Contacts of the helix formed by residues 321 - 335 (chain A) in PDB entry 3RTC
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 ASN 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A PHE* 3.7 42.1 - - - +
319A GLY 4.0 0.2 - - - -
320A ASN* 1.3 80.9 - - - +
322A GLU* 1.3 64.9 + - - +
323A HIS* 3.2 13.6 + - - +
324A VAL* 3.0 25.7 + - - +
325A ARG* 3.0 22.2 + - - +
348A VAL* 4.4 1.3 - - - +
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Residues in contact with GLU 322 (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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321A ASN* 1.3 75.7 - - - +
323A HIS* 1.3 63.5 + - + +
325A ARG* 3.2 31.4 + - - +
326A GLU* 2.9 44.3 + - - +
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Residues in contact with HIS 323 (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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291A LYS* 5.6 13.2 - - + +
293A PHE* 6.1 1.6 - - + -
294A PHE 3.9 5.2 - - - +
295A SER* 3.8 26.6 - - - -
296A LEU 4.2 0.3 + - - -
321A ASN* 3.2 9.3 + - - +
322A GLU* 1.3 78.6 - - + +
324A VAL* 1.3 61.2 + - - +
326A GLU* 3.4 22.2 + - - +
327A PHE* 3.0 29.3 + - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 4.0 6.5 - - + -
294A PHE* 3.5 21.1 - - + +
318A LEU* 3.7 33.9 - - + +
319A GLY 3.3 22.4 - - - +
321A ASN* 3.0 31.9 + - - +
323A HIS* 1.3 73.7 - - - +
325A ARG* 1.3 65.6 + - - +
327A PHE* 3.3 4.9 + - + -
328A VAL* 2.8 40.3 + - + +
344A ASP 5.2 0.7 - - - +
348A VAL* 4.4 8.3 - - + -
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Residues in contact with ARG 325 (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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320A ASN* 4.3 7.7 + - - -
321A ASN 3.0 12.9 + - - +
322A GLU* 3.4 36.2 + - - +
324A VAL* 1.3 77.0 - - - +
326A GLU* 1.3 64.1 + - + +
328A VAL* 4.0 0.3 - - - +
329A ASN* 2.8 45.8 + - - +
347A ASN 3.8 15.6 + - - -
348A VAL* 3.3 48.4 + - + +
349A LEU 4.7 3.6 + - - -
350A ASP* 6.0 1.2 - - - +
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Residues in contact with GLU 326 (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 LEU* 3.8 31.8 + - + +
322A GLU* 2.9 38.7 + - - +
323A HIS* 3.8 20.1 - - - +
325A ARG* 1.3 77.0 - - + +
327A PHE* 1.3 63.8 + - - +
329A ASN* 4.3 2.1 - - - +
330A GLU* 3.0 30.3 + - + +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ILE* 3.9 16.6 - - + -
294A PHE* 3.7 32.5 - + + -
295A SER* 3.4 31.4 - - - -
296A LEU* 4.2 8.2 - - - +
298A ASN 4.0 2.9 - - - -
299A LEU* 3.9 24.6 - - + +
302A CYS* 3.7 35.0 - - + -
314A ILE* 4.2 12.3 - - + -
318A LEU* 4.9 1.8 - - + -
323A HIS 3.0 17.9 + - - +
324A VAL* 3.7 3.8 - - - +
326A GLU* 1.3 78.5 - - - +
328A VAL* 1.3 67.2 + - + +
330A GLU* 3.8 0.5 - - - +
331A PHE* 2.9 45.5 + + + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 4.3 7.9 - - + -
318A LEU* 3.6 31.4 - - + -
324A VAL* 2.8 31.0 + - + +
325A ARG 4.0 0.2 - - - +
327A PHE* 1.3 79.4 - - + +
329A ASN* 1.3 63.9 - - - +
331A PHE* 3.6 3.9 - - - +
332A LEU* 3.0 49.2 + - + +
345A ALA* 4.0 19.7 - - + +
348A VAL* 3.8 21.3 - - + -
349A LEU* 4.9 0.4 - - + -
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Residues in contact with ASN 329 (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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325A ARG* 2.8 33.3 + - - +
