Contacts of the helix formed by residues 282 - 297 (chain A) in PDB entry 3TIN
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 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ILE* 3.7 20.5 - - - +
278A ASN 2.7 19.4 + - - -
280A GLU 3.0 3.4 + - - -
281A ASN* 1.3 81.6 - - - +
283A ILE* 1.3 76.8 + - - +
285A CYS* 4.2 6.5 - - - +
286A GLN* 3.8 22.0 + - - +
325A LEU* 4.4 22.7 - - - +
327A VAL* 4.6 1.1 - - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 5.1 8.1 - - + -
264A PHE* 6.1 0.9 - - + -
267A PHE* 3.9 21.8 - - + -
271A LEU* 3.4 29.8 - - + -
279A LEU* 3.5 10.6 + - + +
282A SER* 1.3 83.1 + - - +
284A LEU* 1.3 75.4 + - + +
285A CYS 3.0 0.9 - - - -
286A GLN* 2.7 18.5 + - - +
287A ILE* 3.1 32.3 + - + +
321A VAL* 4.9 21.8 - - + -
325A LEU* 5.6 6.7 - - + +
327A VAL* 4.3 18.6 - - + -
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 5.8 5.6 - - + -
217A ARG* 6.0 4.9 - - - +
264A PHE* 3.5 34.5 - - + -
279A LEU* 2.9 35.5 + - + +
280A GLU* 3.3 47.1 - - + +
283A ILE* 1.3 82.5 - - + +
285A CYS* 1.3 63.5 + - - +
287A ILE* 4.3 10.1 - - + -
288A LYS* 2.9 37.5 + - + +
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 3.5 20.1 + - + +
281A ASN 5.1 1.6 - - - -
282A SER* 4.2 10.3 - - - +
283A ILE 2.8 5.3 + - - -
284A LEU* 1.3 78.0 - - - +
286A GLN* 1.3 64.4 + - - +
288A LYS* 3.7 17.3 + - - +
289A GLU* 3.8 8.7 + - - +
292A ARG* 5.8 0.2 + - - -
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TRP* 4.3 7.5 - - + +
282A SER 3.8 9.8 + - - +
283A ILE 2.7 12.8 + - - +
285A CYS* 1.3 76.9 - - - +
287A ILE* 1.3 64.5 + - - +
289A GLU* 3.0 21.9 + - + +
290A ILE* 3.2 16.1 + - + +
325A LEU 4.8 1.6 + - - -
326A LYS* 3.7 20.7 - - - +
327A VAL* 2.6 61.2 + - + +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.4 15.3 - - + -
203A SER* 3.7 13.2 - - - +
215A LEU* 4.6 8.5 - - + -
264A PHE* 5.2 6.7 - - + -
283A ILE* 3.1 34.4 + - + +
284A LEU* 4.0 11.0 - - + +
286A GLN* 1.3 71.8 - - - +
288A LYS* 1.3 57.6 + - - +
289A GLU 2.6 16.8 + - - -
290A ILE* 3.3 4.0 + - - +
291A ILE* 3.2 45.5 + - + +
319A PHE* 3.6 38.4 - - + -
327A VAL* 4.3 9.2 - - + -
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 3.9 22.2 - - + -
280A GLU* 4.2 12.6 - - + +
284A LEU* 2.9 36.0 + - + +
285A CYS* 3.8 10.2 + - - +
286A GLN 3.2 0.2 - - - -
287A ILE* 1.3 73.7 - - + +
289A GLU* 1.3 57.3 + - - +
291A ILE* 4.8 2.0 - - - -
292A ARG* 3.1 41.2 + - - +
375A ILE* 4.2 33.1 - - + +
377A LEU* 3.1 26.3 - - + +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TRP* 5.4 7.9 - - + +
285A CYS 4.0 6.1 - - - +
286A GLN* 3.0 15.7 + - + +
287A ILE 2.6 6.9 + - - -
288A LYS* 1.3 74.5 - - - +
290A ILE* 1.3 68.3 + - + +
291A ILE 3.1 1.1 - - - -
292A ARG* 2.9 25.5 + - - +
293A VAL* 2.7 50.0 + - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TRP* 3.4 58.1 - - + -
286A GLN* 3.2 26.1 + - + +
287A ILE 4.0 0.9 - - - +
289A GLU* 1.3 78.0 - - + +
291A ILE* 1.3 67.5 - - - +
293A VAL* 3.0 1.9 + - - +
294A CYS* 2.8 30.4 + - - -
317A PHE* 4.8 0.9 - - + -
