Contacts of the strand formed by residues 266 - 271 (chain C) in PDB entry 4RPP
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 LYS 266 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ASP 3.3 6.5 + - - -
239C MET* 3.3 15.3 - - + +
240C VAL* 2.8 32.2 + - - +
264C ASN 3.7 4.3 + - - +
265C ILE* 1.3 74.2 - - - +
267C ILE* 1.3 57.4 + - - +
268C ILE* 5.0 2.0 - - + -
288C ASP* 3.7 29.8 - - + +
434C SER 4.9 5.1 + - - -
439C HIS* 4.4 16.4 - - - -
462C GLN* 3.3 36.3 + - - +
465C LEU* 4.1 20.4 - - + -
466C TYR* 4.8 14.7 - - + -
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Residues in contact with ILE 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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240C VAL* 3.7 7.2 - - + +
242C ALA* 4.6 7.6 - - + -
251C VAL* 4.1 20.9 - - + +
254C VAL* 3.8 17.3 - - + -
255C ARG* 3.6 63.3 - - + +
258C LEU* 3.7 24.7 - - + -
265C ILE 3.9 1.3 - - - +
266C LYS* 1.3 73.2 - - - +
268C ILE* 1.3 68.8 + - - +
269C SER* 4.6 3.1 - - - +
287C SER* 3.8 1.0 - - - -
288C ASP* 2.9 39.0 + - - +
289C GLY 3.3 4.2 + - - +
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Residues in contact with ILE 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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239C MET* 4.8 3.6 - - + -
240C VAL 2.8 10.9 + - - +
241C PHE* 3.4 27.3 - - + +
242C ALA 2.9 27.6 + - - -
266C LYS* 4.4 7.4 - - + +
267C ILE* 1.3 77.4 - - - +
269C SER* 1.3 61.0 + - - +
270C LYS* 3.5 0.9 + - - +
288C ASP 4.7 2.9 - - - +
289C GLY* 3.4 21.5 - - - +
290C ILE 3.5 31.9 - - - +
291C MET* 3.6 12.1 - - + +
323C PRO* 4.8 4.3 - - + +
325C ILE* 4.1 9.0 - - + -
465C LEU* 3.8 34.8 - - + -
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Residues in contact with SER 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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242C ALA* 3.9 4.5 - - - -
245C ILE* 3.7 14.2 - - - +
251C VAL* 3.4 17.5 - - - +
267C ILE* 4.0 2.8 + - - +
268C ILE* 1.3 70.1 - - - +
270C LYS* 1.3 62.9 + - - +
271C ILE* 3.4 3.0 + - - -
283C ILE* 3.7 19.3 - - - -
287C SER* 2.6 28.2 + - - -
289C GLY 3.0 7.9 + - - -
290C ILE* 3.6 13.1 - - - +
291C MET 3.0 18.2 + - - -
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Residues in contact with LYS 270 (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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73C ARG* 4.4 4.3 - - - +
113C ASP* 2.8 37.0 + - - +
114C THR 4.5 0.4 + - - -
241C PHE* 3.8 16.4 - - + +
242C ALA 2.8 19.9 + - - +
243C SER* 3.3 21.4 + - - +
245C ILE* 3.3 25.1 + - - +
268C ILE 4.4 0.4 - - - +
269C SER* 1.3 69.7 - - - +
271C ILE* 1.3 63.5 + - - +
272C GLU* 3.5 24.5 + - + +
291C MET* 3.5 37.2 - - + +
293C ALA* 4.8 10.5 - - + -
296C ASP* 5.6 3.0 + - - -
328C THR* 6.3 1.8 - - - -
360C MET* 6.3 0.2 - - - -
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Residues in contact with ILE 271 (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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245C ILE* 4.1 8.1 - - + +
269C SER 4.1 8.7 - - - +
270C LYS* 1.3 75.9 - - - +
272C GLU* 1.3 62.2 + - - +
273C ASN 4.1 2.2 - - - +
276C GLY* 3.8 24.9 - - - +
277C VAL* 3.8 7.0 - - + +
280C PHE* 4.0 14.1 - - + -
283C ILE* 4.0 40.6 - - + -
290C ILE* 4.2 4.7 - - + -
291C MET 3.2 6.9 + - - +
293C ALA* 3.7 10.6 + - - +
297C LEU* 3.2 19.3 - - + +
313C MET* 3.6 42.2 - - + -
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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