Contacts of the helix formed by residues 289 - 302 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A THR* 3.8 26.2 - - + +
207A LEU* 3.6 40.7 + - + +
287A ALA 4.9 4.0 - - - -
288A ASP* 1.3 74.8 - - - +
290A LYS* 1.3 67.6 + - - +
291A PRO* 3.4 12.3 - - + -
292A PHE* 3.2 6.4 + - - +
293A LEU* 3.1 22.3 + - - +
55B G 2.7 65.7 + - + +
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Residues in contact with LYS 290 (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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157A SER* 6.1 0.4 - - - +
288A ASP 4.3 0.2 + - - -
289A LYS* 1.3 70.5 - - - +
291A PRO* 1.4 65.7 - - + +
293A LEU* 3.1 13.4 + - + +
294A GLU* 2.8 52.9 + - + +
42B A 2.7 27.1 + - - +
43B C 2.5 36.9 + - - -
44B A 3.7 26.5 - - - +
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Residues in contact with PRO 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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154A PHE 3.5 14.0 - - - +
155A ASN* 3.8 31.6 - - + +
289A LYS* 3.4 13.7 - - + -
290A LYS* 1.4 95.0 - - + +
292A PHE* 1.3 56.3 + - - +
294A GLU* 4.2 10.0 - - + +
295A ARG* 2.9 30.3 + - - +
57B U 3.4 28.2 - - - +
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Residues in contact with PHE 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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288A ASP* 3.8 30.5 - - + -
289A LYS* 3.2 8.9 + - + +
291A PRO* 1.3 78.4 - - - +
293A LEU* 1.3 73.7 + - + +
295A ARG* 4.0 1.4 - - - +
296A ASN* 3.2 41.1 + - - -
55B G 3.3 54.7 - + + +
57B U 3.3 56.6 - + + +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP* 4.3 3.8 - - + +
289A LYS 3.1 19.3 + - - +
290A LYS* 3.1 17.3 + - + +
292A PHE* 1.3 90.8 - - + +
294A GLU* 1.3 64.2 + - + +
296A ASN* 3.1 8.6 + - + +
297A GLU* 3.1 21.7 + - - +
42B A 3.9 66.6 - - + +
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Residues in contact with GLU 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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155A ASN* 5.0 1.9 - - - +
156A THR* 3.9 28.3 + - - +
157A SER* 4.8 9.8 + - - -
290A LYS* 2.8 45.1 + - + +
291A PRO* 4.2 7.5 - - - +
293A LEU* 1.3 72.7 - - + +
295A ARG* 1.3 64.4 + - - +
297A GLU* 3.2 8.9 + - - +
298A VAL* 3.1 24.7 + - + +
347A LEU* 5.8 8.4 - - + +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO 2.9 20.0 + - - +
292A PHE 4.0 0.7 - - - +
294A GLU* 1.3 78.1 - - - +
296A ASN* 1.3 56.8 + - - +
298A VAL* 3.2 23.3 + - - +
299A LYS* 2.9 38.9 + - + +
302A LEU* 4.9 3.8 - - - +
348A LEU 5.2 1.2 + - - -
349A VAL* 4.8 4.0 - - - +
351A ASP* 2.8 45.5 + - - +
57B U 3.3 42.6 - - - +
58B C 3.0 57.7 + - - +
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Residues in contact with ASN 296 (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 PHE* 3.2 44.5 + - - -
293A LEU* 3.1 10.9 + - - +
295A ARG* 1.3 74.0 - - - +
297A GLU* 1.3 66.2 + - - +
299A LYS* 3.4 29.6 + - - +
300A ARG* 3.2 21.0 + - - +
57B U 3.6 11.2 - - - +
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Residues in contact with GLU 297 (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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293A LEU 3.1 11.8 + - - +
294A GLU* 3.6 10.8 - - - +
296A ASN* 1.3 75.1 - - - +
298A VAL* 1.3 67.3 + - - +
300A ARG* 2.6 57.8 + - - -
301A LEU* 3.3 13.3 + - - +
345A LYS* 3.8 25.5 + - - +
347A LEU* 4.8 8.3 - - + -
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Residues in contact with VAL 298 (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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294A GLU* 3.1 15.2 + - + +
295A ARG* 3.2 24.2 + - - +
297A GLU* 1.3 77.3 - - - +
299A LYS* 1.3 58.5 + - - +
301A LEU* 3.2 9.8 + - - +
302A LEU* 2.9 44.7 + - + +
347A LEU* 3.9 29.2 - - + -
348A LEU 3.5 26.5 - - - +
349A VAL* 4.1 12.1 - - + -
356A ILE* 5.2 2.9 - - + -
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 2.9 38.9 + - + +
296A ASN* 3.4 28.8 + - - +
297A GLU 3.3 0.2 - - - -
298A VAL* 1.3 78.2 - - - +
300A ARG* 1.3 63.0 + - - +
302A LEU* 3.4 12.2 + - + +
303A ALA* 3.3 19.6 + - - +
56B A 4.7 2.8 + - - -
57B U 4.4 2.4 + - - -
58B C 2.8 38.5 + - - +
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Residues in contact with ARG 300 (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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296A ASN 3.2 10.1 + - - +
297A GLU* 2.6 48.8 + - - +
299A LYS* 1.3 78.0 - - - +
301A LEU* 1.3 71.8 + - - +
303A ALA* 2.8 22.2 + - - +
304A SER* 2.9 16.9 + - - -
309A GLU* 3.0 40.4 + - - -
36B U 4.8 4.7 - - - +
37B U 3.3 33.7 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 3.3 17.2 + - - +
298A VAL* 3.2 9.8 + - - +
300A ARG* 1.3 80.7 - - - +
302A LEU* 1.3 62.3 + - - +
303A ALA 3.0 1.6 + - - -
304A SER* 3.2 19.2 + - - +
309A GLU* 3.7 37.0 - - + +
310A LEU* 4.3 2.7 - - + +
313A LEU* 4.2 15.7 - - + -
347A LEU* 3.7 30.7 - - + -
356A ILE* 4.5 23.1 - - + -
358A ILE* 4.3 17.0 - - + -
387A ILE* 3.8 15.0 - - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 4.9 4.9 - - - +
298A VAL* 2.9 35.8 + - + +
299A LYS* 3.8 13.0 - - + +
300A ARG 3.3 0.4 - - - -
301A LEU* 1.3 72.8 - - - +
303A ALA* 1.3 57.3 + - - +
304A SER 3.7 0.8 - - - +
349A VAL* 4.2 25.1 - - + -
351A ASP* 4.7 6.5 - - - +
352A PHE* 4.2 15.0 - - + -
356A ILE* 4.5 15.3 - - + -
387A ILE* 3.9 28.9 - - + +
390A MET* 4.5 4.9 - - + -
391A LYS* 4.1 23.3 + - - +
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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