Contacts of the helix formed by residues 183 - 199 (chain C) in PDB entry 6XAV
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 GLY 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C LYS* 3.5 3.0 - - - +
182C ALA* 1.3 80.5 - - - +
184C LYS* 1.3 67.1 + - - +
185C THR* 3.2 3.6 - - - -
186C MET* 3.6 10.5 + - - +
187C LEU* 3.2 22.3 + - - +
345C LEU* 5.4 3.1 - - - +
355C PHE* 4.6 11.5 - - - -
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Residues in contact with LYS 184 (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 ILE* 5.7 3.4 - - + -
178C ALA* 3.7 30.7 - - + +
179C PRO 4.1 12.1 + - - -
180C PRO* 4.7 6.9 - - - +
181C LYS 4.9 3.8 - - - +
182C ALA* 4.9 2.3 - - + +
183C GLY* 1.3 78.0 - - - +
185C THR* 1.3 60.5 + - - +
187C LEU* 3.8 9.6 - - + +
188C LEU* 2.9 31.5 + - - +
265C ASP* 5.9 2.8 - - - -
318C THR* 4.4 29.3 - - + +
319C ALA 4.8 1.3 - - - +
320C LEU* 3.7 31.1 - - + +
345C LEU* 4.9 4.0 - - + -
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Residues in contact with THR 185 (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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366B ARG* 5.5 3.5 + - - -
367B LYS* 6.1 2.9 - - - -
183C GLY* 3.2 1.7 - - - -
184C LYS* 1.3 78.0 - - - +
186C MET* 1.3 68.3 + - - +
188C LEU* 3.3 4.3 + - - +
189C GLN* 3.0 51.1 + - + +
215C GLU* 4.4 23.0 + - + -
218C GLU* 5.1 8.7 - - - +
219C MET* 5.1 6.0 - - + +
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Residues in contact with MET 186 (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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367B LYS* 3.1 33.7 - - - +
183C GLY* 3.6 10.6 + - - +
184C LYS 3.5 0.2 - - - -
185C THR* 1.3 81.7 - - - +
187C LEU* 1.3 61.9 + - - +
189C GLN* 4.0 21.4 - - + +
190C ASN* 3.1 23.7 + - - +
218C GLU* 5.6 1.3 - - - +
355C PHE* 6.2 5.6 - - + -
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Residues in contact with LEU 187 (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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158C THR* 5.3 13.6 - - + +
162C LEU* 5.5 3.4 - - + -
176C ILE* 4.5 21.1 - - + -
183C GLY 3.2 18.0 + - - +
184C LYS* 3.8 8.5 - - + +
185C THR 3.2 0.6 - - - -
186C MET* 1.3 77.9 - - - +
188C LEU* 1.3 66.4 + - + +
190C ASN* 3.4 5.9 + - - +
191C ILE* 3.2 49.6 + - + +
318C THR* 6.0 2.7 - - + -
343C LEU* 5.0 9.9 - - + -
345C LEU* 4.3 30.5 - - + -
356C PRO* 5.4 4.0 - - + -
358C ILE* 4.6 16.4 - - + -
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Residues in contact with LEU 188 (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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184C LYS 2.9 19.4 + - - +
185C THR* 3.9 3.8 - - - +
187C LEU* 1.3 78.9 - - + +
189C GLN* 1.3 60.9 + - - +
191C ILE* 3.3 10.8 + - + +
192C ALA* 2.9 25.4 + - + +
206C VAL* 4.1 15.0 - - + -
219C MET* 3.9 24.2 - - + -
263C LEU* 3.8 36.8 - - + -
265C ASP* 3.3 38.6 - - - +
316C ILE* 5.7 3.8 - - + +
318C THR* 5.4 5.8 - - + -
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Residues in contact with GLN 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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185C THR* 3.0 38.0 + - - +
186C MET* 4.0 22.8 - - + +
188C LEU* 1.3 76.9 - - - +
190C ASN* 1.3 57.7 + - - +
192C ALA* 3.9 5.9 - - - +
193C GLN* 3.0 35.9 + - - +
215C GLU 5.9 0.2 + - - -
218C GLU* 3.6 32.2 + - - +
219C MET* 3.7 24.2 - - + +
222C LEU* 3.5 38.4 - - + +
223C VAL* 4.9 0.7 - - - -
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Residues in contact with ASN 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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149C ARG* 5.0 5.7 - - - +
155C GLU* 3.1 37.1 + - - +
158C THR* 4.1 16.2 - - + +
159C ALA* 4.0 19.6 + - - +
186C MET 3.1 19.1 + - - +
187C LEU* 3.7 7.0 - - - +
188C LEU 3.2 0.2 - - - -
189C GLN* 1.3 78.3 - - - +
191C ILE* 1.3 57.4 + - - +
193C GLN* 3.9 8.4 + - - +
