Contacts of the helix formed by residues 170 - 182 (chain B) in PDB entry 4KYI
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B MET* 4.2 17.9 - - - +
162B GLU* 2.7 38.9 + - - +
163B THR* 3.7 4.4 - - + +
168B ALA 3.4 1.8 + - - -
169B MET* 1.3 86.5 - - - +
171B VAL* 1.3 62.2 + - - +
172B ASN 3.6 1.1 - - - -
173B GLU* 3.2 37.9 + - - +
174B ILE* 3.2 25.1 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.8 41.5 - - + +
40B ARG* 3.6 34.8 - - + +
41B PHE* 3.8 16.2 - - + +
163B THR* 4.8 1.8 - - - -
164B SER 3.9 14.4 - - - +
168B ALA 3.6 9.0 + - - +
169B MET 2.9 13.9 + - - +
170B ASN* 1.3 74.1 - - - +
172B ASN* 1.3 66.5 + - + +
173B GLU* 4.6 0.2 + - - -
174B ILE* 3.2 10.6 - - - +
175B PHE* 3.1 29.1 - - + -
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.1 29.9 + - + +
63B VAL* 5.4 5.1 - - - +
168B ALA 4.9 1.8 + - - +
171B VAL* 1.3 79.9 - - + +
173B GLU* 1.3 72.2 + - - +
175B PHE* 3.8 0.7 + - - +
176B MET* 3.3 45.9 + - - +
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B MET* 3.7 16.9 - - + +
168B ALA 4.9 2.6 - - - +
170B ASN* 3.2 43.7 + - - +
171B VAL 3.2 0.6 + - - -
172B ASN* 1.3 90.9 + - - +
174B ILE* 1.3 57.8 + - - +
176B MET* 4.0 2.2 - - - +
177B ALA* 3.1 29.5 + - - +
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Residues in contact with ILE 174 (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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37B LEU* 6.2 2.0 - - + -
98B ILE* 4.2 17.3 - - + -
130B ALA* 4.2 16.8 - - + -
131B LEU 4.0 11.2 - - - +
132B ALA* 3.7 29.4 - - + -
159B LEU* 4.5 5.8 - - + +
161B MET* 3.6 25.3 - - + -
163B THR* 4.1 10.5 - - + -
170B ASN 3.2 18.0 + - - +
171B VAL* 3.2 10.8 - - - +
173B GLU* 1.3 76.2 - - - +
175B PHE* 1.3 79.4 + - + +
177B ALA* 3.4 3.8 + - + +
178B ILE* 3.2 24.0 + - + +
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Residues in contact with PHE 175 (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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24B LEU* 4.0 25.6 - - + -
26B LEU* 4.7 12.8 - - + -
37B LEU* 4.7 14.8 - - + -
38B VAL* 5.2 4.7 - - + -
41B PHE* 3.5 65.1 - + + -
72B PHE* 4.1 14.8 - + + -
74B ILE* 4.5 7.6 - - + -
98B ILE* 3.6 27.4 - - + -
171B VAL* 3.1 26.9 + - + +
172B ASN 4.1 0.9 - - - +
173B GLU 3.4 0.8 - - - -
174B ILE* 1.3 88.4 - - + +
176B MET* 1.3 57.6 + - - +
178B ILE* 3.0 30.3 + - - +
179B ALA 3.3 3.8 + - - -
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Residues in contact with MET 176 (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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41B PHE* 5.2 3.4 - - + -
63B VAL* 4.7 24.7 - - + -
64B CYS 4.8 3.1 - - - +
65B LEU* 4.1 28.7 - - + +
72B PHE* 5.6 1.1 - - + -
172B ASN* 3.3 36.7 + - - +
173B GLU* 4.4 2.5 - - - +
175B PHE* 1.3 81.3 - - + +
177B ALA* 1.3 62.4 + - - +
179B ALA* 3.1 17.9 + - + +
180B LYS* 3.1 34.6 + - - +
67D ASP* 4.0 21.1 - - + +
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Residues in contact with ALA 177 (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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159B LEU* 3.5 24.7 - - + +
161B MET* 4.0 17.3 - - + -
173B GLU 3.1 21.0 + - - +
174B ILE* 3.5 7.0 - - - +
175B PHE 3.2 0.2 - - - -
176B MET* 1.3 76.4 - - - +
178B ILE* 1.3 60.4 + - - +
180B LYS* 3.6 23.4 - - - +
181B LYS* 3.7 7.8 - - - +
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Residues in contact with ILE 178 (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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24B LEU* 4.1 15.3 - - + -
72B PHE* 5.1 1.1 - - + -
96B ALA* 3.6 28.0 - - + -
98B ILE* 4.0 23.3 - - + -
128B VAL* 3.7 20.4 - - + +
130B ALA* 3.9 23.8 - - + -
159B LEU* 4.2 14.1 - - + -
174B ILE* 3.2 17.7 - - + +
175B PHE* 3.0 10.0 + - - +
177B ALA* 1.3 76.9 - - - +
179B ALA* 1.3 64.7 + - - +
180B LYS 3.1 0.2 - - - -
181B LYS* 3.0 14.6 + - - +
182B LEU* 3.0 19.2 + - + +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 5.6 1.1 - - + -
65B LEU* 3.8 24.3 - - + +
70B VAL* 4.5 17.3 - - + +
72B PHE* 4.2 17.2 - - + -
175B PHE 3.3 2.0 + - - -
176B MET* 3.1 20.5 + - + +
178B ILE* 1.3 79.0 - - - +
180B LYS* 1.3 62.0 + - + +
182B LEU* 3.1 29.9 + - + +
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.9 23.5 - - + +
176B MET* 3.1 43.7 + - - +
177B ALA* 3.6 15.1 - - - +
178B ILE 3.1 0.4 - - - -
179B ALA* 1.3 78.8 - - - +
181B LYS* 1.3 61.5 + - + +
182B LEU 4.7 1.7 - - - -
67D ASP* 5.2 5.4 + - - -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 3.7 32.4 - - + +
159B LEU* 4.1 21.1 - - + -
177B ALA 3.7 12.1 - - - +
178B ILE 3.0 6.8 + - - +
180B LYS* 1.3 77.5 - - + +
182B LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 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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22B PHE* 3.8 54.5 - - + -
70B VAL* 5.8 3.1 - - + -
72B PHE* 3.9 26.5 - - + -
95B GLN* 3.9 24.9 - - + +
96B ALA* 4.8 2.2 - - + -
128B VAL* 3.7 23.3 - - + -
178B ILE* 3.0 20.3 + - + +
179B ALA* 3.1 25.4 + - + +
180B LYS 4.7 2.0 - - - -
181B LYS* 1.3 81.9 - - - +
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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