Contacts of the helix formed by residues 167 - 182 (chain B) in PDB entry 4KMR
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 GLN 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B MSE 1.3 70.1 - - - +
168B HIS* 1.3 59.3 + - - +
169B GLU 3.4 2.0 + - - -
170B ALA* 4.1 14.0 - - + +
171B ALA* 2.8 31.1 + - - +
283B PHE* 5.5 1.1 - - - -
301B PRO 5.4 0.8 + - - -
332B ALA* 3.2 28.8 + - + +
333B PRO 3.1 25.8 + - - +
334B GLU* 3.3 24.9 + - - +
335B PHE* 3.5 33.7 - - + +
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Residues in contact with HIS 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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153B GLY* 6.1 1.6 - - - -
154B GLU* 3.7 25.5 - - - -
165B THR* 4.7 0.2 - - - +
166B MSE 2.9 63.0 + - + +
167B GLN* 1.3 71.6 - - - +
169B GLU* 1.3 59.0 + - - +
171B ALA* 4.1 2.6 - - - +
172B ALA* 3.0 31.7 + - - +
200B VAL* 3.6 32.8 - - + +
203B LEU* 3.8 24.2 - - + -
204B ARG* 3.1 36.2 + - + +
283B PHE* 4.3 1.5 - - - -
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN 3.4 0.4 - - - -
168B HIS* 1.3 79.2 - - - +
170B ALA* 1.3 58.5 + - - +
172B ALA 3.3 1.0 + - - -
173B ARG* 2.9 26.6 + - + +
203B LEU* 3.4 37.9 + - + +
206B ALA* 3.9 21.7 - - - +
207B GLY* 3.5 16.2 - - - +
209B ARG* 5.6 0.3 + - - -
210B GLU* 4.9 7.4 - - - +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN* 3.4 16.6 + - + +
168B HIS 3.4 0.4 - - - -
169B GLU* 1.3 79.7 - - - +
171B ALA* 1.3 58.4 + - - +
173B ARG* 3.4 6.9 + - - +
174B ALA* 3.0 28.6 + - - +
335B PHE* 3.8 19.1 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN 2.8 23.3 + - - +
170B ALA* 1.3 73.7 - - - +
172B ALA* 1.3 58.5 + - - +
174B ALA* 3.3 1.7 + - - +
175B ALA* 2.8 30.5 + - - +
283B PHE* 3.8 25.8 - - + -
299B VAL* 4.2 9.0 - - + +
335B PHE* 3.7 33.9 - - + -
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Residues in contact with ALA 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 HIS 3.0 19.6 + - - +
169B GLU 3.8 3.6 - - - +
171B ALA* 1.3 72.7 - - - +
173B ARG* 1.3 64.3 + - - +
175B ALA* 3.8 0.7 - - - +
176B THR* 2.9 32.0 + - - -
204B ARG* 3.3 37.5 - - - +
207B GLY 4.1 1.6 - - - -
208B TYR 4.2 1.3 - - - +
253B PHE* 3.7 24.8 - - + -
283B PHE* 4.9 0.6 - - - -
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Residues in contact with ARG 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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169B GLU* 2.9 17.8 + - + +
170B ALA* 3.6 7.6 - - - +
172B ALA* 1.3 78.3 - - - +
174B ALA* 1.3 56.6 + - - +
176B THR* 3.4 1.7 + - - -
177B GLU* 2.9 57.5 + - - +
207B GLY* 3.4 23.2 - - - +
210B GLU* 3.7 29.9 + - - +
211B ALA* 3.8 7.3 - - + +
214B ALA* 3.7 27.3 - - - +
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Residues in contact with ALA 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 ALA 3.0 17.0 + - - +
171B ALA 3.7 3.8 - - - +
173B ARG* 1.3 78.0 - - - +
175B ALA* 1.3 58.1 + - - +
177B GLU* 3.4 14.7 + - - +
178B HIS* 2.9 28.2 + - - +
335B PHE* 3.8 23.3 - - + -
337B LEU* 4.6 9.7 - - + +
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Residues in contact with ALA 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 ALA 2.8 20.7 + - - +
