Contacts of the helix formed by residues 193 - 211 (chain C) in PDB entry 2VK1
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 ASP 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B ASN* 4.5 1.9 - - - +
191C PRO 3.9 0.8 + - - -
192C ASN* 1.3 71.7 - - - +
194C ALA* 1.3 66.7 + - - +
195C GLU* 3.4 8.9 + - - +
196C SER* 2.9 42.0 + - - +
197C GLU* 3.0 22.3 + - - +
323C GLY 5.6 1.4 + - - -
324C VAL* 5.3 2.7 - - + +
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ASN 3.2 6.7 + - - +
193C ASP* 1.3 74.0 + - - +
195C GLU* 1.3 69.0 + - + +
197C GLU* 4.0 6.7 - - - +
198C LYS* 3.1 27.1 + - - +
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS* 4.2 37.4 + - + +
317B ARG* 4.8 8.5 + - - -
318B ASN* 3.4 21.9 + - - +
193C ASP* 3.4 7.5 + - - +
194C ALA* 1.3 79.7 - - + +
196C SER* 1.3 62.6 + - - +
198C LYS* 2.9 39.3 + - - +
199C GLU* 3.0 19.6 + - - +
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ASN* 3.4 31.3 + - - +
193C ASP* 2.9 26.5 + - - +
195C GLU* 1.3 75.6 - - - +
197C GLU* 1.3 62.7 + - - +
199C GLU* 3.3 3.6 + - - +
200C VAL* 3.0 26.9 + - - +
321C PHE* 4.5 3.6 - - - -
322C PRO 5.5 1.7 + - - -
324C VAL* 3.5 24.0 - - - -
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ASN* 2.9 41.9 + - + +
193C ASP 3.0 19.3 + - - +
194C ALA* 4.0 5.2 - - - +
196C SER* 1.3 76.6 - - - +
198C LYS* 1.3 59.6 + - - +
200C VAL* 3.2 2.3 + - - +
201C ILE* 2.9 40.7 + - + +
324C VAL* 4.2 10.3 - - + -
328C PHE* 3.3 18.5 - - - +
329C VAL* 4.2 9.0 - - + -
332C LYS* 2.7 40.5 + - - +
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Residues in contact with LYS 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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317B ARG* 5.9 1.0 - - - +
194C ALA* 3.1 17.9 + - - +
195C GLU* 2.9 42.7 + - - +
196C SER 3.3 0.2 - - - -
197C GLU* 1.3 75.8 + - - +
199C GLU* 1.3 58.9 + - - +
201C ILE* 3.4 7.8 + - - +
202C ASP* 2.9 53.6 + - - +
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Residues in contact with GLU 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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316B ILE 4.5 0.5 - - - +
317B ARG* 3.5 22.2 - - - +
318B ASN* 2.9 40.7 + - - +
319B ALA* 4.4 6.8 - - - +
195C GLU 3.0 13.8 + - - +
196C SER 3.3 8.0 + - - +
198C LYS* 1.3 78.5 - - - +
200C VAL* 1.3 60.8 + - - +
202C ASP* 3.9 5.6 - - - +
203C THR* 2.9 45.1 + - + +
321C PHE* 3.8 23.4 - - + -
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Residues in contact with VAL 200 (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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196C SER 3.0 18.1 + - - +
197C GLU* 3.5 9.2 - - - +
199C GLU* 1.3 76.1 - - - +
201C ILE* 1.3 65.3 + - - +
203C THR* 3.3 1.7 + - - -
204C ILE* 3.0 47.3 + - + +
314C MET* 3.9 22.9 - - + -
316C ILE* 4.1 11.2 - - + -
321C PHE* 3.4 43.1 - - + -
324C VAL* 4.2 9.4 - - + -
329C VAL* 4.0 10.1 - - + -
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Residues in contact with ILE 201 (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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197C GLU* 2.9 38.7 + - + +
198C LYS* 3.9 6.1 - - - +
200C VAL* 1.3 76.0 - - - +
202C ASP* 1.3 66.4 + - - +
204C ILE* 3.2 3.9 + - - +
205C LEU* 2.9 44.1 + - + +
329C VAL* 4.1 25.6 - - + +
332C LYS* 3.6 36.3 - - + +
333C LEU* 3.9 19.9 - - + +
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Residues in contact with ASP 202 (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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198C LYS* 2.9 43.8 + - - +
199C GLU* 3.9 5.9 + - - +
201C ILE* 1.3 77.6 - - - +
203C THR* 1.3 54.0 + - + +
205C LEU* 3.4 10.7 + - - +
206C VAL* 2.5 39.6 + - + +
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Residues in contact with THR 203 (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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199C GLU* 2.9 40.4 + - + +