194C SER* 2.7 46.0 + - - -
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Residues in contact with ILE 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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147C MET* 3.8 23.6 - - + -
162C LEU* 3.8 31.0 - - + -
168C ILE* 5.3 10.3 - - + -
176C ILE* 5.8 6.7 - - + -
187C LEU* 3.2 33.9 + - + +
188C LEU* 3.3 13.7 + - + +
190C ASN* 1.3 79.5 - - - +
192C ALA* 1.3 58.9 + - - +
194C SER* 3.2 1.6 + - - -
195C ILE* 2.9 49.4 + - + +
263C LEU* 4.4 13.0 - - + -
316C ILE* 5.8 5.8 - - + -
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Residues in contact with ALA 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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188C LEU* 2.9 19.8 + - + +
189C GLN* 3.9 1.3 - - - +
191C ILE* 1.3 76.1 - - - +
193C GLN* 1.3 63.4 + - - +
195C ILE* 4.6 0.7 - - - +
196C ALA* 3.2 20.4 + - - +
204C LEU* 3.3 20.6 - - + +
206C VAL* 4.7 7.0 - - + -
223C VAL* 3.7 28.1 - - + +
263C LEU* 3.8 21.7 - - + +
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Residues in contact with GLN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ARG* 3.3 19.1 + - - +
155C GLU* 6.0 2.6 - - - +
189C GLN* 3.0 23.5 + - - +
190C ASN* 4.0 5.7 + - - +
192C ALA* 1.3 75.7 - - - +
194C SER* 1.3 63.2 + - - +
196C ALA* 3.6 4.5 + - - +
197C TYR* 3.1 25.8 + - - +
222C LEU* 3.3 45.8 + - + +
223C VAL* 4.6 8.3 - - + +
224C LYS 6.3 0.4 - - - +
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C MET* 3.7 33.8 + - - -
149C ARG* 3.2 26.0 + - - +
159C ALA* 4.4 4.4 - - - +
190C ASN* 2.7 31.5 + - - -
191C ILE* 3.2 4.2 + - - -
193C GLN* 1.3 76.0 - - - +
195C ILE* 1.3 60.2 + - - +
198C ASN* 2.8 36.5 + - - +
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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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145C LEU* 6.2 0.7 - - + -
147C MET* 3.7 20.6 - - + -
191C ILE* 2.9 35.2 + - + +
192C ALA 4.0 3.6 - - - +
194C SER* 1.3 76.6 - - - +
196C ALA* 1.3 58.1 + - - +
199C HIS* 2.8 53.6 + - + +
202C CYS* 4.9 3.6 - - + +
204C LEU* 4.1 25.8 - - + -
261C ILE* 3.8 46.4 - - + -
263C LEU* 4.4 4.3 - - + -
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Residues in contact with ALA 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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192C ALA 3.2 15.5 + - - +
193C GLN* 4.1 4.7 - - - +
195C ILE* 1.3 81.4 - - - +
197C TYR* 1.3 58.6 + - - +
199C HIS 4.4 2.9 - - - -
200C PRO* 3.7 22.0 - - - +
204C LEU* 4.4 7.9 - - + -
224C LYS* 4.0 32.5 - - + +
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Residues in contact with TYR 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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149C ARG* 3.8 37.2 - - - +
151C ASN* 4.4 23.0 + - + +
193C GLN 3.1 19.0 + - - +
194C SER 4.0 0.2 - - - +
196C ALA* 1.3 79.4 - - - +
198C ASN* 1.3 82.3 + - - +
200C PRO* 4.1 6.8 - - - +
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Residues in contact with ASN 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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146C ARG* 3.0 26.4 + - - +
147C MET* 3.3 7.5 + - - -
148C GLU 2.7 35.6 + - - -
149C ARG* 3.5 10.5 - - - +
194C SER 2.8 23.6 + - - +
197C TYR* 1.3 93.7 - - - +
199C HIS* 1.3 72.5 + - + +
200C PRO* 3.5 6.5 - - - +
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Residues in contact with HIS 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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144C ARG 4.1 5.4 - - - -
145C LEU* 3.4 39.8 - - + +
146C ARG* 3.3 33.1 + - + +
147C MET* 5.3 4.3 - - - -
170C ARG* 4.8 6.0 + - - -
195C ILE* 2.8 36.3 + - + +
196C ALA* 4.4 0.7 - - - -
198C ASN* 1.3 89.3 + - + +
200C PRO* 1.3 64.6 - - - +
201C ASP* 3.2 16.1 + - - +
202C CYS* 3.5 24.8 + - + +
261C ILE* 6.0 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