Contacts of the helix formed by residues 280 - 305 (chain A) in PDB entry 5CTR
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 SER 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 1.3 77.1 - - - +
281A VAL* 1.3 67.4 + - - +
282A ILE 3.5 1.8 - - - -
283A GLN* 3.5 16.1 + - - +
284A ASN* 3.4 12.1 + - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 3.2 10.5 + - - +
280A SER* 1.3 71.1 - - - +
282A ILE* 1.3 90.4 + - + +
284A ASN* 2.1 41.0 + - - -
285A TYR* 2.6 16.4 + - + -
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 3.5 0.8 - - - -
281A VAL* 1.3 98.1 - - + +
283A GLN* 1.3 51.0 + - - +
285A TYR* 3.3 15.3 - - + +
286A ASN* 2.4 62.0 + - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 3.5 16.6 + - - +
281A VAL 2.6 4.9 + - - -
282A ILE* 1.3 74.3 - - - +
284A ASN* 1.3 59.6 + - - +
286A ASN* 4.1 9.0 - - - +
287A LYS* 2.8 62.1 + - + +
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Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 4.7 20.9 + - + +
280A SER 3.4 5.9 + - - +
281A VAL* 2.1 31.9 + - - +
283A GLN* 1.3 71.8 - - - +
285A TYR* 1.3 58.9 + - - +
287A LYS* 4.1 3.4 - - - +
288A ALA* 3.1 27.4 + - - +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 2.6 13.7 + - + +
282A ILE* 3.3 21.8 - - + +
284A ASN* 1.3 73.9 - - - +
286A ASN* 1.3 68.8 + - - +
288A ALA* 3.4 4.9 + - + +
289A LEU* 3.0 69.2 + - + +
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 2.4 56.0 + - - +
283A GLN* 3.8 8.1 - - - +
285A TYR* 1.3 83.8 - - - +
287A LYS* 1.3 66.8 + - - +
289A LEU* 3.2 15.0 + - - +
290A GLN* 3.0 25.8 + - - +
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLN* 2.8 55.1 + - + +
284A ASN* 4.5 3.6 - - - +
286A ASN* 1.3 77.8 - - - +
288A ALA* 1.3 63.9 + - - +
290A GLN* 3.5 11.0 + - + +
291A GLN* 3.3 27.2 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASN* 3.1 26.7 + - - +
285A TYR* 3.6 6.7 - - + +
287A LYS* 1.3 76.2 - - - +
289A LEU* 1.3 63.1 + - + +
291A GLN* 3.5 11.4 + - - +
292A LEU* 3.1 24.6 + - - +
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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
----------------------------------------------------------
285A TYR* 3.0 73.0 + - + +
286A ASN* 3.3 16.4 - - - +
288A ALA* 1.3 80.3 - - + +
290A GLN* 1.3 63.7 + - - +
292A LEU* 3.2 18.4 + - + +
293A GLU* 3.1 23.4 + - - +
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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
----------------------------------------------------------
286A ASN 3.0 11.7 + - - +
287A LYS* 3.8 16.8 - - + +
288A ALA 3.4 0.4 - - - -
289A LEU* 1.3 75.4 - - - +
291A GLN* 1.3 61.2 + - - +
293A GLU* 3.3 28.7 + - - +
294A LYS* 3.0 32.1 + - - +
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LYS* 3.3 13.2 + - - +
288A ALA* 3.6 13.9 - - - +
289A LEU 3.2 0.2 - - - -
290A GLN* 1.3 79.2 - - + +
292A LEU* 1.3 62.1 + - - +
294A LYS* 3.3 29.6 + - - +
295A TYR* 3.1 39.4 + - + -
325A ASP* 5.5 5.5 + - - +
328A ARG* 4.4 17.4 + - - +
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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
----------------------------------------------------------
288A ALA 3.1 15.0 + - - +
289A LEU* 3.5 20.9 - - + +
290A GLN 3.2 0.2 - - - -
291A GLN* 1.3 78.8 - - - +
293A GLU* 1.3 64.7 + - + +
295A TYR* 3.6 4.0 + - - +
296A LYS* 3.2 30.0 + - + +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU 3.1 15.8 + - - +
290A GLN* 3.3 30.5 + - - +
292A LEU* 1.3 78.0 - - + +
294A LYS* 1.3 65.6 + - - +
296A LYS* 3.2 50.2 + - - +
297A PRO* 3.4 4.9 - - - +
