Contacts of the helix formed by residues 140 - 152 (chain B) in PDB entry 1KWZ
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B LYS* 6.0 2.0 - - - +
138B PRO* 3.4 1.9 - - - +
139B ARG* 1.3 85.1 - - - +
141B ALA* 1.3 63.7 + - - +
142B GLU* 3.0 20.7 + - - +
143B GLU* 2.8 51.1 + - - +
144B ASN* 3.0 18.9 + - - +
178B TYR* 3.6 18.5 - - - -
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Residues in contact with ALA 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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140B ASN* 1.3 75.3 - - - +
142B GLU* 1.3 70.5 + - - +
144B ASN* 3.2 2.6 + - - +
145B LYS* 3.0 36.6 + - - +
178B TYR* 3.2 31.3 - - + +
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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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109B LYS* 5.5 9.9 - - - +
140B ASN* 3.0 18.3 + - - +
141B ALA* 1.3 93.8 + - - +
143B GLU* 1.3 61.7 + - + +
145B LYS* 3.5 15.6 + - - +
146B ALA* 3.2 19.9 + - - +
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Residues in contact with GLU 143 (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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109B LYS* 5.9 7.9 - - + +
110B LYS* 3.1 39.2 + - - +
112B PHE* 4.1 12.6 - - + -
137B ILE 3.4 0.3 - - - +
138B PRO* 4.1 8.5 - - + -
139B ARG* 2.8 29.8 + - - +
140B ASN* 2.8 34.0 + - - +
142B GLU* 1.3 72.9 - - + +
144B ASN* 1.3 66.4 + - - +
146B ALA* 3.5 8.3 - - - +
147B ILE* 3.0 28.9 + - - +
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Residues in contact with ASN 144 (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 PRO* 3.6 20.9 - - + +
140B ASN 3.0 10.4 + - - +
141B ALA 3.2 10.1 + - - +
143B GLU* 1.3 79.8 - - - +
145B LYS* 1.3 57.7 + - - +
147B ILE* 3.4 0.5 + - - +
148B GLN* 3.0 28.1 + - - +
178B TYR* 3.5 21.4 + - + +
180B ASN* 3.6 8.7 - - - +
198B ILE* 3.5 11.3 - - - +
202B GLY* 3.0 29.9 + - - -
204B TRP* 3.0 25.5 + - - -
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Residues in contact with LYS 145 (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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141B ALA* 3.0 23.5 + - - +
142B GLU* 3.7 15.5 + - - +
143B GLU 3.3 0.2 - - - -
144B ASN* 1.3 74.9 - - - +
146B ALA* 1.3 64.1 + - - +
148B GLN* 3.1 23.2 + - - +
149B GLU* 2.9 36.8 + - - +
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Residues in contact with ALA 146 (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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112B PHE* 3.9 21.3 - - + -
142B GLU 3.2 15.4 + - - +
143B GLU* 3.5 9.0 - - - +
144B ASN 3.3 0.2 - - - -
145B LYS* 1.3 76.3 - - - +
147B ILE* 1.3 61.4 + - - +
149B GLU* 3.1 28.8 - - - +
150B VAL* 3.1 17.1 + - + +
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Residues in contact with ILE 147 (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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112B PHE* 3.6 33.0 - - + -
136B ALA* 3.6 29.6 - - + -
138B PRO* 3.3 37.5 - - + -
143B GLU 3.0 14.5 + - - +
144B ASN 3.8 3.8 - - - +
146B ALA* 1.3 74.5 - - - +
148B GLN* 1.3 57.7 + - - +
150B VAL* 3.2 6.0 + - - +
151B ALA* 2.9 29.4 + - + +
155B ALA* 5.5 0.2 - - + -
157B LEU* 4.3 5.6 - - + -
198B ILE* 4.3 22.7 - - + -
216B VAL* 4.4 14.6 - - + -
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Residues in contact with GLN 148 (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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144B ASN* 3.0 15.2 + - - +
145B LYS* 3.2 29.7 - - - +
147B ILE* 1.3 77.3 - - - +
149B GLU* 1.3 62.4 + - + +
151B ALA* 4.0 2.9 - - - +
152B LYS* 3.1 24.1 + - - +
198B ILE* 4.1 13.7 - - + +
199B VAL 5.0 3.6 - - - +
201B ASN* 3.3 25.9 + - - -
202B GLY* 3.5 21.2 + - - +
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Residues in contact with GLU 149 (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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106B LYS* 4.8 11.4 + - - -
145B LYS* 2.9 31.0 + - + +
146B ALA* 3.1 23.9 - - - +
148B GLN* 1.3 77.7 - - + +
150B VAL* 1.3 61.2 + - + +
152B LYS* 2.7 35.7 + - - +
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Residues in contact with VAL 150 (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 MET 6.0 1.1 - - - +
112B PHE* 3.9 23.1 - - + +
113B VAL* 4.1 21.3 - - - +
114B THR* 3.5 31.0 - - + +
116B HIS* 4.0 9.0 - - - -
146B ALA* 3.1 17.7 + - + +
147B ILE* 3.2 7.1 + - - +
149B GLU* 1.3 84.8 - - + +
151B ALA* 1.3 63.3 + - - +
152B LYS* 4.1 3.1 + - - +
216B VAL* 4.3 7.0 - - + -
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Residues in contact with ALA 151 (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 THR* 4.6 3.4 - - - -
116B HIS* 4.2 10.2 + - - -
147B ILE* 2.9 18.4 + - + +
148B GLN* 4.1 3.1 - - - +
150B VAL* 1.3 77.6 - - - +
152B LYS* 1.3 67.3 + - - +
153B THR* 2.7 33.3 + - - +
155B ALA* 3.8 22.0 - - + -
198B ILE* 5.1 2.5 - - + -
214B THR* 4.6 5.7 - - + +
216B VAL* 4.0 12.8 - - + -
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Residues in contact with LYS 152 (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 HIS* 4.9 11.6 - - + +
148B GLN 3.1 14.0 + - - +
149B GLU* 2.7 29.6 + - - +
150B VAL 4.1 4.6 + - - +
151B ALA* 1.3 79.8 - - - +
153B THR* 1.3 64.8 + - + +
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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