Contacts of the strand formed by residues 251 - 259 (chain C) in PDB entry 3PII
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 ILE 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C VAL* 3.3 8.1 - - + +
233C ALA* 4.2 5.2 - - - -
234C ALA* 3.9 16.4 - - + +
247C ALA 3.5 17.3 - - - +
248C TYR* 3.7 13.3 - - - +
249C ASN 4.0 6.8 - - - +
250C SER* 1.3 83.0 + - - +
252C ARG* 1.3 78.1 + - - +
255C GLY* 3.6 22.7 - - - +
256C ALA 3.4 14.1 - - - +
257C CYS* 3.4 40.4 - - + -
279C ILE* 4.2 16.1 - - + +
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Residues in contact with ARG 252 (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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96B ASP* 3.2 35.0 + - - +
97B TYR* 3.3 24.5 - - - +
167C TRP* 5.4 2.2 - - - -
228C VAL 3.1 25.3 + - - -
229C GLY* 3.7 19.1 + - - +
230C GLY* 2.7 19.4 + - - +
231C VAL 2.7 23.6 + - - +
232C HIS* 3.6 42.7 + - - +
250C SER 3.7 1.0 + - - -
251C ILE* 1.3 82.7 - - - +
253C ARG* 1.3 72.2 + - - +
254C GLY 3.3 0.2 + - - -
255C GLY* 3.0 15.4 + - - -
279C ILE* 4.0 1.2 - - - +
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Residues in contact with ARG 253 (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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97B TYR* 3.0 50.2 + - + -
102B GLN* 4.6 2.8 + - - +
105B LEU* 3.1 41.5 + - + +
106B CYS 4.3 3.0 + - - -
107B GLU* 3.7 35.0 + - - +
109B GLN* 4.9 5.7 - - - +
252C ARG* 1.3 76.4 - - - +
254C GLY* 1.3 59.2 + - - +
255C GLY* 3.4 1.7 + - - -
276C LEU* 5.6 5.5 - - - +
277C ASN* 3.2 44.4 + - + +
279C ILE* 4.2 4.5 - - - -
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Residues in contact with GLY 254 (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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102B GLN* 4.1 17.2 - - - +
105B LEU* 4.1 5.4 - - - +
252C ARG 3.3 0.2 + - - -
253C ARG* 1.3 71.8 - - - +
255C GLY* 1.3 61.9 + - - +
277C ASN 3.1 13.4 + - - -
278C GLY 3.3 17.9 + - - -
279C ILE* 4.0 1.2 - - - +
280C LYS* 3.0 24.7 + - - -
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Residues in contact with GLY 255 (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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232C HIS* 3.2 17.5 - - - -
251C ILE* 3.6 8.2 - - - +
252C ARG* 3.0 19.6 + - - -
253C ARG 3.2 0.4 + - - -
254C GLY* 1.3 81.3 - - - +
256C ALA* 1.3 61.8 + - - -
279C ILE* 3.8 6.2 - - - +
280C LYS* 3.1 23.8 + - - +
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Residues in contact with ALA 256 (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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159C VAL 5.1 0.2 - - - +
160C THR* 4.0 31.2 - - - +
232C HIS 3.3 7.1 + - - -
233C ALA* 3.2 7.3 - - + +
234C ALA 3.1 23.4 + - - +
251C ILE* 3.4 5.8 - - - +
255C GLY* 1.3 75.2 - - - -
257C CYS* 1.3 61.4 + - - +
258C VAL* 4.0 3.1 - - + -
280C LYS* 3.5 19.3 - - + +
282C ILE* 4.5 12.1 - - + -
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Residues in contact with CYS 257 (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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234C ALA 3.8 2.7 - - - -
236C VAL* 4.3 4.0 - - - -
244C PHE* 4.7 11.7 - - + -
247C ALA* 4.2 19.1 - - - -
248C TYR* 4.3 6.7 - - + -
251C ILE* 3.4 23.1 - - + -
256C ALA* 1.3 73.8 - - - +
258C VAL* 1.3 62.0 + - - +
259C LEU* 3.7 23.2 - - - +
279C ILE* 5.1 2.7 - - + -
280C LYS 2.8 15.1 + - - +
281C ILE* 3.5 11.5 - - + -
282C ILE* 3.1 24.0 + - - +
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Residues in contact with VAL 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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156C ALA* 4.2 18.8 - - + +
159C VAL* 4.3 11.7 - - + -
160C THR* 3.9 39.5 - - + +
234C ALA 2.9 11.0 + - - +
235C VAL* 3.5 7.6 - - + +
236C VAL* 2.9 27.5 + - - +
256C ALA* 4.5 8.3 - - + -
257C CYS* 1.3 76.6 - - - +
259C LEU* 1.3 65.4 + - - +
260C VAL* 4.1 0.6 + - + -
282C ILE* 3.3 13.9 - - + +
284C SER* 4.1 24.2 - - - -
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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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269B ILE* 4.9 3.4 - - + -
271B ILE* 4.2 21.5 - - + -
274B THR* 4.9 9.2 - - + -
275B VAL* 3.2 24.6 - - + +
236C VAL* 4.1 11.9 - - + -
239C VAL* 4.2 19.1 - - + -
244C PHE* 4.1 22.7 - - + -
257C CYS* 3.7 31.4 - - + +
258C VAL* 1.3 78.3 - - - +
260C VAL* 1.3 61.3 + - - +
261C GLY 3.7 0.7 - - - -
281C ILE* 4.0 22.0 - - + -
282C ILE 2.9 10.6 + - - +
283C GLY* 4.8 0.2 - - - -
284C SER 3.3 17.0 + - - +
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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