Contacts of the helix formed by residues 280 - 292 (chain A) in PDB entry 2XRG
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 PRO 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.3 11.2 - - + -
100A TRP* 4.5 16.8 - - + -
278A SER 3.4 9.4 - - - +
279A ILE* 1.4 88.5 - - + +
281A HIS* 1.4 64.4 + - - +
282A GLU* 3.3 14.4 - - - +
283A ARG* 3.4 21.5 + - + +
284A ARG* 3.2 22.6 + - - +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE 4.0 0.2 + - - -
280A PRO* 1.4 73.4 - - - +
282A GLU* 1.4 69.6 + - - +
284A ARG* 3.3 29.5 + - - +
285A ILE* 3.3 28.1 + - - +
305A PHE* 3.6 22.4 - + + -
306A TYR 4.0 1.6 - - - -
307A SER* 4.0 17.1 + - - -
308A GLU* 3.2 26.7 + - - -
309A GLN* 5.8 7.6 - - + -
331A ILE* 6.5 0.4 - - + -
334A THR* 4.5 14.5 + - + +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TRP* 3.6 51.2 + - + -
280A PRO* 3.3 9.0 - - - +
281A HIS* 1.4 87.2 + - - +
283A ARG* 1.4 58.4 + - - +
285A ILE* 3.4 8.1 + - - +
286A LEU* 3.0 34.3 + - + +
334A THR* 5.8 0.8 + - - -
337A GLN* 4.1 30.4 + - - +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.6 13.5 - - + -
92A LEU 5.4 1.4 + - - -
93A CYS 3.0 27.7 + - - -
94A LEU* 4.8 7.4 - - + +
95A LYS* 3.9 22.4 - - - +
100A TRP* 3.8 23.0 - - + -
116A ALA 4.7 14.8 + - - -
279A ILE* 4.2 13.7 - - + -
280A PRO* 3.4 28.0 + - + +
282A GLU* 1.4 74.9 - - - +
284A ARG* 1.4 55.0 + - - +
286A LEU* 3.6 37.7 - - - +
287A THR* 2.6 42.9 + - - +
290A GLN* 4.2 15.1 + - - +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TRP* 3.7 57.3 + - + +
276A SER 3.3 18.4 + - - -
277A VAL* 4.2 6.7 + - - +
279A ILE* 3.1 28.4 + - + +
280A PRO 3.2 10.8 + - - +
281A HIS* 3.3 29.7 + - - +
282A GLU 3.3 0.2 - - - -
283A ARG* 1.4 74.8 - - - +
285A ILE* 1.4 62.6 + - - +
287A THR* 3.5 3.1 + - - -
288A ILE* 3.3 31.2 + - - +
305A PHE* 3.7 23.6 - - + -
306A TYR* 3.1 26.9 + - - +
308A GLU* 3.8 19.8 + - - -
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR* 6.3 0.7 - - - -
168A PHE* 4.2 10.5 - - + -
281A HIS 3.3 15.8 + - - +
282A GLU* 3.4 8.7 + - - +
284A ARG* 1.4 73.7 - - - +
286A LEU* 1.4 62.4 + - + +
288A ILE* 3.5 9.0 + - + +
289A LEU* 3.3 35.5 + - + +
305A PHE* 3.7 27.4 - - + -
334A THR* 3.9 23.3 - - + +
337A GLN* 4.4 11.2 - - + +
338A LEU* 3.9 47.0 - - + +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.8 28.0 - - + -
116A ALA 5.6 0.9 - - - +
117A CYS* 4.5 16.8 - - + -
128A ASP* 5.6 4.3 - - - +
129A CYS 4.1 19.5 - - - +
130A CYS* 5.3 2.5 - - - -
131A THR* 5.4 4.9 - - - +
282A GLU* 3.0 23.7 + - + +
283A ARG* 3.6 25.6 - - - +
284A ARG 3.3 0.2 - - - -
285A ILE* 1.4 74.6 - - + +
287A THR* 1.4 58.1 + - - +
