Contacts of the helix formed by residues 317 - 332 (chain A) in PDB entry 5E97
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 ASP 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 2.9 21.3 + - - +
314A ASP* 4.1 11.5 - - - +
315A VAL 3.2 0.4 - - - -
316A LEU* 1.3 73.6 - - - +
318A ILE* 1.3 65.5 + - - +
319A PHE 3.1 0.2 - - - -
320A ILE* 3.0 37.7 + - + +
321A SER 4.0 1.7 + - - -
428A ARG 5.2 4.3 - - - +
429A ARG* 5.0 6.6 - - - +
432A ARG* 2.8 32.8 + - - -
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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
----------------------------------------------------------
270A GLN* 5.8 1.8 - - - +
297A HIS* 4.6 6.1 - - - +
298A TYR 5.4 0.7 - - - +
299A TYR* 3.8 37.9 - - + +
314A ASP 3.4 17.7 - - - +
315A VAL* 3.0 24.9 + - + +
317A ASP* 1.3 77.1 - - - +
319A PHE* 1.3 63.7 + - - +
321A SER* 3.1 24.5 + - - +
322A SER* 3.4 10.5 + - - +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 3.9 11.9 - + - -
297A HIS* 3.7 30.7 - + + -
299A TYR* 3.9 16.8 - - + +
316A LEU 3.3 13.9 + - - +
317A ASP 3.1 0.2 - - - -
318A ILE* 1.3 81.6 - - - +
320A ILE* 1.3 61.7 + - - +
322A SER* 3.2 3.5 + - - -
323A VAL* 3.0 49.3 + - + +
341A LEU* 3.6 24.5 - - + -
368A LYS* 3.9 23.6 - - + -
371A LEU* 3.9 27.6 - - + -
372A SER* 3.3 27.6 - - - -
377A ILE* 5.4 0.2 - - + -
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP* 3.0 39.1 + - + +
319A PHE* 1.3 76.4 - - - +
321A SER* 1.3 62.5 + - - +
323A VAL* 3.3 3.8 + - - +
324A GLN* 3.0 37.2 + - - +
371A LEU* 3.8 35.2 - - + -
375A MET* 3.8 24.9 - - + -
432A ARG* 4.8 0.9 - - - +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP 4.0 1.2 + - - -
318A ILE* 3.1 17.0 + - - +
320A ILE* 1.3 76.2 - - - +
322A SER* 1.3 65.6 + - - +
324A GLN* 3.3 8.7 + - - +
325A LYS* 3.0 49.9 + - - +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLN* 4.5 4.5 + - - +
271A PRO* 3.5 18.9 - - - +
295A TRP* 3.9 23.3 - - - -
297A HIS* 4.0 16.6 + - - -
318A ILE* 3.4 9.1 + - - +
319A PHE 3.2 9.6 + - - -
321A SER* 1.3 78.9 + - - +
323A VAL* 1.3 64.1 + - - +
325A LYS* 3.2 3.0 + - - +
326A VAL* 3.0 26.7 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 4.0 14.4 - - + -
319A PHE* 3.0 54.4 + - + +
320A ILE 3.6 6.3 - - - +
322A SER* 1.3 77.6 - - - +
324A GLN* 1.3 62.0 + - - +
326A VAL* 3.3 3.3 + - - +
327A PHE* 3.1 48.8 + - + -
372A SER* 5.5 0.4 - - - -
375A MET* 3.6 33.0 - - + -
377A ILE* 4.4 11.2 - - + -
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.0 34.4 + - - +
321A SER* 3.8 7.2 - - - +
323A VAL* 1.3 73.6 - - - +
325A LYS* 1.3 59.8 + - + +
327A PHE* 3.3 7.8 + - - +
328A GLN* 2.9 28.1 + - - +
375A MET* 3.5 18.2 - - + +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 3.7 36.0 + - + +
276A ALA* 6.2 0.9 - - + -
321A SER* 3.0 39.7 + - - +
322A SER* 5.0 0.6 - - - +
324A GLN* 1.3 75.7 - - + +
326A VAL* 1.3 66.3 + - - +
328A GLN* 3.3 13.1 + - - +
329A VAL* 3.2 26.2 + - - +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 3.7 19.5 - - + -
279A LEU* 4.5 13.9 - - + -
293A VAL* 5.2 2.0 - - + -
295A TRP* 3.6 41.1 - - + +
322A SER 3.0 14.9 + - - +
323A VAL 3.7 6.3 - - - +
325A LYS* 1.3 74.8 - - - +
327A PHE* 1.3 60.3 + - + +
329A VAL* 3.1 8.0 + - - +
330A VAL* 2.9 35.2 + - + +
339A VAL* 3.8 28.3 - - + -
377A ILE* 6.0 0.2 - - + -
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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
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323A VAL* 3.1 40.9 + - + -
324A GLN* 3.8 8.3 - - - +
326A VAL* 1.3 77.8 - - + +
328A GLN* 1.3 57.1 + - - +
330A VAL* 4.4 2.5 - - + +
331A GLU* 2.8 52.6 + - + +
337A LYS 5.3 1.8 - - - -
339A VAL* 3.5 35.2 - - + -
375A MET* 3.4 22.0 - - + -
376A GLY* 3.6 28.3 - - - -
377A ILE* 4.0 9.9 - - + -
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Residues in contact with GLN 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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280A LYS* 5.3 6.1 - - - +
324A GLN 2.9 14.3 + - - +
325A LYS* 3.5 16.4 - - - +
326A VAL 3.2 0.2 - - - -
327A PHE* 1.3 76.8 - - - +
329A VAL* 1.3 77.2 + - - +
331A GLU* 4.0 3.8 - - - +
332A SER* 3.2 28.7 + - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 5.9 0.9 - - + -
276A ALA* 4.1 28.3 - - + +
279A LEU* 3.8 20.6 - - + -
280A LYS* 3.6 43.1 - - + +
283A LEU* 4.4 4.3 - - + -
325A LYS 3.2 12.7 + - - +
326A VAL* 3.1 9.0 + - - +
328A GLN* 1.3 84.7 - - - +
330A VAL* 1.3 66.0 + - - +
332A SER* 2.9 19.2 + - - -
333A THR* 2.8 16.9 + - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.9 2.5 - - + -
283A LEU* 3.9 20.2 - - + -
293A VAL* 4.3 10.5 - - + -
326A VAL* 2.9 28.1 + - + +
327A PHE* 4.0 4.9 - - + +
329A VAL* 1.3 74.1 - - - +
331A GLU* 1.3 66.0 + - - +
333A THR* 3.0 7.5 + - - -
334A ARG* 2.8 47.9 + - + +
337A LYS* 4.0 24.9 - - + +
339A VAL* 3.9 22.7 - - + -
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Residues in contact with GLU 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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327A PHE* 2.8 40.2 + - + +
328A GLN* 4.1 4.3 - - - +
330A VAL* 1.3 80.0 - - - +
332A SER* 1.3 60.0 + - - +
333A THR 3.5 0.3 + - - -
335A PRO* 3.3 37.7 - - - +
336A GLY* 3.3 22.0 + - - -
337A LYS 5.1 0.9 - - - +
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Residues in contact with SER 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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280A LYS* 3.6 28.6 + - - -
284A LYS* 4.6 5.9 + - - -
328A GLN* 3.2 18.5 + - - -
329A VAL* 2.9 17.9 + - - -
331A GLU* 1.3 76.3 - - - +
333A THR* 1.4 61.0 + - - +
335A PRO* 5.2 0.7 - - - -
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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
------------------------------------------------------------
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