Contacts of the helix formed by residues 183 - 194 (chain I) in PDB entry 2X86
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 183 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170I VAL 4.1 5.4 - - - -
171I TYR* 3.5 24.5 - - - +
175I GLU* 2.7 35.2 + - - -
181I MET 3.9 0.6 + - - -
182I ALA* 1.3 78.2 - - - +
184I VAL* 1.3 64.8 + - - +
185I ALA* 3.5 9.5 - - - +
186I PHE* 3.0 15.9 + - - +
187I HIS* 3.1 18.4 + - - -
211I PHE* 6.5 0.7 - - - -
401I ADP 5.3 1.6 - - - -
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Residues in contact with VAL 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I ALA 3.7 0.2 + - - -
183I SER* 1.3 69.9 - - - +
185I ALA* 1.3 66.6 + - - +
187I HIS* 3.1 9.5 + - + +
188I LEU* 2.9 44.4 + - + +
199I LYS 4.8 0.4 - - - +
200I LEU* 3.9 22.9 - - + -
211I PHE* 5.5 5.8 - - + -
243I PHE* 3.6 32.5 - - + -
246I VAL* 4.9 7.9 - - + -
401I ADP 3.6 36.5 + - + +
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Residues in contact with ALA 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I TYR* 4.6 10.5 - - + -
183I SER* 3.5 11.4 - - - +
184I VAL* 1.3 78.7 - - - +
186I PHE* 1.3 62.9 + - - +
188I LEU* 3.3 3.2 + - - +
189I ASN* 3.0 24.4 + - - +
246I VAL* 4.2 22.6 - - + +
250I THR* 4.6 2.7 - - - -
299I VAL* 4.7 4.7 - - + -
302I TYR* 4.0 19.3 - - + -
303I MET* 3.6 17.9 - - + +
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Residues in contact with PHE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I GLU* 3.6 7.9 - - + +
176I GLY* 3.5 37.9 - - - -
179I GLY* 5.6 2.2 - - - -
182I ALA* 3.8 20.9 - - + -
183I SER* 3.0 14.9 + - - +
185I ALA* 1.3 80.9 - - - +
187I HIS* 1.3 71.9 + + - +
189I ASN* 3.2 5.7 + - - +
190I THR* 3.1 53.7 + - + +
302I TYR* 3.3 28.8 - - - +
306I LEU* 4.1 20.9 - - + -
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Residues in contact with HIS 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I GLY 2.9 26.5 + - - -
180I SER* 3.8 14.5 - - - -
182I ALA* 3.1 23.7 - - - +
183I SER 3.1 13.5 + - - -
184I VAL* 3.1 10.8 + - + +
186I PHE* 1.3 89.1 - + - +
188I LEU* 1.3 59.3 + - + +
190I THR* 3.3 8.6 + - - -
191I GLN* 2.9 46.8 + - - +
199I LYS 6.1 0.7 - - - +
401I ADP 3.2 18.2 + - - -
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Residues in contact with LEU 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I VAL* 2.9 35.7 + - + +
185I ALA* 3.7 3.6 - - - +
187I HIS* 1.3 76.9 - - + +
189I ASN* 1.3 64.5 + - - +
191I GLN* 3.4 16.1 + - - +
192I LEU* 2.9 31.6 + - + +
198I PRO* 3.8 13.9 - - + -
199I LYS 3.4 33.0 - - - +
200I LEU* 5.0 2.5 - - + -
246I VAL* 4.6 2.2 - - + -
247I ALA* 3.8 35.9 - - + +
250I THR* 4.1 19.5 - - + +
251I LEU* 5.5 1.1 - - + -
259I ILE* 4.8 3.8 - - + -
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Residues in contact with ASN 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ALA 3.0 16.7 + - - +
186I PHE 3.6 4.3 - - - +
188I LEU* 1.3 78.6 - - - +
190I THR* 1.3 67.5 + - - +
192I LEU* 3.3 2.9 + - - +
193I ASN* 3.0 43.4 + - - +
250I THR* 4.5 1.5 - - - +
254I HIS* 2.8 34.7 + - - -
303I MET* 3.6 10.1 - - - +
306I LEU* 3.6 39.0 + - + +
307I ASN* 3.4 13.0 + - - -
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Residues in contact with THR 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I PHE* 3.1 48.7 + - + +
187I HIS* 3.4 12.5 + - - -
189I ASN* 1.3 85.0 - - - +
191I GLN* 1.3 67.9 + - - +
193I ASN* 3.4 7.5 + - - +
194I ASN* 3.1 36.1 + - - -
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Residues in contact with GLN 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I HIS* 2.9 31.8 + - - +
188I LEU* 3.4 15.3 - - - +
190I THR* 1.3 79.9 + - - +
192I LEU* 1.3 58.7 + - - +
194I ASN* 3.3 5.3 + - - +
196I GLU* 3.0 55.2 + - - +
197I SER 3.9 13.7 - - - +
198I PRO* 3.3 7.0 - - + +
199I LYS* 3.0 49.3 + - + +
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Residues in contact with LEU 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I LEU 2.9 20.7 + - - +
189I ASN 3.7 3.8 - - - +
191I GLN* 1.3 73.0 - - - +
193I ASN* 1.3 62.6 + - - +
194I ASN 3.1 4.5 - - - -
195I GLY* 3.2 6.9 + - - -
196I GLU 4.2 5.8 - - - +
198I PRO* 3.8 31.0 - - + -
250I THR* 3.9 8.7 - - + -
251I LEU* 3.8 21.3 - - + -
254I HIS* 3.8 38.1 - - + +
256I LYS* 2.8 42.8 + - - +
257I GLY* 4.1 18.6 - - - -
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Residues in contact with ASN 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I ASN* 3.0 40.6 + - - +
190I THR* 3.9 7.0 - - - +
192I LEU* 1.3 76.6 - - - +
194I ASN* 1.3 61.9 + - - +
195I GLY 3.3 1.5 + - - -
254I HIS* 3.4 17.9 + - - -
306I LEU 5.2 1.4 + - - -
307I ASN* 3.4 17.4 + - - +
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Residues in contact with ASN 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I THR* 3.1 27.5 + - - +
191I GLN* 3.6 6.4 - - - +
192I LEU 3.1 1.0 - - - -
193I ASN* 1.3 81.3 - - - +
195I GLY* 1.3 54.7 + - - +
196I GLU* 3.0 32.5 + - - +
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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