Contacts of the helix formed by residues 324 - 338 (chain A) in PDB entry 5F2R
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 ARG 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LEU* 2.9 32.1 + - + +
300A SER 3.7 4.6 + - - -
301A SER* 3.5 10.5 - - - +
302A GLN* 3.1 35.0 + - - +
303A HIS* 2.8 56.5 + - + +
323A THR* 1.3 71.0 - - - +
325A ALA* 1.3 58.6 + - - +
327A PHE* 3.1 10.6 + - + +
328A GLU* 2.9 52.5 + - + +
369A PRO* 4.1 24.3 - - + +
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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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323A THR* 3.2 8.6 + - - +
324A ARG* 1.3 80.5 - - - +
326A LYS* 1.3 56.3 + - - +
328A GLU* 3.3 15.0 + - - +
329A GLU* 2.8 30.6 + - - +
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Residues in contact with LYS 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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265A HIS* 3.3 34.7 + - - +
322A LEU* 3.8 19.3 - - + -
323A THR* 2.8 25.9 + - + +
325A ALA* 1.3 76.2 - - - +
327A PHE* 1.3 58.4 + - - +
329A GLU* 3.2 31.1 + - - +
330A LEU* 3.0 45.3 + - + +
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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
----------------------------------------------------------
258A PHE* 4.1 8.3 - - + -
262A VAL* 3.8 19.3 - - + -
296A LYS* 3.5 41.3 - - + -
299A LEU* 3.9 25.6 - - + -
300A SER* 6.1 0.2 - - - -
322A LEU* 4.2 12.2 - - + +
323A THR 2.9 13.5 + - - +
324A ARG* 3.4 11.4 - - + +
326A LYS* 1.3 78.2 - - - +
328A GLU* 1.3 67.7 + - + +
330A LEU* 3.6 3.1 + - - -
331A ASN* 2.9 50.9 + - - +
335A PHE* 4.0 17.7 - + - -
368A ILE* 4.0 28.5 - - + -
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Residues in contact with GLU 328 (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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324A ARG* 2.9 39.0 + - + +
325A ALA* 3.6 18.6 + - - +
327A PHE* 1.3 80.0 - - + +
329A GLU* 1.3 60.0 + - - +
331A ASN 3.1 0.9 + - - -
332A MET* 2.9 49.3 + - + +
335A PHE* 4.0 9.4 - - + -
368A ILE* 5.7 1.5 - - + +
369A PRO* 5.3 1.6 - - - +
370A LYS* 3.5 46.3 + - + +
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Residues in contact with GLU 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 ALA 2.8 21.3 + - - +
326A LYS* 3.2 39.8 + - - +
328A GLU* 1.3 73.1 - - - +
330A LEU* 1.3 62.9 + - + +
331A ASN 3.3 0.7 + - - -
332A MET* 3.7 13.7 + - - +
333A ASP* 5.4 0.5 - - - +
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Residues in contact with LEU 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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261A ARG* 2.9 43.2 + - + +
262A VAL* 4.3 16.6 - - + -
265A HIS* 3.7 48.5 - - + +
322A LEU* 4.6 3.4 - - + -
326A LYS* 3.0 41.8 + - + +
327A PHE* 3.9 4.5 - - - +
329A GLU* 1.3 78.4 - - + +
331A ASN* 1.3 66.7 + - - +
332A MET 3.7 0.2 - - - -
333A ASP* 3.9 1.0 - - - +
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Residues in contact with ASN 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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258A PHE* 3.1 39.4 + - + -
261A ARG* 3.3 18.0 - - - +
262A VAL* 4.4 0.8 - - - +
327A PHE* 2.9 42.7 + - - +
328A GLU 3.1 3.3 + - - -
330A LEU* 1.3 86.3 - - - +
332A MET* 1.3 63.4 + - - +
333A ASP* 3.3 6.5 - - - -
334A LEU* 3.0 6.6 + - - +
335A PHE* 2.8 45.6 + - + -
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Residues in contact with MET 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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328A GLU* 2.9 32.2 + - + +
329A GLU* 3.7 10.4 + - - +
330A LEU 3.7 1.8 - - - -
331A ASN* 1.3 76.5 - - - +
333A ASP* 1.3 64.4 + - - +
335A PHE* 3.0 13.0 + - + +
336A ARG* 2.9 58.3 + - - +
370A LYS* 3.8 32.5 - - + +
374A LEU* 4.4 12.3 - - - -
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Residues in contact with ASP 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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261A ARG* 2.7 44.8 + - - -
329A GLU 5.4 0.3 - - - +
330A LEU 3.9 1.0 - - - +
331A ASN 3.8 4.2 - - - -
332A MET* 1.3 75.9 + - - +
334A LEU* 1.3 70.4 + - - +
336A ARG* 3.4 6.9 + - - +
337A SER* 3.1 22.3 + - - -
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Residues in contact with LEU 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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253A LEU* 4.4 16.8 - - + +
257A ASP* 4.1 18.4 - - + -
258A PHE* 3.7 27.9 - - + -
261A ARG* 3.7 51.1 - - + +
331A ASN* 3.0 9.6 + - - +
333A ASP* 1.3 80.3 + - - +
335A PHE* 1.3 67.4 + - - +
337A SER* 2.9 25.4 + - - +
338A THR* 3.7 8.5 + - - +
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Residues in contact with PHE 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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258A PHE* 3.7 33.9 - + - -
327A PHE* 4.0 21.5 - + - -
328A GLU* 4.0 17.3 - - + -
331A ASN* 2.8 39.5 + - + -
332A MET* 3.0 12.3 + - + +
334A LEU* 1.3 77.7 - - - +
336A ARG* 1.3 57.3 + - - +
338A THR* 2.7 29.2 + - - -
339A MET* 4.5 2.1 - - - +
368A ILE* 4.1 8.7 - - + -
370A LYS* 3.6 32.8 - - + -
371A ILE* 3.5 24.3 - - + +
374A LEU* 3.6 21.6 - - + +
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Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A MET* 2.9 44.1 + - - +
333A ASP* 4.0 6.5 - - - +
335A PHE* 1.3 76.6 - - - +
337A SER* 1.3 62.2 + - - +
339A MET* 3.0 28.0 + - + +
340A LYS 4.4 0.9 + - - -
374A LEU* 3.4 35.8 - - + +
377A GLU* 5.2 2.4 + - - -
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.5 19.9 - - - +
333A ASP 3.1 15.9 + - - -
334A LEU* 2.9 22.6 + - - +
335A PHE 3.3 0.2 - - - -
336A ARG* 1.3 77.1 - - - +
338A THR* 1.3 59.9 + - - +
339A MET 3.1 1.4 + - - -
340A LYS* 3.3 9.6 + - - +
341A PRO* 3.3 16.5 - - - +
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Residues in contact with THR 338 (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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223A PHE* 3.4 16.6 - - - -
225A LEU* 4.2 26.2 - - + -
230A PHE* 3.2 42.3 - - + -
253A LEU* 4.0 17.5 - - + -
258A PHE* 5.6 1.6 - - + -
334A LEU 3.8 9.0 - - - +
335A PHE* 2.7 23.0 + - - +
336A ARG 3.1 0.4 - - - -
337A SER* 1.3 76.4 + - - +
339A MET* 1.3 70.4 + - - +
340A LYS 3.3 0.4 + - - -
341A PRO* 3.5 2.8 - - - +
342A VAL* 3.5 7.8 - - - +
371A ILE* 5.0 2.5 - - + +
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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