Contacts of the helix formed by residues 167 - 182 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A MSE 1.3 70.0 - - - +
168A HIS* 1.3 64.3 + - - +
169A GLU 3.4 2.2 - - - -
170A ALA* 4.1 12.8 - - + +
171A ALA* 2.9 25.6 + - - +
283A PHE* 5.4 0.7 - - - -
301A PRO* 5.3 1.4 + - - +
332A ALA* 3.1 30.2 + - + +
333A PRO 3.3 24.9 + - - +
334A GLU* 3.8 15.2 - - - +
335A PHE* 3.4 32.7 - - + +
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 3.5 19.5 - - - -
165A THR* 3.7 9.7 + - - -
166A MSE 2.9 56.3 + - + +
167A GLN* 1.3 71.9 - - - +
169A GLU* 1.3 63.1 + - - +
171A ALA* 4.1 2.3 - - - +
172A ALA* 3.0 26.5 + - - +
200A VAL* 3.5 37.1 - - + +
203A LEU* 3.8 21.3 - - + -
204A ARG* 3.0 37.5 + - + +
283A PHE* 4.9 1.6 - - - -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN 3.4 0.6 - - - -
168A HIS* 1.3 79.7 - - - +
170A ALA* 1.3 59.4 + - - +
172A ALA 3.3 0.7 + - - -
173A ARG* 3.0 26.6 + - - +
203A LEU* 3.4 39.7 + - + +
206A ALA* 4.4 9.8 - - + +
207A GLY* 3.5 10.7 - - - +
210A GLU* 2.8 30.3 - - - +
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 3.5 17.9 + - + +
169A GLU* 1.3 79.1 - - - +
171A ALA* 1.3 58.6 + - - +
173A ARG* 3.4 14.5 + - - +
174A ALA* 3.0 29.3 + - - +
210A GLU* 6.0 0.2 - - - -
335A PHE* 3.7 18.1 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN 2.9 20.2 + - - +
168A HIS 4.1 0.2 - - - +
170A ALA* 1.3 78.6 - - - +
172A ALA* 1.3 56.0 - - - +
174A ALA* 3.3 1.9 + - - +
175A ALA* 2.8 30.5 + - - +
283A PHE* 3.6 30.2 - - + -
299A VAL* 4.2 5.7 - - + +
335A PHE* 3.7 35.3 - - + -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A HIS 3.0 20.1 + - - +
169A GLU 3.3 3.6 + - - +
171A ALA* 1.3 72.9 - - - +
173A ARG* 1.3 65.1 + - - +
175A ALA* 3.4 1.0 + - - +
176A THR* 2.9 31.9 + - - -
204A ARG* 3.3 35.9 - - - +
207A GLY 4.2 1.6 - - - -
208A TYR 4.1 1.3 - - - +
253A PHE* 3.7 24.2 - - + -
283A PHE* 4.4 1.2 - - - -
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU 3.0 17.6 + - - +
170A ALA* 3.7 12.8 + - - +
172A ALA* 1.3 77.4 - - - +
174A ALA* 1.3 57.1 + - - +
176A THR* 3.4 0.7 + - - -
177A GLU* 2.9 57.0 + - - +
207A GLY* 3.4 22.8 - - - +
210A GLU* 3.3 34.4 + - - +
211A ALA* 3.9 10.2 - - + +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA 3.0 16.7 + - - +
171A ALA 3.3 1.5 + - - +
173A ARG* 1.3 76.3 - - - +
175A ALA* 1.3 58.3 + - - +
177A GLU* 3.4 15.4 + - - +
178A HIS* 2.9 30.0 + - - +
335A PHE* 3.7 28.3 - - + -
337A LEU* 4.7 9.4 - - + +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA 2.8 17.4 + - - +
172A ALA 3.7 0.4 - - - +
173A ARG 3.3 0.4 - - - -
174A ALA* 1.3 76.5 - - - +
176A THR* 1.3 63.0 + - - +
178A HIS* 3.1 8.3 + - - +
179A LEU* 3.1 25.8 + - - +
253A PHE* 3.6 29.4 - - + -
281A MSE 3.6 30.4 - - + +
299A VAL* 4.5 4.7 - - + +
337A LEU* 4.8 3.6 - - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 2.9 17.7 + - - -
175A ALA* 1.3 75.3 - - - +
177A GLU* 1.3 57.3 + - - +
179A LEU* 3.1 10.4 + - - +
180A LEU* 2.9 33.1 + - + +
187A VAL* 4.6 7.4 - - + -
208A TYR* 3.6 40.2 - - + +
211A ALA* 3.6 23.8 - - + -
212A LEU* 4.1 14.8 - - + -
253A PHE* 3.7 9.9 - - - +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 2.9 45.7 + - - +
174A ALA* 3.6 17.7 + - - +
176A THR* 1.3 78.1 - - - +
178A HIS* 1.3 57.4 + - - +
180A LEU* 3.4 9.7 + - + +
181A GLY* 2.8 27.2 + - - -
211A ALA* 4.1 13.4 - - + +
214A ALA* 6.0 2.5 - - + +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA 2.9 13.9 + - - +
175A ALA* 3.1 9.6 + - - +
177A GLU* 1.3 76.7 - - - +
179A LEU* 1.3 64.1 + - + +
181A GLY* 3.2 10.0 + - - -
182A LEU* 3.3 24.7 + - + +
281A MSE 4.3 8.3 - - - -
297A THR* 4.1 10.5 - - + +
337A LEU* 3.8 23.0 - - + +
339A VAL* 3.5 28.5 - - + +
343A THR* 2.8 46.9 + - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 3.1 14.6 + - - +
176A THR* 3.1 7.4 + - - +
178A HIS* 1.3 78.1 - - + +
180A LEU* 1.3 62.9 + - - +
182A LEU* 3.2 18.3 + - + +
184A ARG* 3.4 18.9 + - - +
187A VAL* 3.8 28.7 - - + -
251A ALA* 4.2 17.5 - - + -
252A VAL 4.4 1.1 - - - +
253A PHE* 3.9 23.3 - - + +
279A ALA* 4.2 18.6 - - + -
281A MSE 4.0 16.2 - - + -
343A THR* 3.7 31.0 - - + -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 2.9 31.1 + - + +
177A GLU* 3.9 7.4 - - + +
179A LEU* 1.3 75.6 - - - +
181A GLY* 1.3 56.7 + - - +
183A GLY* 2.9 21.5 + - - -
184A ARG 3.3 20.5 + - - +
185A ARG* 5.4 0.2 - - + -
187A VAL* 4.1 14.6 - - + -
211A ALA* 3.5 34.8 - - + +
212A LEU* 4.2 4.7 - - + +
215A ALA* 3.9 16.4 - - + -
217A LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU 2.8 17.9 + - - -
178A HIS* 3.6 4.0 - - - -
179A LEU 3.2 0.4 - - - -
180A LEU* 1.3 76.4 - - - +
182A LEU* 1.3 59.1 + - - +
183A GLY 3.2 1.9 + - - -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.3 24.2 + - + +
179A LEU* 3.4 15.9 - - + +
180A LEU 3.1 0.6 - - - -
181A GLY* 1.3 77.5 - - - +
183A GLY* 1.3 58.8 + - - +
184A ARG* 3.4 18.0 + - + +
279A ALA* 4.2 15.7 - - + -
343A THR* 3.2 46.2 - - - +
344A GLY* 5.3 2.0 - - - -
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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