Contacts of the strand formed by residues 254 - 264 (chain C) in PDB entry 3I5D
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 GLY 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C MET* 4.4 8.1 - - - +
253C GLY* 1.3 73.2 - - - -
255C VAL* 1.3 66.7 + - - +
281C ARG* 4.3 4.7 - - - -
283C ASP* 3.4 17.7 - - - -
295C TYR* 3.6 9.5 - - - +
319C GLY 3.1 5.5 + - - +
320C ILE* 3.1 9.9 - - - +
321C ARG 2.9 22.3 + - - -
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Residues in contact with VAL 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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66A SER* 5.1 3.8 - - - +
68A THR* 4.5 9.0 - - - +
254C GLY* 1.3 79.1 - - - +
256C MET* 1.3 59.2 + - - +
281C ARG* 3.7 2.7 - - - +
282C LEU* 2.8 59.2 + - + +
283C ASP* 2.9 27.9 + - + +
295C TYR* 3.5 30.5 - - + -
321C ARG* 3.2 31.2 - - + +
323C ASP* 5.3 2.5 - - - +
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Residues in contact with MET 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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238C ILE* 4.1 18.6 - - + +
239C VAL* 4.1 12.1 - - + -
242C ALA* 3.6 20.9 - - + -
249C MET* 4.0 20.0 - - - -
255C VAL* 1.3 73.2 - - - +
257C GLY* 1.3 62.6 + - - +
258C VAL* 3.7 1.3 + - + +
279C PHE* 4.4 2.2 - - + -
280C ARG 2.9 35.0 - - - +
281C ARG* 3.7 15.0 - - - -
282C LEU* 4.1 2.2 - - - -
320C ILE* 3.7 19.7 - - + +
321C ARG 2.9 6.2 + - - +
322C PHE* 3.5 29.4 - - + +
323C ASP* 2.9 27.7 + - - +
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Residues in contact with GLY 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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256C MET* 1.3 71.3 - - - +
258C VAL* 1.3 62.0 + - - +
259C GLN* 3.5 4.2 + - - +
279C PHE* 3.5 6.9 - - - +
280C ARG* 2.7 37.7 + - - +
282C LEU* 3.5 13.2 - - - +
323C ASP 3.6 1.8 - - - -
325C MET* 3.3 26.0 - - - -
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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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102C PHE* 5.9 0.7 - - + -
192C ILE* 4.3 21.3 - - + -
233C PHE* 5.6 1.3 - - + -
238C ILE* 4.2 23.1 - - + -
256C MET 4.5 1.8 - - - +
257C GLY* 1.3 72.8 - - - -
259C GLN* 1.3 60.9 + - - +
260C ILE* 3.6 14.8 + - + +
277C TYR* 5.2 6.1 - - + -
278C THR 3.8 4.9 - - - +
279C PHE* 4.2 22.4 - - + -
322C PHE* 4.3 21.3 - - + -
323C ASP 2.9 13.8 + - - +
324C VAL* 3.5 15.7 - - + +
325C MET 3.0 20.8 + - - -
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Residues in contact with GLN 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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257C GLY 3.5 1.8 + - - +
258C VAL* 1.3 72.2 - - - +
260C ILE* 1.3 61.6 + - - +
261C ARG* 4.1 0.4 - - + -
276C ARG 3.5 1.7 - - - +
277C TYR* 3.5 5.5 - - - +
278C THR* 2.9 61.1 + - - +
280C ARG* 2.9 45.2 + - - +
325C MET* 3.3 32.5 - - + +
327C PHE* 4.4 21.6 - - + -
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Residues in contact with ILE 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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192C ILE* 4.4 11.4 - - + -
194C ASN* 3.8 23.3 - - + +
207C ASN* 5.7 0.7 - - + +
258C VAL* 4.4 9.6 - - + +
259C GLN* 1.3 75.5 - - - +
261C ARG* 1.3 60.7 + - - +
262C TRP* 3.3 28.5 - - + +
275C PRO* 3.9 19.7 - - + -
276C ARG 3.8 2.5 - - - +
277C TYR* 3.8 29.4 - - + -
324C VAL* 4.1 13.9 - - + -
325C MET 2.9 8.6 + - - +
326C VAL* 3.4 18.7 - - + +
327C PHE* 3.1 29.8 + - - +
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Residues in contact with ARG 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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199A PRO* 5.7 1.6 - - - -
259C GLN 5.7 0.2 - - - -
260C ILE* 1.3 74.2 - - - +
262C TRP* 1.3 62.5 + - - +
263C ASP* 2.7 41.5 + - - +
274C VAL 3.9 1.9 - - - +
275C PRO* 3.6 2.1 - - - +
276C ARG* 2.9 61.6 + - - +
278C THR* 5.0 7.8 + - - +
327C PHE* 3.2 43.3 - - + -
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Residues in contact with TRP 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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63C VAL* 4.1 9.0 - - + -
194C ASN* 3.0 35.3 + - - -
196C ILE* 3.5 41.0 - - + +
198C TYR* 2.7 32.6 + - + +
205C LYS* 4.5 10.8 - - + -
206C ARG* 3.8 6.7 - - - -
207C ASN* 3.7 20.0 - - + -
260C ILE* 3.3 11.7 - - + +
261C ARG* 1.3 69.6 - - - +
263C ASP* 1.3 60.3 + - - +
264C CYS* 3.8 2.0 - - - -
273C CYS* 4.1 21.8 - - - -
274C VAL* 4.2 5.2 - - - -
275C PRO* 3.2 46.9 - - + -
326C VAL* 3.7 21.1 - - + -
327C PHE 2.9 10.2 + - - -
328C GLY* 3.2 0.9 - - - -
329C GLN 3.1 15.4 + - - -
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Residues in contact with ASP 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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261C ARG* 2.7 46.5 + - - +
262C TRP* 1.3 77.5 - - - +
264C CYS* 1.3 63.9 + - - +
272C TRP 5.7 0.5 - - - +
274C VAL 4.6 6.1 + - - +
327C PHE* 5.4 0.7 - - - -
328C GLY* 3.6 6.1 - - - -
329C GLN* 3.3 21.6 + - - +
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Residues in contact with CYS 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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58C GLN* 5.4 0.9 - - - +
198C TYR* 4.5 11.9 - - + +
203C PHE* 5.1 3.4 - - + -
262C TRP* 3.8 4.0 - - - -
263C ASP* 1.3 81.9 - - - +
265C ASP* 1.3 63.7 + - - +
266C LEU* 3.7 1.6 - - - -
272C TRP 5.8 0.9 - - - -
273C CYS* 2.0 62.6 - - + +
274C VAL 4.0 3.6 - - - -
329C GLN 3.3 6.8 + - - +
330C ALA* 3.2 34.7 - - + +
331C GLY 3.8 0.9 + - - -
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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