Contacts of the helix formed by residues 276 - 298 (chain F) in PDB entry 5TJG
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 276 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.3 50.0 - - + +
274F ARG* 6.1 0.2 - - - +
275F ILE* 1.3 98.1 - - + +
277F VAL* 1.3 65.3 + - + +
278F HIS* 4.6 2.7 - - + +
279F MET* 3.5 19.8 + - + +
280F VAL* 3.2 20.1 + - - +
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ARG* 3.3 32.3 - - - +
267F ALA* 3.9 30.5 - - + +
268F ASP* 4.3 6.1 - - - +
274F ARG* 5.7 0.9 - - - +
275F ILE 5.3 0.4 - - - +
276F PRO* 1.3 72.4 - - + +
278F HIS* 1.3 72.5 + - + +
280F VAL* 3.0 5.7 + - - +
281F GLU* 3.0 44.0 + - + +
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Residues in contact with HIS 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F PRO* 3.5 3.2 - - + +
277F VAL* 1.3 81.9 - - + +
279F MET* 1.3 52.9 + - + +
281F GLU* 3.3 25.6 + - - +
282F THR* 2.7 40.3 + - - +
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Residues in contact with MET 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 4.4 12.8 - - - -
275F ILE* 3.6 19.3 - - + -
276F PRO* 3.5 29.5 + - + +
277F VAL 3.2 0.6 - - - -
278F HIS* 1.3 78.4 - - + +
280F VAL* 1.3 52.5 + - - +
282F THR* 3.4 9.4 - - + -
283F ILE* 2.7 51.3 + - + +
322F THR* 5.1 13.5 - - + -
325F ILE* 3.7 35.0 - - + -
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ILE* 5.2 11.2 - - + +
267F ALA* 4.2 27.4 - - + +
271F ARG* 4.8 15.3 - - + +
275F ILE* 3.8 22.9 - - + +
276F PRO 3.2 16.5 + - - +
277F VAL* 3.0 9.5 + - - +
279F MET* 1.3 76.0 - - - +
281F GLU* 1.3 58.8 + - + +
283F ILE* 3.2 8.1 + - + +
284F ASN* 2.9 45.2 + - - +
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F VAL* 3.0 34.5 + - + +
278F HIS* 3.5 25.4 + - - +
280F VAL* 1.3 76.9 - - + +
282F THR* 1.3 62.7 + - - +
284F ASN* 3.3 9.7 + - - +
285F LYS* 3.0 42.0 + - - +
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Residues in contact with THR 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F HIS* 2.7 27.2 + - - +
279F MET* 3.2 11.5 + - + +
281F GLU* 1.3 73.6 - - - +
283F ILE* 1.3 63.7 + - + +
285F LYS* 3.2 16.5 + - - +
286F LEU* 3.0 26.3 + - + +
310F MET* 5.1 0.2 - - - +
314F TRP* 3.4 38.0 - - + -
318F ARG* 4.7 6.5 + - - +
322F THR* 4.9 7.9 - - + -
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Residues in contact with ILE 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F ARG* 4.5 18.2 - - - +
275F ILE* 4.8 12.6 - - + -
279F MET* 2.7 37.0 + - + +
280F VAL* 3.2 7.8 + - + +
282F THR* 1.3 74.5 - - + +
284F ASN* 1.3 62.1 + - - +
286F LEU* 3.3 11.2 + - + +
287F SER* 2.8 31.6 + - - -
322F THR* 4.1 15.5 - - - +
325F ILE* 4.6 2.7 - - + -
326F ALA* 3.6 44.6 - - + +
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Residues in contact with ASN 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220F ARG* 5.3 14.8 + - - +
280F VAL* 2.9 36.6 + - - +
281F GLU* 3.6 8.2 - - - +
282F THR 3.2 0.2 - - - -
283F ILE* 1.3 78.6 - - - +
285F LYS* 1.3 65.7 + - + +
287F SER* 3.2 7.3 + - - -
288F ARG* 3.0 25.6 + - - +
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Residues in contact with LYS 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F GLU* 3.0 34.0 + - - +
282F THR* 3.5 15.3 + - - +
284F ASN* 1.3 77.8 - - + +
286F LEU* 1.3 59.7 + - - +
288F ARG* 3.5 5.9 + - - +
289F THR* 3.0 25.6 + - - -
310F MET* 4.0 18.1 - - + +
314F TRP* 6.5 0.4 - - + -
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Residues in contact with LEU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F THR* 3.0 19.0 + - + +
283F ILE* 3.7 11.0 - - + +
285F LYS* 1.3 77.1 - - - +
287F SER* 1.3 63.6 + - - +
289F THR* 3.4 11.8 + - - -
290F ALA* 3.5 13.5 + - - +
306F ILE* 4.6 7.1 - - + +
310F MET* 3.6 33.7 - - + -
314F TRP* 3.6 25.8 - - + -
319F VAL* 3.7 26.0 - - + -
322F THR* 3.2 31.4 - - - +
323F LEU* 4.8 9.4 - - + +
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Residues in contact with SER 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F ILE* 2.8 21.7 + - - -
284F ASN* 3.2 10.3 + - - -
286F LEU* 1.3 76.7 - - - +
