Contacts of the helix formed by residues 129 - 143 (chain B) in PDB entry 4K2S
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 THR 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B GLY 3.8 3.6 - - - +
128B GLN* 1.3 87.0 - - + +
130B ILE* 1.3 65.9 + - - +
131B GLU* 3.5 10.9 + - - +
132B ASP* 3.0 40.7 + - - +
133B CYS* 3.0 11.1 + - - +
152B SER* 4.1 4.0 - - - -
153B GLY 5.5 0.9 - - - -
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Residues in contact with ILE 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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129B THR* 1.3 72.7 - - - +
131B GLU* 1.3 58.0 + - - +
133B CYS* 3.1 4.3 + - - +
134B LEU* 2.9 33.2 + - + +
152B SER* 3.9 21.2 - - - +
192B HIS* 4.0 20.8 + - + +
195B LYS* 3.7 18.6 - - + +
196B LEU* 3.7 36.6 - - + +
199B ALA* 3.5 28.7 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B THR* 3.1 9.5 + - - +
130B ILE* 1.3 80.3 - - - +
132B ASP* 1.3 65.7 + - - +
134B LEU* 3.2 6.6 + - - +
135B GLY* 3.1 19.1 + - - -
203B ARG* 2.9 43.0 + - - -
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Residues in contact with ASP 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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126B THR 4.4 0.2 - - - +
127B GLY* 3.6 16.4 - - - -
128B GLN* 3.3 13.8 - - - +
129B THR* 3.0 37.3 + - - +
131B GLU* 1.3 78.3 - - - +
133B CYS* 1.3 64.0 + - - +
135B GLY* 3.3 10.5 + - - -
136B GLU* 3.3 15.6 + - - +
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Residues in contact with CYS 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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125B CYS* 3.5 26.0 - - - -
126B THR 4.1 2.5 - - - -
127B GLY* 3.8 10.0 - - - +
129B THR 3.0 11.2 + - - +
130B ILE 3.4 7.9 - - - +
132B ASP* 1.3 78.1 - - - +
134B LEU* 1.3 56.9 + - - +
136B GLU* 3.0 5.0 + - - +
137B VAL* 2.9 25.7 + - - +
150B VAL* 3.8 25.8 - - - -
151B GLN 3.6 18.4 - - - +
152B SER* 4.2 1.3 - - - -
196B LEU* 4.1 15.5 - - + -
200B VAL* 5.5 1.1 - - - -
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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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130B ILE* 2.9 24.4 + - + +
131B GLU* 3.2 12.8 + - - +
133B CYS* 1.3 76.7 - - - +
135B GLY* 1.3 62.1 + - - +
137B VAL* 3.3 2.2 + - + -
138B ALA* 3.0 19.9 + - - +
196B LEU* 5.2 1.3 - - + -
199B ALA* 3.9 24.7 - - + +
200B VAL* 3.8 42.8 - - + +
203B ARG* 3.5 43.7 + - + +
204B PHE* 3.2 24.7 - - + -
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Residues in contact with GLY 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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131B GLU* 3.1 14.5 + - - -
132B ASP 3.3 4.5 + - - -
133B CYS 3.2 0.4 - - - -
134B LEU* 1.3 75.2 - - - +
136B GLU* 1.3 59.4 + - - +
138B ALA* 3.5 7.5 + - - +
139B ARG* 3.1 26.5 + - - +
203B ARG* 5.0 1.9 - - - +
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Residues in contact with GLU 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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124B HIS 4.9 1.4 - - - +
125B CYS* 3.7 8.1 - - + -
126B THR* 3.3 39.2 + - + +
132B ASP 3.3 8.0 + - - +
133B CYS 3.0 9.4 + - - +
135B GLY* 1.3 76.7 - - - +
137B VAL* 1.3 65.0 + - - +
139B ARG* 2.8 45.2 + - - +
140B HIS* 2.8 35.4 + - - -
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Residues in contact with VAL 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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125B CYS* 3.6 14.8 - - + -
133B CYS* 2.9 21.0 + - - +
134B LEU* 3.3 3.6 + - - +
136B GLU* 1.3 76.1 - - - +
138B ALA* 1.3 62.5 + - - +
140B HIS* 3.1 2.4 + - - +
141B VAL* 2.9 31.0 + - + +
148B VAL* 4.2 5.4 - - + -
150B VAL* 3.7 30.3 - - + -
200B VAL* 4.9 6.1 - - + -
204B PHE* 3.5 35.7 - - + -
208B LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 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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134B LEU 3.0 13.1 + - - +
135B GLY* 3.6 12.3 - - - +
137B VAL* 1.3 74.2 - - - +
139B ARG* 1.3 62.2 + - - +
141B VAL* 3.4 4.8 + - - +
142B GLU* 3.1 28.9 + - + +
203B ARG* 6.1 1.1 - - - -
204B PHE* 3.4 20.0 - - + -
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Residues in contact with ARG 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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135B GLY 3.1 14.1 + - - +
136B GLU* 2.8 43.0 + - - +
137B VAL 3.1 0.4 - - - -
138B ALA* 1.3 77.4 - - - +
140B HIS* 1.3 80.0 + - - +
142B GLU* 3.3 10.5 + - + +
143B LEU* 3.3 42.0 + - + +
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Residues in contact with HIS 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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123B ALA* 3.4 22.3 - - + +
124B HIS 3.5 20.4 + - - -
125B CYS* 3.5 16.1 - - - -
136B GLU* 2.8 35.9 + - - +
137B VAL 3.9 2.2 - - - +
139B ARG* 1.3 106.5 + - - +
141B VAL* 1.3 67.2 + - - +
142B GLU 3.1 1.3 - - - -
143B LEU* 2.9 20.8 + - + +
144B GLY 3.2 0.2 + - - -
145B TYR* 3.2 42.1 + + + -
148B VAL* 4.3 8.3 - - + -
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Residues in contact with VAL 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 VAL* 2.9 31.6 + - + +
138B ALA* 3.7 6.7 - - - +
140B HIS* 1.3 75.7 - - - +
142B GLU* 1.3 68.5 + - - +
144B GLY* 3.1 18.7 + - - -
145B TYR 4.0 12.6 - - - +
148B VAL* 5.0 2.2 - - + -
204B PHE* 4.7 9.9 - - + -
208B LEU* 4.0 29.2 - - + -
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Residues in contact with GLU 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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138B ALA* 3.1 17.1 + - + +
139B ARG* 3.4 13.7 - - - +
140B HIS 3.1 0.8 - - - -
141B VAL* 1.3 90.2 - - - +
143B LEU* 1.3 59.9 + - + +
144B GLY 3.2 1.4 + - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.3 30.9 + - + +
140B HIS* 2.9 24.7 + - + +
142B GLU* 1.3 78.7 - - + +
144B GLY* 1.3 57.6 + - - +
145B TYR* 3.6 24.6 - - + -
360B PHE* 4.9 7.4 - - + -
362B ASP* 4.4 6.1 + - - +
363B GLY 4.2 8.8 + - - -
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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