Contacts of the helix formed by residues 161 - 175 (chain B) in PDB entry 5KAL
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 CYS 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B PHE* 4.4 9.7 - - + -
158B ASN* 3.1 43.4 + - + +
159B PRO 3.0 1.0 + - - -
160B PRO* 1.3 79.0 - - - +
162B ARG* 1.3 64.1 + - - +
164B LEU* 2.9 22.0 + - + +
165B SER 3.5 2.4 + - - -
195B VAL* 5.6 0.3 - - - +
199B LEU* 4.1 34.4 - - + +
204B HIS* 5.3 4.3 - - - -
205B LEU* 5.7 1.6 - - + -
236B GLU* 5.6 1.1 - - - -
240B GLN* 4.4 25.8 - - - +
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Residues in contact with ARG 162 (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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57B VAL 5.0 0.2 - - - -
58B TYR* 2.9 50.4 + - + +
60B VAL* 4.6 0.6 - - - +
155B PHE* 3.8 36.9 - - + -
159B PRO* 2.9 42.2 + - - +
160B PRO 2.9 0.4 + - - -
161B CYS* 1.3 76.8 - - - +
163B TRP* 1.3 65.6 + - - +
165B SER* 2.9 6.7 + - - -
166B MET* 2.9 29.1 + - - +
225B LEU* 3.5 25.2 + - - +
226B PRO 2.9 20.6 + - - -
227B LEU* 3.6 34.1 - - + +
228B GLU 4.6 1.8 - - - +
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Residues in contact with TRP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.9 47.6 - + + -
160B PRO* 2.9 28.8 + - + +
162B ARG* 1.3 76.0 - - - +
164B LEU* 1.3 67.3 + - - +
166B MET* 2.9 26.0 + - + +
167B SER* 2.9 23.7 + - - -
227B LEU* 3.9 30.3 - - + +
228B GLU 3.2 26.0 + - - -
229B GLU* 4.3 13.2 - - + -
230B PRO* 3.8 29.9 - - + +
237B LEU* 4.2 22.2 - - + -
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Residues in contact with LEU 164 (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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160B PRO 4.4 0.2 + - - -
161B CYS* 2.9 12.5 + - + +
163B TRP* 1.3 79.4 - - - +
165B SER* 1.3 66.5 + - - +
167B SER* 3.0 11.5 + - - -
168B ILE* 3.1 27.9 + - + +
195B VAL* 4.3 16.6 - - + -
198B TYR* 4.4 14.6 - - + -
199B LEU* 4.2 23.1 - - + -
237B LEU* 4.5 11.6 - - + +
240B GLN* 4.1 26.5 - - + +
241B VAL* 3.6 39.5 - - + +
244B PHE* 4.8 6.5 - - + -
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.7 16.4 + - - -
155B PHE* 3.9 23.3 - - - -
161B CYS 3.5 1.4 + - - -
162B ARG 2.9 9.2 + - - -
164B LEU* 1.3 77.7 - - - +
166B MET* 1.3 67.6 + - - +
168B ILE* 3.0 5.5 + - - +
169B LYS* 2.9 19.8 + - - +
192B ASN* 2.6 28.8 + - - -
195B VAL* 4.4 22.0 - - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 4.1 19.7 - - + -
58B TYR* 3.7 33.9 - - + -
60B VAL* 5.4 2.2 - - + -
62B GLU* 4.0 24.5 - - + +
162B ARG* 2.9 23.9 + - - +
163B TRP* 3.3 35.9 - - + +
165B SER* 1.3 72.8 - - - +
167B SER* 1.3 68.5 + - - +
169B LYS* 3.0 12.8 + - - +
170B ARG* 3.1 12.0 + - - +
227B LEU* 3.8 27.6 - - + -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.4 14.6 - - - +
16B PHE* 3.7 27.2 - - - -
163B TRP 2.9 17.7 + - - -
164B LEU* 3.3 10.1 - - - -
166B MET* 1.3 73.9 - - - +
168B ILE* 1.3 70.7 + - - +
170B ARG* 3.0 7.7 + - - +
171B TRP* 2.9 21.3 + - - +
237B LEU* 4.3 15.0 - - - +
241B VAL* 5.2 5.2 - - - -
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Residues in contact with ILE 168 (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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164B LEU* 3.5 28.0 - - + +
165B SER* 3.0 7.9 + - - +
167B SER* 1.3 76.6 - - - +
169B LYS* 1.3 66.0 + - - +
