Contacts of the helix formed by residues 117 - 132 (chain B) in PDB entry 3A4T
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 GLU* 2.9 18.1 + - - +
116B ILE* 1.3 80.8 - - - +
118B LYS* 1.3 53.5 + - - +
119B THR* 3.4 9.0 + - - -
120B ARG* 3.2 33.1 + - - +
121B THR* 2.8 37.9 + - - -
140B ASN* 3.6 1.1 - - - -
501B SFG 4.2 1.8 - - - -
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Residues in contact with LYS 118 (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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116B ILE 3.4 4.6 + - - -
117B SER* 1.3 70.6 + - - +
119B THR* 1.3 62.8 + - - +
121B THR* 3.6 13.2 - - - -
122B LYS* 3.3 44.4 + - - +
140B ASN* 3.5 26.2 - - - +
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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
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117B SER* 3.3 8.1 + - - -
118B LYS* 1.3 76.8 - - - +
120B ARG* 1.3 72.0 + - + +
122B LYS* 3.1 38.5 + - + +
123B ALA* 3.6 4.3 + - - +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 3.3 33.3 + - + +
94B PRO* 3.6 15.7 - - - +
115B GLU* 3.9 2.0 - - - +
117B SER* 3.2 22.1 + - - +
119B THR* 1.3 84.6 - - + +
121B THR* 1.3 56.8 + - - +
123B ALA* 3.0 13.8 + - + +
124B LEU 3.0 22.5 + - - -
501B SFG 3.0 54.7 + - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 3.4 19.2 - - - +
117B SER 2.8 23.1 + - - -
118B LYS* 3.6 10.1 - - - +
119B THR 3.2 0.2 - - - -
120B ARG* 1.3 74.3 - - - +
122B LYS* 1.3 57.8 + - + +
124B LEU* 3.3 8.9 + - - +
125B LYS* 2.8 36.5 + - + +
138B ILE* 3.9 24.2 - - + -
139B ILE 4.8 0.3 + - - -
140B ASN* 3.6 26.0 + - + +
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Residues in contact with LYS 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 LYS* 3.3 46.5 + - - +
119B THR* 3.1 28.2 + - + +
121B THR* 1.3 78.2 - - + +
123B ALA* 1.3 54.9 + - - +
125B LYS* 3.6 8.9 - - - +
126B SER* 3.1 27.2 + - - -
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Residues in contact with ALA 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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94B PRO* 3.3 21.5 - - + +
119B THR 3.6 1.9 + - - +
120B ARG* 3.0 19.9 + - + +
122B LYS* 1.3 77.8 - - - +
124B LEU* 1.3 57.4 + - - +
126B SER* 3.7 6.9 - - - -
127B ASN* 3.0 27.1 + - - +
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Residues in contact with LEU 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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92B ALA* 3.8 23.6 - - + +
93B ALA* 3.9 8.7 - - + +
94B PRO 3.3 8.8 + - - -
95B GLY* 3.6 27.1 - - - +
98B THR* 4.0 11.2 - - - +
113B ALA* 4.3 11.7 - - + +
115B GLU* 4.2 18.4 - - + -
120B ARG 3.0 11.5 + - - +
121B THR* 3.5 7.6 - - - +
123B ALA* 1.3 72.6 - - - +
125B LYS* 1.3 60.5 + - - +
127B ASN* 3.1 1.9 + - - +
128B ILE* 2.9 45.0 + - + +
138B ILE* 4.0 28.3 - - + -
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Residues in contact with LYS 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 THR* 2.8 24.7 + - + +
122B LYS* 3.6 9.2 - - - +
124B LEU* 1.3 71.9 - - - +
126B SER* 1.3 55.2 + - - +
128B ILE* 3.7 1.4 - - - +
129B ASN* 2.7 73.0 + - - +
138B ILE* 3.5 31.0 - - + -
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Residues in contact with SER 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 LYS 3.1 16.1 + - - -
123B ALA* 3.7 8.5 - - - -
124B LEU 3.3 0.2 - - - -
125B LYS* 1.3 79.2 - - - +
127B ASN* 1.4 54.8 + - - +
129B ASN* 3.7 4.1 - - - +
130B ARG* 2.7 43.4 + - - +
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Residues in contact with ASN 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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60B TYR* 4.3 5.9 + - - -
66B MET* 4.0 16.8 - - - +
94B PRO* 2.6 39.0 - - - +
95B GLY* 4.6 2.7 - - - +
99B THR* 4.0 13.2 - - + -
123B ALA* 3.0 14.0 + - - +
124B LEU 3.1 0.8 + - - +
126B SER* 1.4 74.6 + - - +
128B ILE* 1.3 66.6 + - - +
130B ARG* 2.8 40.7 + - - +
131B MET* 2.9 30.2 + - + +
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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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95B GLY* 5.3 0.2 - - - -
98B THR* 4.2 23.6 - - + -
99B THR* 3.4 26.5 - - + +
124B LEU* 2.9 33.4 + - + +
125B LYS* 3.7 4.7 - - - +
127B ASN* 1.3 72.3 - - - +
129B ASN* 1.3 72.9 + - - +
132B GLY 3.3 2.3 + - - -
133B VAL* 3.1 62.7 + - + +
136B THR* 4.2 13.9 - - + +
138B ILE* 4.2 17.9 - - + -
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Residues in contact with ASN 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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19B LYS* 5.3 1.0 + - - -
125B LYS* 2.7 59.9 + - - +
126B SER* 4.0 3.8 - - - +
128B ILE* 1.3 85.1 - - - +
130B ARG* 1.3 62.8 + - - +
131B MET 3.2 0.9 + - - -
132B GLY* 3.3 9.9 + - - -
133B VAL 4.8 2.8 - - - +
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Residues in contact with ARG 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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149A TYR* 5.5 1.8 - - - -
19B LYS* 3.4 15.4 + - - -
60B TYR* 2.9 65.1 + - - +
61B LEU* 3.5 25.3 - - - +
62B PHE 3.6 1.6 - - - +
63B GLY* 3.2 18.9 + - - +
65B TYR 2.9 21.0 + - - -
66B MET* 3.4 22.6 - - - -
126B SER* 2.7 25.6 + - - +
127B ASN* 2.8 34.3 - - - +
129B ASN* 1.3 72.5 - - - +
131B MET* 1.4 78.2 + - - +
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Residues in contact with MET 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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14B ARG* 3.6 27.6 - - - +
16B ASN* 2.7 38.6 + - + +
18B LEU* 4.0 7.6 - - - +
19B LYS* 3.9 6.9 - - - +
63B GLY* 3.8 11.9 - - - +
65B TYR 3.7 5.8 - - - +
66B MET* 3.8 27.6 - - + +
99B THR* 3.9 27.4 - - + +
127B ASN* 2.9 20.7 + - + +
128B ILE 4.1 1.3 - - - +
130B ARG* 1.4 110.9 - - - +
132B GLY* 1.3 61.2 + - - +
133B VAL* 3.4 3.5 + - + -
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Residues in contact with GLY 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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18B LEU* 4.1 2.9 - - - +
19B LYS* 3.9 13.8 - - - +
107B ASN* 2.8 23.0 + - - -
129B ASN* 3.3 13.2 + - - -
130B ARG 3.4 1.8 + - - -
131B MET* 1.3 80.1 - - - +
133B VAL* 1.3 60.3 + - - +
134B LEU* 3.6 11.4 + - - +
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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