Contacts of the helix formed by residues 313 - 327 (chain A) in PDB entry 3RFU
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 THR 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A VAL* 5.3 2.1 - - - +
261A ASP* 2.8 31.9 + - - +
307A LEU 5.0 0.7 - - - -
308A HIS 3.2 15.7 + - - -
309A VAL* 4.7 1.9 - - - -
310A GLY* 2.9 30.6 + - - +
311A SER 3.6 0.5 - - - +
312A ASP* 1.3 84.0 - - - +
314A MET* 1.3 64.7 + - - +
315A LEU* 4.0 5.7 + - + +
316A ALA* 3.2 27.6 - - + +
317A ARG* 3.4 17.9 + - - +
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Residues in contact with MET 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP* 3.6 5.2 + - - +
275A MET* 6.5 0.7 - - + -
276A VAL* 4.7 5.4 - - + -
292A ILE* 3.5 37.5 - - + -
313A THR* 1.3 76.3 + - - +
315A LEU* 1.3 66.3 + - - +
317A ARG* 3.0 42.9 + - - +
318A ILE* 3.0 39.9 + - + +
601A MET* 3.5 29.2 - - + -
602A PRO* 3.3 35.2 - - + -
603A GLU* 4.6 4.5 - - + +
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Residues in contact with LEU 315 (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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220A LEU* 4.6 17.0 - - + +
221A LYS 4.5 16.6 - - - +
222A LEU* 4.7 11.0 - - + +
261A ASP* 5.2 1.3 + - - +
275A MET* 4.0 22.6 - - + +
292A ILE* 5.4 0.4 - - - +
293A GLY 5.3 1.8 + - - +
294A ALA* 4.3 24.0 - - + -
313A THR* 4.0 5.8 + - + +
314A MET* 1.3 78.7 - - - +
316A ALA* 1.3 65.0 + - - +
318A ILE* 2.9 25.7 + - + +
319A VAL* 2.9 25.2 + - + +
626A VAL* 5.1 9.0 - - + -
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Residues in contact with ALA 316 (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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310A GLY 3.6 9.9 - - - +
311A SER* 4.4 9.4 - - - +
313A THR* 3.2 23.8 - - + +
314A MET 3.3 1.2 - - - -
315A LEU* 1.3 78.8 - - - +
317A ARG* 1.3 56.6 + - - +
319A VAL* 3.2 11.8 - - - +
320A GLN* 3.0 34.6 + - - +
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER 4.3 10.2 + - - +
312A ASP* 4.0 10.8 + - - +
313A THR 3.4 21.2 + - - +
314A MET* 3.0 39.4 + - - +
316A ALA* 1.3 75.5 - - - +
318A ILE* 1.3 61.2 + - + +
320A GLN* 3.9 6.4 - - + +
321A MET* 3.0 44.6 + - + +
601A MET* 5.1 0.8 - - - +
603A GLU* 2.8 45.2 + - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 4.8 9.6 - - + -
275A MET* 5.1 12.1 - - + +
276A VAL* 5.3 2.5 - - + -
314A MET* 3.0 46.6 + - + +
315A LEU* 2.9 21.2 + - + +
317A ARG* 1.3 74.9 - - - +
319A VAL* 1.3 62.6 + - - +
321A MET* 2.9 32.0 + - + +
322A VAL* 2.9 18.5 + - + +
602A PRO* 4.1 12.8 - - + -
626A VAL* 4.7 17.0 - - + +
629A ALA* 5.3 0.7 - - + -
630A PRO* 4.3 22.3 - - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 5.1 17.3 - - + +
220A LEU* 4.0 23.3 - - + +
315A LEU* 2.9 24.7 - - + +
316A ALA* 3.2 21.1 - - - +
318A ILE* 1.3 76.0 - - - +
320A GLN* 1.3 57.7 + - + +
322A VAL* 3.2 13.3 - - + +
323A SER* 3.0 27.0 + - - -
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 5.4 11.7 + - - +
316A ALA* 3.0 21.2 + - - +
317A ARG* 4.0 6.0 - - - +
319A VAL* 1.3 77.2 - - + +
321A MET* 1.3 60.1 + - - +
323A SER* 3.4 9.0 + - - +
324A ASP* 2.9 48.1 + - - +
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Residues in contact with MET 321 (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 MET* 5.7 0.2 - - + -
317A ARG* 3.0 32.9 + - + +
318A ILE* 2.9 24.7 + - + +
320A GLN* 1.3 76.2 - - - +
322A VAL* 1.3 60.4 + - - +
324A ASP* 3.1 10.0 + - - +
325A ALA* 2.9 27.0 + - - +
603A GLU* 3.5 50.3 - - + +
606A SER* 4.7 6.3 - - - +
607A ARG* 6.3 0.4 - - - -
630A PRO* 3.9 24.0 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 3.4 34.3 - - + -
217A ARG* 6.2 1.8 - - + -
220A LEU* 4.4 13.0 - - + -
318A ILE* 2.9 23.0 + - + +
319A VAL* 3.2 19.7 - - + +
321A MET* 1.3 73.7 - - - +
323A SER* 1.3 52.9 + - - +
325A ALA* 3.4 8.8 - - - +
326A GLN* 2.6 43.8 + - + +
629A ALA* 5.0 5.4 - - + +
630A PRO* 4.5 18.7 - - + +
633A ALA* 4.5 5.4 - - + -
651A SER* 4.9 1.1 - - - +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 6.5 0.4 - - - -
319A VAL* 3.0 20.9 + - - -
320A GLN* 3.4 12.9 + - - +
321A MET 3.1 0.4 - - - -
322A VAL* 1.3 80.4 - - - +
324A ASP* 1.3 64.5 + - - +
326A GLN* 3.5 7.6 + - - +
327A ARG* 3.1 24.3 + - - +
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Residues in contact with ASP 324 (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 GLN* 2.9 32.8 + - - +
321A MET* 3.5 11.0 - - - +
323A SER* 1.3 80.1 + - - +
325A ALA* 1.3 53.6 + - - +
327A ARG* 2.8 29.8 - - - +
328A SER* 3.6 7.4 + - - -
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Residues in contact with ALA 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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321A MET 2.9 13.1 + - - +
322A VAL* 3.4 10.1 - - - +
324A ASP* 1.3 75.0 - - - +
326A GLN* 1.3 56.8 + - - +
327A ARG 2.7 20.1 - - - +
328A SER* 4.4 1.4 + - - -
329A ARG* 3.5 11.6 + - - +
630A PRO 4.3 2.5 - - - +
633A ALA* 3.7 14.5 - - + +
634A LYS* 3.7 43.4 - - + +
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Residues in contact with GLN 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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212A THR* 5.3 6.3 + - - -
214A SER* 5.8 0.6 - - - +
216A ILE* 3.0 47.5 - - - +
217A ARG* 4.8 4.0 + - - +
322A VAL* 2.6 29.7 + - + +
323A SER* 4.0 7.4 - - - +
325A ALA* 1.3 72.0 - - - +
327A ARG* 1.3 57.5 + - - +
329A ARG* 3.1 31.9 + - - +
633A ALA* 4.2 13.0 - - + -
650A GLU 5.3 2.0 + - - -
651A SER* 6.1 0.6 - - - +
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Residues in contact with ARG 327 (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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323A SER 3.1 16.6 + - - +
324A ASP* 2.8 11.1 - - - +
325A ALA 2.7 15.5 - - - +
326A GLN* 1.3 75.7 - - - +
328A SER* 1.3 84.9 + - - +
329A ARG 3.0 6.9 + - - -
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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