Contacts of the helix formed by residues 259 - 267 (chain L) in PDB entry 5PRC
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 TRP 259 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C PHE* 3.8 22.9 - + - -
164L TYR* 3.0 35.6 + + + +
166L ASN 3.7 15.7 - - - +
167L TRP* 4.0 8.9 - + - -
169L TYR* 3.8 2.7 - - - -
170L ASN* 3.4 41.9 - - + +
171L PRO* 3.6 23.6 - - + -
247L GLY* 6.0 0.2 - - - -
250L ALA* 4.4 11.0 - - + -
251L SER* 3.3 27.8 + - - -
255L TRP* 3.7 26.0 - + + -
257L ARG 3.7 0.2 + - - -
258L GLY* 1.3 69.6 - - - -
260L PRO* 1.3 73.5 - - - +
261L GLU 3.2 0.4 - - - -
262L TRP* 3.0 63.7 + + + +
263L TRP* 3.5 7.1 - - - -
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Residues in contact with PRO 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ALA 3.1 19.7 - - - +
182C TYR* 3.6 24.0 - - + +
183C SER 4.6 0.4 - - - +
234C MET* 4.0 11.7 - - + -
164L TYR 4.1 0.2 - - - +
165L LEU* 4.8 1.8 - - + -
166L ASN* 3.9 29.2 - - + +
169L TYR* 3.6 31.8 - - + -
258L GLY* 3.6 5.6 - - - -
259L TRP* 1.3 91.0 - - + +
261L GLU* 1.3 55.4 + - - +
263L TRP* 2.8 31.5 + - - +
264L GLY 4.1 0.3 + - - -
90M TRP* 5.1 0.2 - - - -
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Residues in contact with GLU 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C CYS* 5.0 0.9 - - - -
181C ALA* 3.8 6.5 + - + +
182C TYR* 3.6 39.3 + - + +
238C ASP* 4.2 15.1 - - - +
255L TRP* 4.1 7.8 - - + -
257L ARG* 3.7 39.3 + - + +
258L GLY* 3.6 14.1 + - - +
259L TRP 3.2 0.8 - - - -
260L PRO* 1.3 74.7 - - - +
262L TRP* 1.3 67.8 + - - +
264L GLY* 2.8 17.6 + - - -
265L TRP 4.4 0.2 + - - -
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Residues in contact with TRP 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C CYS* 3.0 43.2 + - + +
2C PHE* 3.7 17.6 - + - -
171L PRO* 3.6 21.1 - - + -
255L TRP* 3.4 28.9 - + + -
258L GLY 3.8 0.8 + - - -
259L TRP* 3.0 44.5 + + + +
261L GLU* 1.3 77.0 - - - +
263L TRP* 1.3 100.0 + + - +
264L GLY 2.9 6.8 + - - -
265L TRP* 3.0 56.7 + + - -
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Residues in contact with TRP 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L TYR* 2.7 25.1 + - + -
171L PRO* 3.8 10.3 - - + -
174L MET* 3.7 31.4 - - + -
259L TRP 3.5 15.7 - - - -
260L PRO* 2.8 13.0 + - + +
262L TRP* 1.3 102.1 - + - +
264L GLY* 1.3 54.3 + - - +
265L TRP* 3.1 26.9 - + - -
266L TRP* 2.7 36.4 + + + +
267L LEU* 3.1 10.5 + - - +
89M PHE* 4.2 18.8 - + - -
90M TRP* 3.9 22.1 - + + -
178M TRP* 3.9 23.6 - + - -
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Residues in contact with GLY 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C TYR* 3.8 23.8 - - - -
260L PRO 4.1 1.0 + - - -
261L GLU 2.8 16.1 + - - -
263L TRP* 1.3 77.6 - - - +
265L TRP* 1.3 56.9 + - - +
267L LEU* 4.0 5.2 - - - -
268L ASP* 2.7 42.5 + - - +
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Residues in contact with TRP 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C CYS* 3.6 27.9 - - + +
262L TRP* 3.0 68.8 + + - -
263L TRP* 3.7 23.7 - + - -
264L GLY* 1.3 74.8 - - - +
266L TRP* 1.3 92.3 + + + +
268L ASP 4.5 0.6 - - - -
269L ILE* 3.6 22.3 + - + +
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Residues in contact with TRP 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L TRP* 2.7 23.3 + + + +
265L TRP* 1.3 110.4 - + + +
267L LEU* 1.3 74.1 + - - +
268L ASP 2.9 3.1 + - - -
269L ILE* 3.1 14.0 + - + +
272L TRP* 3.1 50.6 + + - -
85M PHE* 3.7 36.3 - + - -
86M ARG* 2.7 26.8 + - + -
88M PHE* 6.3 0.4 - - + -
90M TRP* 4.3 13.8 - + - -
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Residues in contact with LEU 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C VAL* 4.2 26.2 - - + -
177C ALA* 4.7 8.3 - - + -
178C LYS* 5.0 1.1 - - + -
182C TYR* 4.0 25.4 - - + -
263L TRP 3.1 5.0 + - - +
264L GLY* 4.0 13.5 - - - -
266L TRP* 1.3 84.8 - - - +
268L ASP* 1.3 57.9 + - - +
272L TRP* 3.3 4.0 + - - -
86M ARG* 2.7 65.8 + - + +
87M GLN* 4.6 2.2 - - + -
90M TRP* 3.9 41.3 - - + -
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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