Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 2XMS
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A SER* 1.3 77.7 - - - +
179A ILE* 1.3 65.9 + - - +
180A PRO* 3.2 13.9 - - - +
181A GLU* 3.0 39.1 + - - +
182A MET* 3.1 21.8 + - - +
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Residues in contact with ILE 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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178A SER* 1.3 72.0 - - - +
180A PRO* 1.3 72.5 - - + +
182A MET* 3.2 7.9 + - + +
183A ILE* 3.0 41.7 + - + +
213A LEU* 4.6 10.5 - - + -
217A GLU* 3.2 57.0 - - + +
220A TRP* 4.7 12.8 - - + +
221A ASN* 6.2 0.2 - - - +
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Residues in contact with PRO 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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178A SER* 3.2 14.6 - - - +
179A ILE* 1.3 93.3 - - + +
181A GLU* 1.3 55.8 + - + +
183A ILE* 3.4 2.5 + - + +
184A LEU* 2.9 36.9 + - + +
207A ILE* 4.0 16.1 - - + +
208A THR* 3.9 39.0 - - + +
213A LEU* 3.8 29.2 - - + -
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Residues in contact with GLU 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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176A THR 4.2 4.0 - - - +
177A SER* 3.5 15.6 + - - +
178A SER* 3.0 41.4 + - - +
180A PRO* 1.3 77.4 - - + +
182A MET* 1.3 59.2 + - - +
184A LEU* 3.5 12.1 + - + +
185A GLY* 3.0 23.0 + - - -
193A LEU* 5.1 2.4 - - - +
204A ARG* 6.3 0.7 - - - +
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Residues in contact with MET 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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170A HIS* 3.5 50.7 - - + +
173A THR* 4.0 15.7 - - + -
174A GLY* 3.7 27.1 - - - -
177A SER* 3.6 22.9 - - - +
178A SER 3.1 12.2 + - - +
179A ILE* 3.7 6.5 - - - +
181A GLU* 1.3 74.7 - - - +
183A ILE* 1.3 64.5 + - - +
185A GLY* 3.3 3.7 + - - +
186A HIS* 3.1 20.8 + - - +
220A TRP* 3.8 20.8 - - + +
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Residues in contact with ILE 183 (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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57A VAL* 3.6 28.7 - - + +
58A GLY* 3.9 9.6 - - - -
179A ILE* 3.0 32.6 + - + +
180A PRO* 3.8 4.7 - - + +
182A MET* 1.3 74.4 - - - +
184A LEU* 1.3 63.5 + - - +
186A HIS* 3.0 20.0 + - + +
187A LEU* 3.1 19.1 + - + +
207A ILE* 4.4 11.7 - - + -
213A LEU* 5.0 0.4 - - + -
216A ILE* 3.4 29.4 - - + +
220A TRP* 3.8 35.9 - - + -
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Residues in contact with LEU 184 (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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180A PRO* 2.9 25.1 + - + +
181A GLU* 3.6 11.7 - - + +
183A ILE* 1.3 77.3 - - - +
185A GLY* 1.3 56.4 + - - +
187A LEU* 3.3 2.6 + - - +
188A PHE* 2.9 59.1 + - + +
193A LEU* 3.6 20.5 - - + +
200A ILE 5.3 0.7 - - - +
203A TYR 4.0 8.5 - - - +
204A ARG* 3.9 41.3 - - + +
207A ILE* 3.7 27.4 - - + -
208A THR* 4.6 6.3 - - - +
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU 3.0 15.0 + - - -
182A MET* 3.3 4.9 + - - -
183A ILE 3.2 0.4 - - - -
184A LEU* 1.3 73.0 - - - +
186A HIS* 1.3 62.0 + - - +
188A PHE 3.3 16.6 - - - +
190A GLN* 4.1 11.4 - - - +
193A LEU* 3.9 10.2 - - - +
252A PRO* 3.8 12.8 - - - +
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Residues in contact with HIS 186 (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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56A ASP* 2.8 37.4 + - - +
57A VAL* 4.3 13.0 - - + +
132A GLY* 4.7 4.7 - - - -
156A ASN* 5.2 0.2 + - - -
182A MET 3.1 6.7 + - - +
183A ILE 3.0 9.7 + - - +
185A GLY* 1.3 77.5 - - - +
187A LEU* 1.3 70.3 + - + +
220A TRP* 3.6 28.5 - + + -
223A TYR* 3.6 38.0 - + - -
252A PRO* 4.4 4.0 - - - +
253A HIS* 3.0 59.4 + + - -
280A GLN* 5.0 0.5 - - - +
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Residues in contact with LEU 187 (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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56A ASP* 3.5 31.6 - - + +
57A VAL 3.5 24.2 - - - +
59A LEU* 4.2 14.1 - - + -
183A ILE* 3.1 15.5 + - + +
184A LEU* 3.8 2.7 - - - +
186A HIS* 1.3 81.6 - - + +
188A PHE* 1.3 82.1 + - + +
207A ILE* 3.5 31.9 - - + -
252A PRO* 5.1 0.4 - - - -
279A GLY* 3.1 30.6 - - - +
280A GLN* 3.3 21.0 - - - +
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Residues in contact with PHE 188 (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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184A LEU* 2.9 36.2 + - + +
185A GLY* 3.3 21.0 - - - +
187A LEU* 1.3 92.8 - - + +
189A SER* 1.3 65.2 + - - +
190A GLN* 3.8 0.5 + - - +
192A GLU* 3.5 17.3 - - + +
193A LEU* 3.9 15.8 - - + +
199A LEU* 4.1 16.8 - - + -
200A ILE* 3.5 29.2 - - + -
203A TYR* 3.7 40.6 - + + -
252A PRO* 3.5 6.9 - - - +
279A GLY* 4.0 0.7 - - - -
280A GLN* 3.6 29.8 - - + -
283A LEU* 4.4 2.2 - - + -
284A THR* 5.9 0.2 - - + -
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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