319A PHE* 3.5 34.3 - - + -
327A VAL* 4.2 9.0 - - + +
329A LEU* 3.6 34.1 - - + +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 4.2 10.1 - - - +
205A VAL* 3.6 29.2 - - + -
213A ILE* 4.2 3.4 - - + -
215A LEU* 4.7 9.9 - - + -
287A ILE* 3.2 36.3 + - + +
288A LYS* 4.9 0.9 - - - +
290A ILE* 1.3 80.8 - - - +
292A ARG* 1.3 66.4 + - - +
293A VAL 3.0 1.4 + - - -
294A CYS* 3.2 0.9 + - - +
295A LEU* 3.1 42.9 + - + +
317A PHE* 3.8 32.8 - - + -
319A PHE* 4.1 4.0 - - + -
377A LEU* 3.8 15.9 - - + -
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 5.4 5.7 - - + +
285A CYS 5.8 0.2 + - - -
288A LYS* 3.1 43.9 + - - +
289A GLU* 2.9 32.5 + - - +
291A ILE* 1.3 77.7 - - - +
293A VAL* 1.3 57.7 + - + +
295A LEU* 4.3 4.2 - - - +
296A SER* 2.7 41.8 + - - +
375A ILE* 6.2 0.2 - - - +
377A LEU* 3.2 54.7 + - + +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 5.2 5.2 - - - +
87A LEU* 4.5 19.1 - - + -
90A THR* 5.4 5.8 - - + -
93A TRP* 4.4 20.6 - - + +
289A GLU* 2.7 48.4 + - + +
290A ILE* 3.5 7.0 - - - +
292A ARG* 1.3 73.0 - - + +
294A CYS* 1.3 65.8 + - - +
295A LEU 3.2 1.6 - - - -
296A SER* 3.8 3.9 - - - -
297A CYS* 3.0 26.1 + - + +
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Residues in contact with CYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.7 33.6 - - + +
77A LEU* 5.5 2.0 - - - -
80A LEU* 4.9 3.3 - - + +
81A ILE* 5.7 3.1 - - - -
87A LEU* 6.2 3.4 - - - -
93A TRP* 3.7 24.0 - - - -
290A ILE* 2.8 39.2 + - - +
291A ILE 4.0 2.9 - - - +
293A VAL* 1.3 75.5 - - - +
295A LEU* 1.3 59.6 + - - +
297A CYS* 3.6 7.2 + - - +
298A LEU* 3.3 21.5 + - - +
317A PHE* 4.4 9.6 - - + -
329A LEU* 4.0 13.0 - - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.8 21.5 - - + -
205A VAL* 3.8 15.3 - - + -
207A VAL* 4.2 5.4 - - + -
211A TYR* 2.6 34.8 + - + +
213A ILE* 3.5 33.0 - - + -
291A ILE* 3.1 32.1 + - + +
292A ARG 4.3 2.0 - - - +
294A CYS* 1.3 74.9 - - - +
296A SER* 1.3 56.4 + - - +
297A CYS 3.1 4.5 - - - -
298A LEU* 2.9 6.0 + - + +
299A GLU 2.8 15.8 + - - -
302A ILE* 5.9 0.7 - - + -
315A PHE* 4.2 26.0 - - + -
317A PHE* 4.4 9.6 - - + -
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 4.9 2.1 - - - -
213A ILE* 5.6 4.7 - - - +
292A ARG* 2.7 30.6 + - - +
293A VAL* 3.9 5.6 - - - -
295A LEU* 1.3 76.0 - - - +
297A CYS* 1.3 59.6 + - - +
298A LEU 3.2 0.6 + - - -
299A GLU* 4.0 14.1 + - - +
300A PRO* 3.8 14.2 - - - +
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Residues in contact with CYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.8 29.4 - - - +
84A SER* 3.7 30.5 - - - -
87A LEU* 4.5 10.5 - - + -
293A VAL* 3.0 19.6 + - + +
294A CYS* 3.8 7.2 - - - +
295A LEU 3.1 0.2 - - - -
296A SER* 1.3 77.7 - - - +
298A LEU* 1.3 60.5 + - - +
300A PRO* 4.0 8.3 - - - +
301A ALA* 5.5 0.3 + - - +
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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
------------------------------------------------------------
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