Contacts of the helix formed by residues 257 - 267 (chain C) in PDB entry 6ACQ
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 HIS 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ASN* 2.8 25.1 + - - +
199C VAL* 3.7 20.9 - - + -
200C GLY* 3.5 24.5 + - - -
203C ALA* 3.3 27.1 - - + +
204C GLU* 5.7 3.0 + - - +
255C ARG* 3.6 2.3 + - - -
256C PRO* 1.3 76.3 - - - +
258C THR* 1.3 81.9 + - + +
259C LEU* 3.1 17.8 + - + +
260C LEU* 3.4 5.0 + - + +
261C LYS* 3.3 21.1 + - - +
204F GLU* 4.1 19.7 + - - -
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Residues in contact with THR 258 (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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181A GLU 5.8 1.1 - - - +
182A ALA* 5.2 7.6 - - + -
183A PRO* 4.1 28.8 - - + +
248A GLU* 3.9 17.0 + - - +
249A THR* 4.4 9.1 - - - +
256C PRO 3.6 2.3 + - - -
257C HIS* 1.3 82.5 + - + +
259C LEU* 1.3 61.3 + - + +
261C LYS* 3.3 13.5 - - - +
262C LYS* 3.2 25.2 + - - +
204F GLU* 4.3 18.6 - - - +
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Residues in contact with LEU 259 (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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155A ILE* 4.4 3.8 - - + -
199C VAL* 3.8 12.3 - - + +
202C LEU* 3.9 27.8 - - + -
203C ALA* 4.0 22.9 - - + -
257C HIS* 3.1 17.3 + - + +
258C THR* 1.3 80.5 - - + +
260C LEU* 1.3 65.6 + - - +
262C LYS* 3.1 26.0 + - - +
263C TYR* 2.9 54.6 + - + +
277C PHE* 4.7 0.2 - - + -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 6.0 2.9 - - + -
196C ASN* 4.0 20.0 - - + +
199C VAL* 3.9 21.5 - - + +
235C LEU* 4.0 44.0 - - + +
238C CYS* 4.5 8.1 - - + -
239C LEU* 3.9 37.9 - - + +
242C MET* 4.6 4.7 - - + -
256C PRO* 4.5 3.6 - - + -
257C HIS* 3.4 11.0 + - + +
259C LEU* 1.3 77.9 - - - +
261C LYS* 1.3 64.9 + - - +
263C TYR* 3.2 6.8 + - - +
264C VAL* 3.1 23.1 + - + +
277C PHE* 4.8 7.4 - - + -
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Residues in contact with LYS 261 (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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247A SER 3.5 14.6 + - - -
248A GLU* 2.8 46.3 + - - +
249A THR 5.3 0.2 - - - -
250A GLY* 5.2 1.2 - - - +
239C LEU* 4.1 25.0 - - + +
243C ASP* 5.1 2.6 + - - -
256C PRO* 3.9 30.8 - - - +
257C HIS 3.3 8.6 + - - +
258C THR* 3.3 13.7 - - - +
260C LEU* 1.3 79.7 - - - +
262C LYS* 1.3 56.1 + - - +
264C VAL* 3.4 2.1 + - - +
265C ARG* 3.0 50.8 + - - +
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Residues in contact with LYS 262 (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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122A THR* 3.5 29.7 - - + +
153A ARG 4.7 2.4 + - - -
155A ILE* 3.9 26.1 - - + +
180A ALA* 4.4 10.5 - - - +
181A GLU* 2.9 51.8 + - + +
258C THR* 3.2 11.9 + - - +
259C LEU* 3.1 29.0 + - + +
261C LYS* 1.3 77.5 - - - +
263C TYR* 1.3 65.7 + - - +
265C ARG* 3.3 8.5 + - - +
266C ALA* 3.1 18.4 + - - +
206F ILE* 5.8 0.8 - - - +
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Residues in contact with TYR 263 (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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155A ILE* 3.7 15.4 - - + +
202C LEU* 4.5 7.3 - - - +
209C VAL* 5.9 1.7 - - - +
235C LEU* 4.1 14.8 - - + -
259C LEU* 2.9 49.8 + - + +
260C LEU* 3.6 8.3 - - - +
262C LYS* 1.3 74.7 - - - +
264C VAL* 1.3 63.8 + - - +
266C ALA* 3.1 15.0 + - - +
268C TRP* 3.2 47.1 + + + +
276C GLY 3.4 32.1 - - - -
277C PHE* 3.4 41.0 + + - -
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Residues in contact with VAL 264 (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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235C LEU* 3.6 39.3 - - + +
236C ASP* 3.8 13.0 - - + +
239C LEU* 3.9 26.0 - - + -
260C LEU* 3.1 17.4 + - + +
261C LYS 3.8 3.1 - - - +
263C TYR* 1.3 76.1 - - - +
265C ARG* 1.3 60.5 + - + +
267C GLY* 2.9 20.8 + - - -
269C LEU* 3.7 16.8 - - + +
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Residues in contact with ARG 265 (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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92A MET* 6.1 0.4 - - - +
120A SER* 3.8 23.5 + - - +
122A THR* 3.7 14.2 - - + +
123A GLU* 3.1 44.8 + - + +
126A SER* 2.7 29.8 + - - -
181A GLU* 4.8 4.2 + - - -
248A GLU* 2.8 40.6 + - - -
258C THR 5.7 0.2 + - - -
261C LYS* 3.0 41.3 + - - +
262C LYS* 3.5 8.2 - - - +
263C TYR 3.3 0.2 - - - -
264C VAL* 1.3 78.6 - - + +
266C ALA* 1.3 50.2 + - - +
267C GLY 3.2 0.2 - - - -
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Residues in contact with ALA 266 (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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122A THR* 3.6 7.4 - - + +
126A SER* 3.4 13.4 + - - -
155A ILE* 3.6 25.1 - - + -
156A ALA* 5.6 2.9 - - + -
262C LYS 3.1 11.4 + - - +
263C TYR 3.3 10.3 - - - +
264C VAL 3.1 0.6 - - - -
265C ARG* 1.3 78.2 - - - +
267C GLY* 1.3 58.6 + - - +
268C TRP* 3.5 27.0 + - + +
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Residues in contact with GLY 267 (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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126A SER* 4.9 0.7 - - - -
264C VAL 2.9 14.7 + - - -
265C ARG 3.2 0.8 + - - -
266C ALA* 1.3 78.7 - - - +
268C TRP* 1.3 63.8 + - - +
269C LEU* 3.1 21.0 + - - +
273C SER* 3.4 17.7 + - - -
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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
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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