Contacts of the helix formed by residues 289 - 302 (chain C) in PDB entry 5TF6
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 LYS 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C THR* 3.9 21.0 + - + +
207C LEU* 3.5 43.1 + - + +
288C ASP* 1.3 77.2 - - - +
290C LYS* 1.3 66.4 + - - +
291C PRO* 3.4 11.0 - - + -
292C PHE* 3.3 14.4 + - - +
293C LEU* 3.3 14.6 + - - +
55D G 2.8 62.2 + - - +
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Residues in contact with LYS 290 (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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157C SER* 5.8 3.8 - - - +
288C ASP 6.0 0.2 - - - +
289C LYS* 1.3 73.6 - - - +
291C PRO* 1.3 72.7 - - + +
293C LEU* 3.1 15.4 + - + +
294C GLU* 2.8 46.4 + - + +
42D A 3.2 25.0 + - - +
43D C 2.7 32.8 + - - -
44D A 3.9 25.5 - - - +
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Residues in contact with PRO 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PHE 3.4 13.7 - - - +
155C ASN* 3.6 35.9 - - + +
156C THR 5.8 0.9 - - - +
289C LYS* 3.4 13.2 - - + -
290C LYS* 1.3 95.7 - - + +
292C PHE* 1.3 56.5 + - - +
294C GLU* 4.2 6.1 - - + +
295C ARG* 3.0 31.5 + - - +
57D U 3.3 26.2 - - - +
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Residues in contact with PHE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASP* 3.7 32.1 - - + -
289C LYS* 3.3 10.2 + - - +
291C PRO* 1.3 77.0 - - - +
293C LEU* 1.3 68.0 + - + +
295C ARG* 3.4 2.3 + - - +
296C ASN* 3.0 48.7 + - - -
55D G 3.3 55.4 + + + +
57D U 3.4 54.3 - + + +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASP* 4.1 18.4 - - + +
289C LYS 3.5 19.3 - - - +
290C LYS* 3.1 20.5 + - + +
292C PHE* 1.3 86.0 - - + +
294C GLU* 1.3 61.5 + - + +
296C ASN* 3.1 7.8 + - - +
297C GLU* 2.9 27.3 + - - +
42D A 4.0 55.4 - - + +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR* 3.7 32.5 + - - +
157C SER* 5.4 6.8 + - - -
290C LYS* 2.8 43.7 + - + +
291C PRO* 4.2 4.7 - - + +
293C LEU* 1.3 73.4 - - + +
295C ARG* 1.3 64.1 + - - +
297C GLU* 3.2 18.8 + - - +
298C VAL* 3.1 26.2 + - + +
347C LEU* 5.2 12.8 - - + +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C PRO 3.0 20.7 + - - +
292C PHE 3.9 0.2 - - - +
294C GLU* 1.3 78.9 - - - +
296C ASN* 1.3 62.4 + - - +
298C VAL* 3.2 21.5 + - - +
299C LYS* 2.9 32.4 + - + +
302C LEU* 5.3 4.7 - - - +
348C LEU 5.0 5.9 + - - -
349C VAL* 5.0 1.6 - - - +
351C ASP* 2.6 41.6 + - - -
57D U 3.3 40.4 - - - +
58D C 3.0 60.7 + - - +
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Residues in contact with ASN 296 (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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292C PHE* 3.0 52.0 + - - -
293C LEU* 3.1 7.7 + - - +
295C ARG* 1.3 74.8 - - - +
297C GLU* 1.3 64.2 + - - +
298C VAL 3.2 0.5 + - - -
299C LYS* 3.3 32.8 + - - +
300C ARG* 3.3 23.0 + - - +
57D U 3.5 9.7 + - - +
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Residues in contact with GLU 297 (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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293C LEU 2.9 13.8 + - - +
294C GLU* 3.2 18.9 + - - +
296C ASN* 1.3 77.9 - - - +
298C VAL* 1.3 62.4 + - + +
300C ARG* 3.3 28.7 + - - +
301C LEU* 3.4 13.1 + - + +
344C ARG* 5.0 2.6 + - - -
345C LYS* 2.8 45.8 + - - +
347C LEU* 4.3 17.6 - - + +
358C ILE* 5.8 0.3 - - - +
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Residues in contact with VAL 298 (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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294C GLU 3.1 15.7 + - - +
295C ARG* 3.2 26.2 + - - +
297C GLU* 1.3 73.8 - - - +
299C LYS* 1.3 67.9 + - - +
301C LEU* 3.0 8.4 + - - +
302C LEU* 2.9 32.7 + - + +
347C LEU* 3.9 37.0 - - + -
348C LEU 4.0 19.7 - - - +
349C VAL* 4.2 15.5 - - + -
356C ILE* 4.9 3.4 - - + -
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Residues in contact with LYS 299 (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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295C ARG* 2.9 30.5 + - + +
296C ASN* 3.3 32.0 + - - +
298C VAL* 1.3 77.3 - - - +
300C ARG* 1.3 60.0 + - - +
302C LEU* 3.5 12.9 + - + +
303C ALA* 3.3 20.6 + - - +
56D A 4.6 3.4 + - - -
57D U 4.4 5.6 + - - +
58D C 3.0 42.2 + - - +
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Residues in contact with ARG 300 (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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296C ASN 3.3 9.9 + - - +
297C GLU* 3.3 22.3 + - - +
298C VAL 3.1 1.0 - - - -
299C LYS* 1.3 76.9 - - - +
301C LEU* 1.3 74.2 + - - +
303C ALA* 3.2 7.5 + - - +
304C SER* 3.0 31.2 + - - -
309C GLU* 2.7 44.1 + - - -
36D U 4.4 20.9 + - - +
37D U 3.8 29.1 + - - -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C GLU* 3.4 12.3 + - + +
298C VAL* 3.0 10.2 + - - +
300C ARG* 1.3 89.4 - - - +
302C LEU* 1.3 59.8 + - - +
304C SER* 3.1 19.1 + - - +
309C GLU* 3.3 42.8 - - + +
310C LEU* 4.5 2.1 - - + +
313C LEU* 4.2 19.3 - - + -
347C LEU* 3.9 18.2 - - + -
356C ILE* 4.7 14.1 - - + -
358C ILE* 3.8 29.6 - - + -
387C ILE* 3.6 15.9 - - + +
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ARG* 5.3 4.7 - - - +
298C VAL* 2.9 23.7 + - + +
299C LYS* 3.6 14.1 - - + +
301C LEU* 1.3 77.3 - - - +
303C ALA* 1.3 56.2 + - - +
304C SER 3.5 0.4 - - - +
305C ARG* 5.9 0.5 + - - -
349C VAL* 4.3 22.7 - - + -
351C ASP* 4.9 7.6 - - - +
352C PHE* 4.3 22.0 - - + -
356C ILE* 4.4 16.6 - - + -
387C ILE* 4.1 28.5 - - + +
390C MET* 4.7 4.3 - - + -
391C LYS* 3.8 20.5 + - - +
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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