S3 3.9 9.4 - - + +
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Residues in contact with TYR 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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111A LYS* 4.6 13.3 + - - +
115A GLU* 3.9 37.4 - - - +
133B PHE* 3.1 28.1 + - + +
134B THR* 3.0 9.4 + - - +
136B CYS* 1.3 77.3 - - - +
138B ILE* 1.3 62.1 + - - +
140B ASN 3.5 13.3 - - - +
142B PRO* 5.4 1.2 - - - +
147B VAL* 3.8 29.6 - - + -
150B ALA* 3.4 40.6 + - + +
151B GLU* 3.4 14.9 + - + +
154B GLU* 2.7 32.0 + - - +
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Residues in contact with ILE 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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111A LYS* 5.0 1.0 + - - -
112A LYS* 3.4 35.4 + - + +
115A GLU* 3.8 16.8 - - + +
116A ASN* 3.2 32.3 - - - +
1170A EDO 3.7 24.9 - - - +
100B ILE* 3.9 16.6 - - + -
101B ILE* 4.1 7.9 - - + -
134B THR* 2.8 40.6 + - + +
135B ASN* 3.2 11.0 + - - +
137B TYR* 1.3 74.0 - - - +
139B TYR* 1.3 63.0 + - - +
140B ASN 3.8 1.6 + - - +
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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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112A LYS* 5.5 3.4 + - - +
94B LEU* 3.4 24.9 - - + +
96B ASP* 2.7 39.9 + - - -
97B TYR* 3.7 50.0 - + + -
100B ILE* 4.0 25.7 - - + +
101B ILE* 4.2 6.5 - - + -
135B ASN 3.0 16.0 + - - +
138B ILE* 1.3 81.2 - - - +
140B ASN* 1.3 76.4 + - - +
141B LYS 4.2 0.3 + - - -
1169B 9S3 4.0 11.9 - - + -
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Residues in contact with ASN 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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111A LYS* 5.4 0.9 + - - -
136B CYS* 2.9 34.1 + - - +
137B TYR 3.5 15.2 - - - +
138B ILE 4.6 1.3 - - - +
139B TYR* 1.3 94.2 - - - +
141B LYS* 1.3 64.9 + - - +
142B PRO* 3.5 4.2 - - - +
144B ASP* 4.4 3.3 - - - +
146B ILE* 3.4 27.2 - - + +
147B VAL* 3.6 10.9 - - + +
1169B 9S3 3.0 44.9 + - - +
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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
------------------------------------------------------------
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