288F ARG* 1.3 62.2 + - - +
290F ALA* 3.8 10.5 + - - +
291F ARG* 4.1 12.1 + - - +
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Residues in contact with ARG 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F ASN 3.0 15.9 + - - +
285F LYS* 4.0 6.3 - - - +
286F LEU 3.3 0.2 - - - -
287F SER* 1.3 78.6 - - - +
289F THR* 1.3 60.6 + - - +
291F ARG* 3.1 51.8 - - - +
292F GLN* 3.0 44.3 + - - +
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Residues in contact with THR 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LYS 3.0 15.0 + - - -
286F LEU 3.4 4.8 + - - -
287F SER 3.4 0.2 - - - -
288F ARG* 1.3 80.4 + - - +
290F ALA* 1.3 62.9 + - - +
291F ARG 3.2 1.0 + - - -
292F GLN* 3.5 24.8 + - - +
293F LEU* 3.4 23.4 + - + +
306F ILE* 3.7 23.1 - - + -
309F ALA* 3.9 26.5 - - + +
310F MET* 3.7 10.8 - - - -
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F LEU 3.5 12.8 + - - +
287F SER* 3.8 7.4 + - - +
288F ARG 3.4 0.6 - - - -
289F THR* 1.3 78.1 - - - +
291F ARG* 1.3 58.0 + - - +
293F LEU* 3.9 12.1 - - - +
294F GLN* 3.2 26.8 + - - +
300F GLU* 6.1 0.2 - - - +
301F PRO* 4.4 18.7 - - + +
306F ILE* 4.1 7.1 - - + +
323F LEU* 6.4 2.0 - - + -
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Residues in contact with ARG 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ARG* 5.7 7.5 - - - +
376C ARG* 6.1 0.7 - - - +
287F SER 4.1 7.7 + - - +
288F ARG* 3.1 60.4 + - - +
290F ALA* 1.3 78.7 - - - +
292F GLN* 1.3 69.9 + - - +
294F GLN* 3.6 8.5 - - - +
295F GLN* 3.3 19.2 + - - +
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Residues in contact with GLN 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F ARG* 3.0 46.5 + - - +
289F THR* 3.5 33.0 + - - +
291F ARG* 1.3 88.2 + - + +
293F LEU* 1.3 64.3 + - + +
295F GLN* 3.4 8.0 + - - +
296F GLU* 3.1 42.2 + - - +
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Residues in contact with LEU 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F THR* 3.4 21.3 + - + +
290F ALA* 3.9 3.6 - - - +
292F GLN* 1.3 79.8 - - + +
294F GLN* 1.3 60.2 + - - +
295F GLN 3.2 0.4 - - - -
296F GLU* 3.6 15.3 - - + +
297F LEU* 2.7 60.6 + - + +
299F ARG 4.5 0.7 - - - +
301F PRO* 3.4 40.8 - - + -
305F GLU* 5.0 4.0 - - + +
306F ILE* 3.7 30.3 - - + +
309F ALA* 5.1 4.5 - - + -
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Residues in contact with GLN 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ASN* 3.1 29.4 - - - +
376C ARG* 3.1 44.9 + - - +
290F ALA 3.2 21.9 + - - +
291F ARG* 3.6 9.9 - - - +
293F LEU* 1.3 79.3 - - - +
295F GLN* 1.3 53.9 + - + +
298F GLY* 2.7 39.2 + - - +
299F ARG* 3.2 33.9 - - - +
300F GLU* 3.3 12.0 - - + +
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Residues in contact with GLN 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C ARG* 4.5 17.0 + - - -
370C ALA 3.4 15.4 + - - +
371C LYS* 3.9 28.2 - - + +
372C LEU 5.8 0.6 - - - -
373C VAL 3.1 31.3 + - - -
374C ASN* 4.0 22.1 + - - +
291F ARG 3.3 11.4 + - - +
292F GLN* 3.6 11.0 - - - +
293F LEU 3.2 0.4 - - - -
294F GLN* 1.3 81.0 - - + +
296F GLU* 1.3 64.1 + - + +
298F GLY* 3.8 5.7 + - - -
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Residues in contact with GLU 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F GLN* 3.1 33.1 + - - +
293F LEU* 3.3 12.8 + - - +
295F GLN* 1.3 81.0 - - + +
297F LEU* 1.3 64.8 + - + +
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Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 5.4 5.2 - - - -
293F LEU* 2.7 40.3 + - + +
296F GLU* 1.3 78.4 - - + +
298F GLY* 1.3 59.7 + - - +
299F ARG* 3.0 53.5 + - + +
301F PRO* 4.8 1.1 - - + -
305F GLU* 3.5 27.4 - - - +
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Residues in contact with GLY 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 5.5 9.1 - - - -
374C ASN* 4.6 5.2 - - - -
375C SER* 3.6 29.7 + - - -
376C ARG 5.2 0.2 + - - -
294F GLN* 2.7 30.7 + - - +
295F GLN* 3.8 5.5 + - - -
296F GLU 3.4 2.8 - - - -
297F LEU* 1.3 72.4 - - - +
299F ARG* 1.3 56.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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