Contacts of the helix formed by residues 130 - 139 (chain B) in PDB entry 2KXN
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 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B THR* 1.3 80.4 - - - +
131B GLU* 1.3 68.1 + - + +
132B ARG* 3.1 26.1 + - - +
133B ASP* 2.9 26.3 + - - +
134B LEU* 3.0 15.2 + - - +
149B ILE* 3.4 13.5 - - + -
151B TYR* 4.6 12.1 - - - +
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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
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130B THR* 1.3 73.5 - - + +
132B ARG* 1.3 109.7 + - - +
133B ASP 3.3 0.2 - - - -
134B LEU* 3.9 7.0 - - - -
135B ARG* 3.1 29.8 + - - +
147B VAL* 3.4 40.5 - - + +
148B SER* 4.6 2.5 - - - +
149B ILE* 3.1 30.7 - - + +
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Residues in contact with ARG 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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130B THR* 3.1 23.3 + - - +
131B GLU* 1.3 107.7 + - - +
133B ASP* 1.3 58.1 + - - +
135B ARG* 4.2 5.7 + - - +
136B GLU* 3.5 24.4 + - - +
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Residues in contact with ASP 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 THR* 3.5 22.9 - - + +
130B THR* 2.9 14.8 + - - +
132B ARG* 1.3 78.1 - - - +
134B LEU* 1.3 64.2 + - - +
135B ARG 3.2 2.0 - - - -
136B GLU* 3.3 28.2 + - - +
137B VAL* 3.6 17.4 + - - +
184B LEU* 4.4 11.1 - - - +
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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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122B VAL* 4.0 34.3 - - + -
125B LEU* 3.6 31.4 - - + -
129B THR* 3.8 19.5 - - + -
130B THR 3.0 19.2 + - - +
131B GLU* 4.2 8.5 - - + +
133B ASP* 1.3 76.3 - - - +
135B ARG* 1.3 63.4 + - - +
136B GLU 3.2 0.2 - - - -
137B VAL* 4.7 4.3 - - + +
138B PHE* 3.0 40.4 + - + +
147B VAL* 4.9 7.9 - - + -
149B ILE* 4.4 1.8 - - + -
162B ALA* 4.6 3.4 - - + -
164B VAL* 5.5 1.9 - - + +
182B MET* 6.3 1.3 - - - -
184B LEU* 4.2 16.8 - - + -
189B ILE* 5.4 1.1 - - + -
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Residues in contact with ARG 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 19.6 + - - +
132B ARG* 4.5 6.7 - - - +
133B ASP 3.2 0.4 - - - -
134B LEU* 1.3 77.4 - - - +
136B GLU* 1.3 60.5 + - + +
138B PHE* 4.1 2.9 - - - -
139B SER* 3.1 26.7 + - - -
144B ILE* 3.4 56.4 + - + +
145B ALA 4.3 3.8 + - - -
146B ASP* 4.1 19.8 - - - +
147B VAL* 4.3 17.4 - - + +
164B VAL* 6.4 0.9 - - - -
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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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132B ARG 3.5 22.0 - - - +
133B ASP* 3.3 18.3 + - - +
134B LEU 3.2 0.4 - - - -
135B ARG* 1.3 78.8 - - + +
137B VAL* 1.3 66.9 + - + +
138B PHE 3.2 0.2 - - - -
139B SER* 3.3 15.7 + - - -
140B LYS* 3.5 14.8 - - - +
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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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133B ASP* 3.6 22.7 + - - +
134B LEU* 3.7 3.6 + - + +
135B ARG 3.6 0.2 - - - -
136B GLU* 1.3 80.4 - - + +
138B PHE* 1.3 67.7 + - + +
140B LYS* 3.4 31.8 - - + +
141B TYR* 3.2 26.6 - - + +
179B ALA* 6.0 0.4 - - + -
182B MET* 4.1 30.3 - - + -
184B LEU* 6.4 1.1 - - + -
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Residues in contact with PHE 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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120B LEU* 5.5 2.7 - - + -
121B GLY 4.6 2.0 - - - -
122B VAL* 3.4 29.4 - - + -
134B LEU* 3.0 36.4 + - + +
135B ARG* 4.5 1.3 - - - +
137B VAL* 1.3 82.8 - - + +
139B SER* 1.3 58.8 + - - +
140B LYS 3.0 5.2 - - - -
141B TYR* 3.1 25.5 + + - +
142B GLY 3.5 9.0 + - - +
144B ILE* 3.6 18.6 - - + +
164B VAL* 3.9 21.5 - - + -
166B PHE* 3.9 22.9 - + + -
175B ALA* 4.9 5.8 - - + -
179B ALA* 4.4 12.8 - - + -
182B MET* 4.9 9.9 - - - -
191B VAL* 3.4 39.5 - - + -
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Residues in contact with SER 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 ARG* 3.1 22.3 + - - -
136B GLU* 3.3 9.8 + - - -
138B PHE* 1.3 77.2 - - - +
140B LYS* 1.3 58.6 + - - +
141B TYR 3.2 0.4 - - - -
142B GLY* 3.2 22.3 + - - +
143B PRO* 5.5 1.9 - - - +
144B ILE* 3.7 10.3 - - - +
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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