289A LEU* 3.4 13.2 + - + +
290A GLN* 3.0 44.5 + - + +
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.8 40.3 - - + -
275A TRP* 4.2 10.4 - - + -
279A ILE* 5.8 0.2 - - - +
283A ARG* 2.6 24.9 + - - +
284A ARG* 3.8 5.3 - - - -
285A ILE 3.4 0.4 - - - -
286A LEU* 1.4 71.7 - - - +
288A ILE* 1.4 61.1 + - - +
290A GLN* 3.3 13.8 + - + +
291A TRP* 3.0 64.7 + - + +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 4.1 26.9 - - + -
275A TRP* 4.4 13.7 - - + -
284A ARG 3.3 20.5 + - - +
285A ILE* 3.9 13.2 - - + +
286A LEU 3.4 0.2 - - - -
287A THR* 1.4 74.8 - - - +
289A LEU* 1.3 61.4 + - + +
291A TRP* 3.2 16.6 + - + +
292A LEU* 3.2 28.9 + - + +
303A TYR* 4.0 30.0 - - + -
304A ALA 4.2 20.4 - - - +
305A PHE* 4.5 16.8 - - + -
338A LEU* 5.0 9.0 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY* 4.8 4.2 - - - +
131A THR* 5.9 3.6 - - - +
166A ILE* 6.5 0.2 - - + -
285A ILE* 3.3 36.3 + - + +
286A LEU* 3.9 13.7 - - + +
287A THR 3.4 0.2 - - - -
288A ILE* 1.3 76.6 - - + +
290A GLN* 1.3 59.9 + - + +
292A LEU* 3.7 14.7 + - + +
293A SER* 3.8 10.9 + - - -
337A GLN 4.8 3.1 - - - +
338A LEU* 4.5 13.2 - - + +
341A GLY* 3.9 32.1 - - - -
342A LEU* 4.1 15.7 - - + +
345A LEU* 3.8 35.6 - - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 6.1 2.9 - - - -
127A GLY 3.4 21.5 - - - +
128A ASP* 5.0 12.3 - - + +
283A ARG* 4.2 15.7 + - - +
286A LEU* 3.0 39.0 + - + +
287A THR* 3.5 12.6 + - + +
288A ILE 3.2 0.2 - - - -
289A LEU* 1.3 73.9 - - + +
291A TRP* 1.4 66.0 + - + +
292A LEU 3.3 0.4 - - - -
293A SER* 2.7 23.9 + - - +
294A LEU* 3.8 9.5 + - - +
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A CYS 5.4 0.6 + - - -
63A PHE* 3.3 32.5 + - + +
64A GLU 5.6 0.4 - - - -
65A LEU* 4.5 24.7 - - + +
77A ASN* 3.9 9.6 - - - -
271A GLY* 5.2 2.2 - - - -
272A THR* 3.7 31.2 - - - -
275A TRP* 4.2 17.7 - + - -
287A THR* 3.0 41.6 + - + +
288A ILE* 3.2 13.0 + - + +
290A GLN* 1.4 77.4 - - + +
292A LEU* 1.3 61.2 + - - +
294A LEU* 3.4 40.5 - - + +
299A ARG* 3.5 13.9 - - - +
300A PRO* 4.5 4.7 - - + -
303A TYR* 3.8 33.9 - + + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 4.8 6.2 - - + -
164A PRO* 4.1 17.3 - - + -
166A ILE* 4.4 12.8 - - + -
288A ILE* 3.2 36.9 + - + +
289A LEU* 3.9 22.4 - - + +
290A GLN 3.3 0.6 - - - -
291A TRP* 1.3 75.0 - - - +
293A SER* 1.3 57.1 + - - +
294A LEU 3.4 0.4 - - - +
299A ARG* 3.3 27.3 + - - +
303A TYR* 3.6 27.4 - - + +
342A LEU* 4.6 5.6 - - + -
345A LEU* 5.1 5.8 - - + -
347A LEU* 3.9 31.7 - - + +
351A VAL* 4.9 2.0 - - + -
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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