Contacts of the helix formed by residues 257 - 269 (chain C) in PDB entry 4GKH
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 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C PHE* 5.7 1.0 - - - +
226C TYR* 2.8 28.5 + - + +
255C ASN 3.2 4.6 + - - +
256C PRO* 1.3 69.8 - - - +
258C MSE 1.3 56.5 + - - +
259C ASN* 3.3 12.1 + - - +
260C LYS* 3.1 42.9 + - + +
261C LEU* 2.9 27.7 + - - +
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Residues in contact with MSE 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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164A SER* 4.3 28.0 - - - +
233C TRP* 4.7 13.7 - - + -
256C PRO* 3.2 24.1 + - - +
257C ASP* 1.3 72.8 + - - +
259C ASN* 1.3 57.4 + - - +
261C LEU* 3.6 29.5 - - + +
262C GLN* 2.8 31.8 + - - +
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Residues in contact with ASN 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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185C LEU* 3.2 52.2 + - - +
187C PRO 5.1 0.4 + - - -
188C PHE* 3.7 22.0 - - - +
257C ASP* 3.2 9.5 + - - +
258C MSE 1.3 76.0 - - - +
260C LYS* 1.3 61.0 + - - +
262C GLN* 3.4 5.2 + - - +
263C PHE* 2.9 28.9 + - - +
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Residues in contact with LYS 260 (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 PHE* 3.5 38.4 - - + -
189C SER* 3.3 18.0 + - - +
191C ASP* 3.8 11.3 - - - +
224C ASP* 2.8 28.2 + - - +
226C TYR* 3.8 32.9 - - + -
257C ASP* 3.1 33.8 + - - +
259C ASN* 1.3 76.6 - - - +
261C LEU* 1.3 65.8 + - - +
263C PHE* 3.4 4.4 + - - +
264C HIS* 2.8 34.1 + - - +
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Residues in contact with LEU 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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226C TYR* 4.0 8.2 - - + -
230C ALA* 3.6 33.7 - - + +
233C TRP* 3.8 50.3 - - + +
248C PHE* 3.8 26.7 - - + -
256C PRO* 5.6 0.2 - - + -
257C ASP 2.9 16.6 + - - +
258C MSE 3.6 28.0 - - + +
260C LYS* 1.3 76.9 - - - +
262C GLN* 1.3 64.0 + - - +
264C HIS* 3.3 2.8 + - - -
265C LEU* 3.0 30.9 + - + +
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Residues in contact with GLN 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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170C ARG* 4.7 9.7 - - - +
185C LEU* 3.9 21.9 - - + +
258C MSE 2.8 20.8 + - - +
259C ASN* 3.4 4.8 + - - +
261C LEU* 1.3 74.2 - - - +
263C PHE* 1.3 64.3 + - - +
265C LEU* 3.3 8.4 + - - +
266C MSE 2.9 55.7 + - + +
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Residues in contact with PHE 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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145C ARG* 4.0 25.6 - - + -
149C LEU* 4.1 22.2 - - + -
182C MSE 3.6 35.9 - - + -
185C LEU* 3.5 15.3 - - + +
186C LEU* 3.6 24.5 - - + -
188C PHE* 3.6 32.8 - + + -
259C ASN 2.9 17.9 + - - +
260C LYS 3.7 3.4 - - - +
261C LEU 3.3 0.2 - - - -
262C GLN* 1.3 77.0 - - - +
264C HIS* 1.3 71.1 + - - +
266C MSE 3.3 3.5 + - - +
267C LEU* 2.9 46.7 + - + +
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Residues in contact with HIS 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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145C ARG* 5.4 4.6 - - - +
188C PHE* 3.8 16.1 - + - -
223C ALA* 6.2 0.2 - - - +
224C ASP* 3.8 25.4 + - + +
226C TYR* 3.7 16.8 - - + +
227C GLN* 3.4 42.6 + - + +
230C ALA* 3.6 24.8 - - + +
231C ILE* 5.2 2.6 - - + +
260C LYS* 2.8 27.3 + - + +
263C PHE* 1.3 97.1 - + - +
265C LEU* 1.3 64.4 + - - +
267C LEU* 3.8 7.9 - - + +
268C ASP* 3.1 22.9 + - - +
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Residues in contact with LEU 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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167C ASP* 4.2 3.7 - - - +
169C GLU* 5.1 5.8 - - - +
170C ARG* 3.8 18.4 - - - +
230C ALA* 3.4 31.0 - - + +
231C ILE* 4.4 5.8 - - + +
233C TRP* 3.8 31.2 - - + -
234C ASN* 3.5 28.5 - - + +
261C LEU* 3.0 27.4 + - + +
262C GLN* 3.7 7.2 - - + +
264C HIS* 1.3 73.4 - - - +
266C MSE 1.3 66.5 + - - +
268C ASP* 3.3 13.8 + - + +
269C GLU* 3.3 16.8 + - - +
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Residues in contact with MSE 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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170C ARG* 3.5 25.6 - - - +
173C TRP* 4.3 11.9 - - + -
178C VAL* 3.6 25.8 - - + +
181C GLU* 3.7 15.9 - - + -
182C MSE 3.5 46.2 - - + +
185C LEU* 4.0 7.2 - - - -
262C GLN* 2.9 47.6 + - + +
263C PHE 3.7 3.1 - - - +
265C LEU* 1.3 76.5 - - - +
267C LEU* 1.3 64.8 + - - +
269C GLU* 3.1 27.3 + - - +
270C PHE* 3.4 9.4 - - - -
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Residues in contact with LEU 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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145C ARG* 5.2 4.5 - - + -
148C ARG* 3.8 35.9 - - + +
149C LEU* 4.1 18.4 - - + -
152C ALA* 4.0 10.8 - - + -
182C MSE 3.5 10.9 - - - -
227C GLN* 4.3 16.8 - - - +
263C PHE* 2.9 39.1 + - + +
264C HIS* 3.8 8.7 - - + +
265C LEU 3.3 0.2 - - - -
266C MSE 1.3 77.8 - - - +
268C ASP* 1.3 61.3 + - - +
270C PHE* 3.1 17.0 + - - -
271C PHE* 3.3 32.6 - - + -
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Residues in contact with ASP 268 (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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148C ARG* 5.0 2.5 + - - +
197C GLY 5.0 0.5 - - - +
198C ASP* 5.0 2.8 - - - +
219C ARG* 4.5 9.0 + - - -
227C GLN* 4.9 4.5 + - - +
231C ILE* 3.5 39.9 - - + +
264C HIS 3.1 16.6 + - - +
265C LEU* 3.3 8.3 + - + +
266C MSE 3.2 0.6 - - - -
267C LEU* 1.3 72.1 - - - +
269C GLU* 1.3 65.5 + - - +
270C PHE 3.0 3.7 + - - -
271C PHE* 3.1 33.0 + - - +
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Residues in contact with GLU 269 (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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161C VAL* 3.5 14.7 - - - +
162C ASP* 4.7 3.8 + - - +
165C ASP 3.9 5.0 - - - +
166C PHE* 3.4 40.5 - - + -
167C ASP* 2.8 36.4 + - - +
170C ARG* 2.6 35.1 + - - +
178C VAL* 4.4 6.7 - - + -
265C LEU 3.3 9.2 + - - +
266C MSE 3.1 18.1 + - - +
268C ASP* 1.3 78.9 - - - +
270C PHE* 1.3 60.9 + - + +
271C PHE* 3.3 4.1 + - - +
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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