Contacts of the helix formed by residues 180 - 189 (chain B) in PDB entry 4KZX
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 ASP 180 (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* 4.5 0.9 - - - -
130B THR* 2.8 9.3 + - - +
131B ASP* 2.5 38.4 - - - +
179B ASN* 1.3 72.0 - - - +
181B LEU* 1.3 64.1 + - - +
182B LYS* 2.8 14.9 + - - +
183B GLU* 2.8 34.7 + - - +
184B VAL* 3.2 10.2 + - - +
227B LYS* 5.7 7.4 - - - +
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Residues in contact with LEU 181 (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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99B ASN* 4.7 6.3 - - - +
100B PHE* 3.2 55.6 - - + +
129B THR* 4.6 2.1 + - - -
131B ASP* 3.2 7.2 + - - +
133B TYR* 3.3 55.1 - - + +
135B LEU* 4.0 20.9 - - + -
180B ASP* 1.3 73.9 - - - +
182B LYS* 1.3 59.7 + - - +
184B VAL* 3.7 7.1 - - + +
185B VAL* 2.9 33.8 + - - +
217B MET* 3.8 8.3 - - + -
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Residues in contact with LYS 182 (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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36B PRO* 4.3 5.1 - - - +
37B ALA* 4.7 1.6 - - - +
38B MET* 3.9 39.0 - - + +
99B ASN* 4.3 3.4 + - - -
100B PHE* 5.9 2.2 - - - +
131B ASP* 4.8 0.2 + - - -
180B ASP* 2.8 19.9 + - - +
181B LEU* 1.3 78.0 - - - +
183B GLU* 1.3 52.5 + - + +
185B VAL* 3.1 16.2 - - + +
186B ASN* 2.7 47.1 + - - +
231B LEU* 1.5 60.2 - - + +
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Residues in contact with GLU 183 (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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179B ASN* 1.8 70.0 - - + +
180B ASP* 2.8 21.0 + - - +
182B LYS* 1.3 70.8 - - + +
184B VAL* 1.3 56.1 + - - +
186B ASN* 3.5 15.1 - - + +
187B LYS* 2.6 41.3 + - - +
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Residues in contact with VAL 184 (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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100B PHE* 5.6 1.6 - - + -
129B THR* 4.8 4.3 - - + -
135B LEU* 4.8 7.2 - - + -
137B LEU* 4.8 14.4 - - + -
175B GLU 4.8 4.0 - - - +
176B VAL* 4.2 33.4 - - + -
179B ASN* 4.4 9.8 - - + +
180B ASP 3.2 13.2 + - - +
181B LEU* 3.7 13.7 - - + +
183B GLU* 1.3 78.2 - - - +
185B VAL* 1.3 60.3 + - + +
187B LYS* 3.0 9.5 + - - +
188B LEU* 2.7 56.1 + - + +
215B VAL* 5.4 2.7 - - + -
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Residues in contact with VAL 185 (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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38B MET* 4.7 6.1 - - + +
39B PHE* 4.3 24.0 - - + -
84B PHE* 5.4 4.4 - - + -
100B PHE* 4.0 37.7 - - + -
181B LEU* 2.9 25.7 + - + +
182B LYS* 3.1 22.7 - - + +
184B VAL* 1.3 74.7 - - - +
186B ASN* 1.3 65.0 + - - +
188B LEU* 3.0 20.4 + - - +
189B ILE* 3.2 31.6 + - + +
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Residues in contact with ASN 186 (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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38B MET* 1.9 74.6 - - - +
182B LYS* 2.7 26.6 + - - +
183B GLU* 3.7 14.5 - - + +
185B VAL* 1.3 72.1 - - - +
187B LYS* 1.3 56.6 + - - +
189B ILE* 4.2 7.2 - - - +
190B PRO* 2.9 26.8 - - - +
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Residues in contact with LYS 187 (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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175B GLU* 2.5 64.0 + - + +
178B THR* 4.3 0.6 + - - -
179B ASN* 3.0 31.6 - - - +
183B GLU* 2.6 23.7 + - - +
184B VAL* 3.1 11.2 - - - +
186B ASN* 1.3 70.7 - - - +
188B LEU* 1.3 62.8 + - + +
189B ILE 3.1 3.7 + - - -
190B PRO* 3.5 4.3 - - - +
191B ASP* 3.3 14.7 + - - -
192B SER* 3.4 23.6 + - - +
193B ILE* 4.0 14.5 + - + -
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Residues in contact with LEU 188 (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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71B LEU* 5.1 0.5 - - - +
82B ARG* 3.1 9.9 + - - -
84B PHE* 5.2 8.8 - - + -
100B PHE* 4.9 11.9 - - + -
103B MET* 4.2 17.1 - - + +
137B LEU* 6.5 0.4 - - + -
184B VAL* 2.7 44.2 + - + +
185B VAL* 3.0 9.3 + - - +
187B LYS* 1.3 71.2 - - + +
189B ILE* 1.3 56.6 + - - +
191B ASP* 2.7 27.7 - - - +
193B ILE* 4.6 14.6 - - + -
212B VAL* 3.2 35.6 - - + +
215B VAL* 4.0 22.0 - - + -
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Residues in contact with ILE 189 (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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38B MET 4.3 18.4 - - - +
39B PHE* 4.9 4.0 - - + -
71B LEU* 4.8 16.8 - - + +
75B GLN* 3.8 38.6 - - + +
82B ARG* 2.8 23.6 + - - +
84B PHE* 4.8 4.9 - - + -
185B VAL* 3.3 33.2 - - + +
186B ASN* 4.3 8.7 - - - +
188B LEU* 1.3 75.3 - - - +
190B PRO* 1.4 70.9 - - + +
191B ASP* 3.1 4.5 + - - -
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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