326A GLU* 4.3 2.7 - - - +
328A VAL* 1.3 74.8 - - - +
330A GLU* 1.3 60.8 + - - +
332A LEU* 3.5 1.2 + - - -
333A LYS* 3.1 30.4 + - - +
348A VAL* 2.9 24.8 + - - +
349A LEU* 3.6 14.0 - - - +
350A ASP* 2.8 37.3 + - + +
353A VAL* 3.9 18.7 - - + +
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Residues in contact with GLU 330 (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 LEU* 3.9 22.7 - - + -
299A LEU* 4.0 17.7 - - + +
326A GLU* 3.0 20.5 + - + +
327A PHE 4.1 0.7 - - - +
329A ASN* 1.3 74.2 - - - +
331A PHE* 1.3 64.8 + - - +
333A LYS* 3.5 31.7 + - - +
334A THR* 2.9 33.8 + - - -
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Residues in contact with PHE 331 (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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238A ILE* 3.3 23.3 - - + -
299A LEU* 3.6 13.8 - - + +
302A CYS* 3.8 31.4 - - + -
303A LEU* 3.6 30.1 - - + -
306A SER* 3.5 15.7 - - - -
312A VAL* 4.0 7.2 - - + -
314A ILE* 3.8 20.0 - - + -
327A PHE* 2.9 27.8 + + + +
328A VAL* 3.6 3.8 - - - +
330A GLU* 1.3 78.4 - - - +
332A LEU* 1.3 68.4 + - + +
334A THR* 3.1 4.1 + - - -
335A LEU* 2.8 55.7 + - + +
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Residues in contact with LEU 332 (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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314A ILE* 4.2 16.6 - - + -
328A VAL* 3.0 33.1 + - + +
331A PHE* 1.3 88.5 - - + +
333A LYS* 1.3 61.2 + - - +
334A THR 3.4 0.2 + - - -
335A LEU* 3.7 7.3 + - + +
339A ALA* 3.8 28.9 - - + -
341A ILE* 3.9 21.5 - - + -
349A LEU* 3.7 28.9 - - + -
353A VAL* 4.0 14.4 - - + -
354A LEU* 6.0 0.2 - - + -
357A ARG* 2.9 38.1 + - - +
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Residues in contact with LYS 333 (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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329A ASN 3.1 18.1 + - - +
330A GLU* 3.6 30.3 - - - +
331A PHE 3.2 0.2 - - - -
332A LEU* 1.3 79.7 - - - +
334A THR* 1.3 59.8 + - - +
335A LEU 4.9 0.9 - - - +
336A GLU* 5.9 0.2 - - - +
353A VAL* 3.8 18.5 - - + +
356A GLU* 3.2 42.5 + - - +
357A ARG* 4.9 6.5 - - - +
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Residues in contact with THR 334 (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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299A LEU* 5.1 2.1 - - - +
303A LEU* 4.0 30.3 - - + +
330A GLU* 2.9 22.5 + - - -
331A PHE 3.1 3.8 + - - -
333A LYS* 1.3 78.0 - - - +
335A LEU* 1.3 66.3 + - - +
336A GLU* 3.2 14.5 + - - +
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Residues in contact with LEU 335 (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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303A LEU* 4.1 7.2 - - + +
306A SER* 3.5 34.8 - - - +
312A VAL* 3.8 19.1 - - + -
331A PHE* 2.8 45.3 + - + +
332A LEU* 3.7 3.7 + - + +
333A LYS 3.6 1.3 - - - +
334A THR* 1.3 75.3 - - - +
336A GLU* 1.3 61.6 + - - +
337A LYS* 3.5 36.5 + - + +
339A ALA* 4.2 15.5 - - + -
357A ARG* 2.7 31.8 + - - +
359A SER* 4.5 1.4 + - - -
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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