172B ALA 3.8 0.4 - - - +
174B ALA* 1.3 71.9 - - - +
176B THR* 1.3 63.5 + - - +
178B HIS* 3.2 13.9 + - - +
179B LEU* 3.2 12.7 + - - +
253B PHE* 3.6 28.7 - - + -
281B MSE 3.6 36.9 - - + +
299B VAL* 4.5 4.9 - - + -
337B LEU* 5.0 3.8 - - - -
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Residues in contact with THR 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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172B ALA 2.9 19.2 + - - -
175B ALA* 1.3 75.4 - - - +
177B GLU* 1.3 58.6 + - - +
179B LEU* 3.2 10.9 + - - +
180B LEU* 2.9 43.5 + - + +
187B VAL* 4.6 7.9 - - + -
208B TYR* 3.6 39.7 - - + +
211B ALA* 3.6 24.0 - - + -
212B LEU* 4.1 8.1 - - + -
253B PHE* 3.7 9.6 - - - +
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Residues in contact with GLU 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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173B ARG* 2.9 51.8 + - - +
174B ALA* 3.6 17.3 - - - +
176B THR* 1.3 75.4 - - - +
178B HIS* 1.3 57.1 + - - +
180B LEU* 3.7 10.2 - - + +
181B GLY* 2.9 27.9 + - - -
211B ALA* 4.0 13.2 - - + +
214B ALA* 5.8 0.7 - - + +
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA 2.9 12.7 + - - +
175B ALA* 3.2 9.8 + - - +
177B GLU* 1.3 76.1 - - - +
179B LEU* 1.3 64.1 + - + +
181B GLY* 3.3 9.9 + - - -
182B LEU* 3.5 21.4 + - + +
281B MSE 4.2 7.6 - - - -
297B THR* 4.0 12.4 - - + +
337B LEU* 3.6 21.7 - - + +
339B VAL* 3.9 25.7 - - + +
343B THR* 2.8 48.4 + - + -
345B GLY 5.6 1.3 - - - -
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Residues in contact with LEU 179 (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 ALA 3.2 11.4 + - - +
176B THR* 3.2 7.9 + - - +
178B HIS* 1.3 78.2 - - + +
180B LEU* 1.3 62.3 + - - +
182B LEU* 3.2 22.7 + - + +
184B ARG* 3.5 14.8 - - - +
187B VAL* 4.0 21.1 - - + -
251B ALA* 4.2 12.3 - - + -
252B VAL 4.1 8.5 - - - +
253B PHE* 3.9 28.0 - - + +
279B ALA* 4.1 20.2 - - + +
281B MSE 4.0 17.7 - - + -
343B THR* 3.7 30.1 - - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR* 2.9 31.9 + - + +
177B GLU* 3.7 8.3 - - + +
179B LEU* 1.3 75.0 - - - +
181B GLY* 1.3 57.0 + - - +
183B GLY* 2.9 22.5 + - - -
184B ARG 3.3 21.1 + - - +
185B ARG* 5.6 1.1 - - - +
187B VAL* 4.0 13.9 - - + -
211B ALA* 3.6 34.3 - - + +
212B LEU* 4.2 4.5 - - + -
215B ALA* 3.9 15.5 - - + -
217B LEU* 3.6 25.4 - - + -
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Residues in contact with GLY 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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177B GLU 2.9 16.7 + - - -
178B HIS* 3.3 4.4 + - - -
179B LEU 3.2 1.0 - - - -
180B LEU* 1.3 76.8 - - - +
182B LEU* 1.3 62.2 + - - +
183B GLY 3.2 1.8 + - - -
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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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178B HIS* 3.5 23.1 - - + +
179B LEU* 3.4 14.4 - - - +
180B LEU 3.2 0.6 - - - -
181B GLY* 1.3 79.0 - - - +
183B GLY* 1.3 59.1 + - - +
184B ARG* 3.5 20.9 + - + +
279B ALA* 3.8 29.4 - - + -
343B THR* 3.4 36.1 - - - +
345B GLY 6.0 0.7 - - - +
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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