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Residues in contact with LYS 294 (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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290A GLN* 3.0 20.0 + - + +
291A GLN* 3.3 28.5 + - - +
293A GLU* 1.3 77.8 - - - +
295A TYR* 1.3 94.4 + - - +
297A PRO* 3.4 14.7 - - - +
298A TYR* 4.0 9.7 - - - -
319A PHE* 4.1 16.2 - - + -
323A ILE* 3.6 23.0 - - + +
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 3.1 30.3 + - + +
292A LEU* 4.0 4.0 - - - +
294A LYS* 1.3 94.1 + - - +
296A LYS* 1.3 59.0 + - - +
297A PRO* 3.4 1.3 - - - -
298A TYR* 3.2 11.2 + - - +
299A GLU* 3.0 31.6 + - + +
316A TYR* 3.7 24.7 - + - +
319A PHE* 3.5 31.4 - + - -
320A GLU* 3.1 18.0 + - - -
323A ILE* 3.1 23.4 - - + +
328A ARG* 3.1 51.6 - - - +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.2 25.0 + - + +
293A GLU* 3.2 41.7 + - - +
295A TYR* 1.3 74.0 - - - +
297A PRO* 1.4 74.8 - - + +
299A GLU* 3.1 10.2 + - - +
300A GLU* 3.0 23.1 + - - +
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU 3.4 8.7 - - - +
294A LYS 3.4 12.3 - - - +
295A TYR 3.6 0.2 - - - -
296A LYS* 1.4 100.9 - - + +
298A TYR* 1.3 67.6 + - + +
300A GLU* 3.3 9.5 + - + +
301A ALA* 3.0 28.3 + - - +
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS 4.0 16.6 - - - -
295A TYR* 3.2 9.4 + + - +
297A PRO* 1.3 83.1 - - + +
299A GLU* 1.3 66.3 + - - +
301A ALA* 4.0 6.4 - - + +
302A LEU* 3.1 26.9 + - - +
312A GLU 5.8 0.7 - - - -
315A ALA* 4.2 15.9 - - + -
316A TYR* 4.0 38.2 - + + -
319A PHE* 3.2 60.0 - + + +
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Residues in contact with GLU 299 (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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292A LEU 6.0 0.2 - - - +
295A TYR* 3.0 22.9 + - + +
296A LYS* 3.5 11.4 - - - +
298A TYR* 1.3 77.1 - - - +
300A GLU* 1.3 60.2 + - - +
302A LEU* 3.1 32.8 - - - +
303A LEU* 3.4 7.6 + - - +
316A TYR* 2.6 25.3 + - - +
328A ARG* 5.4 1.2 + - - -
335A ARG* 3.0 33.1 + - - -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS 3.0 12.5 + - - +
297A PRO* 3.7 9.8 - - - +
299A GLU* 1.3 75.9 - - - +
301A ALA* 1.3 59.6 + - - +
303A LEU* 3.1 9.3 + - + +
304A GLN* 3.0 53.6 + - + +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO 3.0 15.7 + - - +
298A TYR* 4.0 7.9 - - + +
300A GLU* 1.3 73.3 - - - +
302A LEU* 1.3 65.6 + - - +
304A GLN* 3.5 6.1 + - - +
305A ALA* 3.3 24.9 + - - +
312A GLU* 3.9 11.8 - - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A TYR 3.1 10.2 + - - +
299A GLU* 3.1 32.8 - - - +
301A ALA* 1.3 77.4 - - - +
303A LEU* 1.3 89.4 + - + +
305A ALA* 3.7 2.3 + - - +
309A ARG* 2.9 34.0 + - + +
312A GLU* 4.4 19.0 - - + +
313A TYR* 5.0 14.8 - - + +
316A TYR* 3.7 24.7 - - + -
335A ARG* 3.2 30.1 - - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU 3.4 11.2 + - - +
300A GLU* 3.1 12.6 + - + +
302A LEU* 1.3 92.8 - - + +
304A GLN* 1.3 73.3 + - - +
305A ALA 3.4 4.7 + - - +
309A ARG* 5.0 3.4 + - - +
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Residues in contact with GLN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.0 44.3 + - + +
301A ALA* 3.5 5.8 + - - +
302A LEU 3.4 0.4 - - - -
303A LEU* 1.3 88.3 - - - +
305A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA 3.3 14.9 + - - +
302A LEU 4.0 6.3 - - - +
303A LEU 3.3 7.2 - - - +
304A GLN* 1.3 82.7 - - - +
306A GLU* 1.3 67.3 + - + +
309A ARG* 4.1 10.3 + - + -
312A GLU* 3.4 35.2 - - + +
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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
------------------------------------------------------------
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