200C VAL 3.7 3.1 - - - -
202C ASP* 1.3 79.1 - - + +
204C ILE* 1.3 61.6 + - - +
206C VAL* 3.4 9.9 + - - +
207C LEU* 3.1 25.7 + - - +
316C ILE* 3.7 28.5 - - + +
317C ARG* 4.3 11.3 + - - +
321C PHE* 5.6 2.2 - - + -
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Residues in contact with ILE 204 (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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200C VAL* 3.0 36.3 + - + +
201C ILE* 3.6 3.8 - - - +
203C THR* 1.3 71.8 - - - +
205C LEU* 1.3 66.5 + - - +
207C LEU* 3.1 10.9 + - + +
208C ASP* 2.9 32.0 + - - +
281C LEU* 6.4 0.2 - - + -
283C LEU* 4.7 15.5 - - + -
307C VAL* 3.8 31.6 - - + -
309C PHE* 4.0 12.1 - - + -
314C MET* 3.8 8.5 - - + -
316C ILE* 4.0 8.5 - - + -
329C VAL* 4.1 6.5 - - + -
333C LEU* 3.8 24.0 - - + -
337C ILE* 5.0 2.2 - - + -
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Residues in contact with LEU 205 (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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201C ILE* 2.9 36.9 + - + +
202C ASP* 3.7 12.6 - - - +
204C ILE* 1.3 75.0 - - - +
206C VAL* 1.3 57.3 + - - +
208C ASP* 3.0 22.4 - - - +
209C LYS* 3.0 27.4 + - - +
333C LEU* 3.8 20.2 - - + +
336C ALA* 4.0 29.6 - - + +
337C ILE* 4.1 12.1 - - + +
340C ALA* 3.8 22.5 - - + +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ASP* 2.5 35.8 + - + +
203C THR* 3.5 11.2 - - - +
205C LEU* 1.3 74.8 - - + +
207C LEU* 1.3 66.8 + - + +
209C LYS* 3.4 22.6 + - + +
210C ASP* 3.4 14.8 + - + +
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Residues in contact with LEU 207 (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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203C THR* 3.1 18.6 + - - +
204C ILE* 3.1 10.0 + - - +
206C VAL* 1.3 77.7 - - + +
208C ASP* 1.3 64.2 - - - +
210C ASP* 3.3 8.0 + - + +
211C ALA* 3.2 22.9 + - - +
281C LEU* 3.8 15.4 - - + +
283C LEU* 6.4 0.2 - - + -
305C ASN* 3.3 32.1 + - - +
307C VAL* 3.9 17.7 - - + -
316C ILE* 3.7 17.5 - - + -
317C ARG* 3.4 30.1 - - - +
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Residues in contact with ASP 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ILE* 2.9 19.7 + - - +
205C LEU* 3.0 14.6 - - - +
207C LEU* 1.3 74.9 - - - +
209C LYS* 1.3 67.4 + - - +
210C ASP 3.1 0.5 + - - -
211C ALA* 3.4 14.6 + - - +
240C PHE* 3.6 32.1 - - - -
281C LEU* 4.0 15.5 - - - +
283C LEU* 4.5 4.7 - - - +
337C ILE* 4.0 23.8 - - - +
340C ALA* 4.0 16.5 - - + +
341C ALA* 4.1 6.2 - - - +
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Residues in contact with LYS 209 (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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205C LEU* 3.0 24.4 + - - +
206C VAL* 3.7 15.7 - - + +
208C ASP* 1.3 80.6 - - - +
210C ASP* 1.3 59.8 + - + +
211C ALA 3.8 2.4 + - - +
212C LYS* 5.6 1.0 + - - +
336C ALA* 5.2 1.6 + - - +
339C ASP* 3.9 15.0 + - - -
340C ALA* 3.4 42.5 - - - +
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Residues in contact with ASP 210 (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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206C VAL* 3.4 13.4 + - + +
207C LEU* 3.3 7.4 + - + +
208C ASP 3.0 0.6 - - - -
209C LYS* 1.3 79.7 - - + +
211C ALA* 1.3 58.7 + - - +
212C LYS* 2.9 38.4 + - - +
280C ASP* 4.5 0.9 - - - +
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Residues in contact with ALA 211 (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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207C LEU 3.2 14.2 + - - +
208C ASP 3.4 10.0 + - - +
209C LYS 4.6 2.3 - - - +
210C ASP* 1.3 78.1 - - - +
212C LYS* 1.3 64.3 + - - +
214C PRO* 3.8 21.0 - - + +
240C PHE* 6.0 0.3 - - - -
280C ASP* 3.6 18.8 - - - +
281C LEU* 3.8 22.9 - - + -
305C ASN* 5.5 0.9 - - - +
344C TYR* 4.6 10.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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