Contacts of the helix formed by residues 188 - 200 (chain C) in PDB entry 2X1L
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 PRO 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C ILE 4.0 0.7 - - - +
187C GLY* 1.3 88.1 - - - +
189C ASP* 1.3 67.4 + - - +
190C ALA* 4.6 4.0 - - + +
191C ARG* 3.0 38.6 + - + +
192C ARG 3.2 8.5 + - - -
290C PHE* 3.6 17.0 - - + -
291C ALA 3.5 19.3 - - - +
334C PHE 5.8 0.7 - - - +
335C GLY* 4.5 11.4 - - - +
603C 2HP 3.4 21.3 - - - +
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Residues in contact with ASP 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PRO* 1.3 71.7 - - - +
190C ALA* 1.3 63.1 + - - +
192C ARG* 2.8 56.4 + - - +
193C ASN* 3.0 23.2 + - - +
603C 2HP 2.8 34.2 + - - +
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PRO* 3.3 3.4 + - + +
189C ASP* 1.3 77.5 - - - +
191C ARG* 1.3 81.2 + - - +
193C ASN* 3.5 12.6 + - - +
194C GLU* 3.4 27.2 + - - +
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Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ILE* 4.1 2.5 - - + -
187C GLY 4.4 1.6 - - - +
188C PRO* 3.0 37.4 + - + +
190C ALA* 1.3 92.7 - - - +
192C ARG* 1.3 62.3 + - - +
194C GLU* 2.8 42.5 + - - +
195C ILE* 3.3 26.5 + - - +
264C LYS* 3.9 47.8 - - - +
267C ILE* 3.3 35.2 - - + -
291C ALA* 4.4 8.3 - - + -
335C GLY 4.2 10.7 + - - -
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Residues in contact with ARG 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C TYR* 4.3 11.9 + - + +
182C HIS 5.2 0.2 - - - -
183C PRO* 2.8 59.3 + - - +
186C ILE* 3.5 46.8 + - + +
188C PRO 3.2 5.3 + - - +
189C ASP* 2.8 47.7 + - - +
191C ARG* 1.3 75.0 - - - +
193C ASN* 1.3 67.9 + - - +
195C ILE* 3.3 2.6 + - - +
196C VAL* 3.0 38.2 + - + +
288C ARG* 5.8 0.2 - - - +
603C 2HP 5.0 0.6 + - - -
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Residues in contact with ASN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ASP* 3.0 22.7 + - - +
190C ALA* 3.7 11.9 - - - +
191C ARG 3.4 0.2 - - - -
192C ARG* 1.3 88.6 + - - +
194C GLU* 1.3 56.6 + - + +
196C VAL* 3.6 8.2 + - - +
197C SER* 3.0 29.1 + - - -
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Residues in contact with GLU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ALA* 3.4 12.9 + - - +
191C ARG* 2.8 50.9 + - - +
192C ARG 3.2 0.4 - - - -
193C ASN* 1.3 75.8 - - + +
195C ILE* 1.3 62.4 + - + +
197C SER* 3.4 7.2 + - - -
198C PHE* 3.0 27.8 + - - +
267C ILE* 5.8 2.1 - - - +
268C ARG* 5.5 1.2 + - - -
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Residues in contact with ILE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C TYR* 3.6 32.1 - - + +
186C ILE* 3.8 13.0 - - + -
191C ARG 3.3 14.3 + - - +
192C ARG 3.3 7.3 + - - +
194C GLU* 1.3 76.4 - - + +
196C VAL* 1.3 58.4 + - - +
198C PHE* 3.1 4.9 + - + +
199C VAL* 2.9 29.5 + - - +
267C ILE* 3.9 21.3 - - + -
268C ARG* 3.8 31.0 - - + +
271C THR* 3.4 27.1 - - - +
272C VAL* 3.9 9.2 - - + -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C LEU* 3.9 8.7 - - + +
179C TYR* 3.8 36.8 - - + -
192C ARG* 3.0 29.0 + - + +
193C ASN* 3.8 8.1 - - - +
195C ILE* 1.3 74.5 - - - +
197C SER* 1.3 56.5 + - - +
199C VAL 3.9 0.2 - - - -
200C SER* 2.7 45.8 + - - +
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Residues in contact with SER 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASN 3.0 18.0 + - - -
194C GLU* 3.6 8.1 - - - -
196C VAL* 1.3 77.4 - - - +
198C PHE* 1.3 61.7 + - - +
200C SER* 3.8 6.2 + - - -
201C GLY* 3.7 12.3 + - - -
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLU 3.0 17.0 + - - +
195C ILE* 3.1 6.9 + - - +
197C SER* 1.3 74.2 - - - +
199C VAL* 1.3 75.1 + - + +
201C GLY* 3.4 12.6 + - - -
202C GLY 4.2 7.8 + - - +
203C LEU* 3.7 25.5 - - + +
268C ARG* 3.5 60.3 - - + +
272C VAL* 4.3 14.1 - - + -
273C TYR* 5.4 9.2 - + - -
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Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C THR* 3.4 42.3 - - + +
175C LEU* 4.4 6.7 - - + -
176C LEU* 3.8 17.7 - - + -
179C TYR* 3.7 24.0 - - + +
195C ILE 2.9 19.5 + - - +
198C PHE* 1.3 78.9 - - + +
200C SER* 1.3 60.7 + - - +
202C GLY* 3.1 17.3 + - - -
203C LEU* 3.9 15.9 - - + -
272C VAL* 3.8 23.8 - - + -
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Residues in contact with SER 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C THR* 5.8 0.2 - - - -
176C LEU* 3.6 22.7 - - - +
196C VAL* 2.7 29.6 + - - +
197C SER* 4.0 8.0 - - - -
198C PHE 3.3 0.4 - - - -
199C VAL* 1.3 75.9 - - - +
201C GLY* 1.3 58.5 - - - +
202C GLY 3.2 2.2 + - - -
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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