Contacts of the strand formed by residues 277 - 284 (chain C) in PDB entry 3GXM
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 ARG 277 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C TRP* 2.9 24.4 + - + +
229C ALA* 3.0 12.1 - - + -
230C VAL* 2.7 33.5 + - - +
275C ASN 4.3 9.4 + - - +
276C VAL* 1.3 76.4 - - - +
278C LEU* 1.3 56.7 + - - +
279C LEU* 4.8 1.1 - - + -
306C HIS* 3.2 47.5 + - + +
501C SO4 3.0 40.4 + - - +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C VAL* 3.5 29.6 - - + +
232C ALA* 4.1 10.5 - - + +
260C ILE* 3.7 34.1 - - + -
264C LEU* 3.6 33.9 - - + -
265C GLY* 5.1 2.7 - - - +
268C LEU* 4.3 11.2 - - + -
276C VAL 3.8 1.9 + - - +
277C ARG* 1.3 74.3 - - - +
279C LEU* 1.3 68.3 + - - +
304C TYR* 3.6 25.2 + - + +
305C VAL* 3.7 5.6 - - + +
306C HIS* 2.8 32.5 + - - +
307C GLY 3.5 1.6 + - - -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LEU* 4.1 21.3 - - + -
228C TRP* 4.2 6.3 - - + -
229C ALA* 4.3 12.1 - - + -
230C VAL 2.9 15.7 + - - +
231C THR* 3.5 7.1 - - + -
232C ALA* 3.2 26.9 + - - +
278C LEU* 1.3 78.9 - - - +
280C MET* 1.3 61.0 + - - +
305C VAL* 5.0 0.2 - - - -
306C HIS* 4.3 9.2 - - + -
307C GLY* 3.3 31.4 - - - +
309C ALA* 4.1 27.4 - - + +
335C MET* 4.0 15.0 - - + -
337C PHE* 4.1 23.6 - - + -
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Residues in contact with MET 280 (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 ALA* 4.9 2.0 - - - -
256C GLN* 3.8 13.5 - - - +
260C ILE* 4.4 15.3 - - + -
278C LEU 4.3 0.2 + - - -
279C LEU* 1.3 75.1 - - - +
281C LEU* 1.3 83.6 + - + +
282C ASP* 2.9 3.7 + - - -
288C LEU* 5.4 0.4 - - + -
291C TRP* 3.8 16.8 - - + +
292C ALA* 3.8 24.0 - - + -
295C VAL* 3.8 28.7 - - + -
296C LEU* 4.0 17.0 - - - -
305C VAL* 3.7 11.2 - - + -
307C GLY 2.9 21.4 + - - +
308C ILE* 3.7 18.3 - - + -
309C ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ALA* 5.6 0.2 - - - +
233C GLU 3.5 3.1 - - - +
236C PRO* 3.0 29.5 - - - +
256C GLN* 3.1 21.8 + - - +
280C MET* 1.3 81.6 - - + +
282C ASP* 1.3 64.6 + - - +
283C ASP* 3.7 24.9 - - + +
284C GLN 3.8 13.0 - - - +
287C LEU* 3.8 12.1 - - + -
288C LEU* 3.8 32.8 - - + -
291C TRP* 3.5 39.0 - - + -
308C ILE* 4.1 6.7 - - + -
309C ALA 3.5 11.0 - - - +
310C VAL* 4.2 4.5 - - + -
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Residues in contact with ASP 282 (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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120C ARG* 2.8 23.3 + - - -
177C SER* 3.2 1.7 + - - -
231C THR* 2.7 39.0 + - + +
233C GLU 3.4 11.9 - - - +
234C ASN* 3.5 7.1 - - - -
235C GLU* 2.8 22.0 + - - -
280C MET 2.9 5.1 + - - -
281C LEU* 1.3 71.3 - - - +
283C ASP* 1.3 56.2 + - - +
309C ALA* 2.8 22.4 + - - -
311C HIS* 2.7 21.4 + - - -
339C SER* 2.5 30.4 + - - -
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Residues in contact with ASP 283 (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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235C GLU* 3.4 22.5 - - - +
236C PRO* 3.5 1.8 - - + +
237C SER* 2.6 47.2 + - - -
281C LEU* 3.3 28.0 - - + +
282C ASP* 1.3 78.8 - - - +
284C GLN* 1.3 96.1 + - - +
287C LEU* 3.5 6.0 - - - +
309C ALA 3.4 2.8 + - - -
310C VAL* 3.4 6.4 - - - -
311C HIS* 3.0 26.1 + - - -
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Residues in contact with GLN 284 (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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235C GLU* 3.1 27.9 + - - +
237C SER* 5.7 0.4 - - - +
281C LEU* 3.8 5.0 - - - +
283C ASP* 1.3 93.0 + - - +
285C ARG* 1.3 66.0 + - - +
286C LEU* 3.1 26.4 + - + -
287C LEU* 3.3 19.1 + - + +
311C HIS* 3.3 21.7 + - - +
313C TYR* 2.9 38.1 + - - +
314C LEU* 3.2 36.6 - - + +
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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
------------------------------------------------------------
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