171B TRP* 3.0 25.4 + - + +
172B SER* 2.8 21.0 + - - -
191B PHE* 4.0 30.7 - - + -
195B VAL* 4.5 12.8 - - + -
241B VAL* 5.1 11.7 - - + -
244B PHE* 4.0 35.0 - - + -
245B LEU* 5.7 4.0 - - + -
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Residues in contact with LYS 169 (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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54B SER* 3.7 23.4 + - - -
58B TYR* 4.0 15.5 - - - +
62B GLU* 2.8 32.7 + - - +
65B SER* 4.5 6.6 + - - +
165B SER* 2.9 12.0 + - - +
166B MET* 3.4 9.2 - - - +
168B ILE* 1.3 76.0 - - - +
170B ARG* 1.3 67.5 + - - +
172B SER* 2.6 27.3 + - - +
173B LYS* 3.2 30.2 + - - +
188B SER* 3.9 31.6 - - - +
191B PHE* 5.6 6.3 - - + +
192B ASN* 5.6 4.9 - - - +
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Residues in contact with ARG 170 (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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12B LEU* 4.9 6.7 - - - +
15B SER* 3.0 44.3 + - - -
16B PHE* 3.6 40.4 - - + -
166B MET 3.1 6.9 + - - +
167B SER* 3.0 10.7 + - - +
169B LYS* 1.3 78.3 - - - +
171B TRP* 1.3 64.7 + - - +
173B LYS* 2.9 22.4 + - + +
174B GLN* 3.1 36.3 + - + +
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Residues in contact with TRP 171 (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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167B SER 2.9 11.9 + - - +
168B ILE* 3.3 29.8 - - + +
170B ARG* 1.3 75.5 - - - +
172B SER* 1.3 76.5 + - - +
174B GLN* 2.9 24.9 + - + +
175B THR* 3.2 39.3 + - + +
177B LEU* 3.7 28.9 - - + -
191B PHE* 4.6 14.8 - + - -
244B PHE* 6.1 2.5 - + - -
245B LEU* 5.2 16.8 - - + -
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Residues in contact with SER 172 (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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168B ILE 2.8 15.1 + - - -
169B LYS* 2.6 23.3 + - - -
171B TRP* 1.3 79.3 - - - +
173B LYS* 1.3 59.3 + - - +
175B THR* 3.6 6.9 + - - -
177B LEU* 3.2 13.5 + - - -
178B ASN* 2.9 42.3 + - - -
191B PHE* 3.6 38.3 - - - -
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Residues in contact with LYS 173 (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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64B GLY 5.0 5.5 + - - -
65B SER* 4.5 12.9 + - - +
169B LYS* 3.2 30.7 + - + +
170B ARG* 2.9 12.8 + - + +
172B SER* 1.3 79.4 + - - +
174B GLN* 1.3 62.1 + - + +
175B THR 3.4 0.4 + - - -
176B GLY 4.0 2.3 + - - -
178B ASN* 3.8 31.2 - - + +
180B SER* 3.9 15.7 - - - +
181B VAL* 3.8 21.1 - - + +
188B SER* 4.2 7.9 + - - -
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Residues in contact with GLN 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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170B ARG* 3.1 36.1 + - + +
171B TRP* 2.9 16.4 + - + +
173B LYS* 1.3 78.4 - - + +
175B THR* 1.3 63.3 + - + +
176B GLY 3.5 0.2 - - - -
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Residues in contact with THR 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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171B TRP* 3.2 45.1 + - + +
172B SER* 3.6 3.6 + - - -
174B GLN* 1.3 79.9 - - + +
176B GLY* 1.3 59.6 + - - +
177B LEU* 3.4 29.4 + - - +
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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