Contacts of the helix formed by residues 333 - 350 (chain A) in PDB entry 3EDY
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 2.6 40.9 + - - +
26A ASP* 3.4 22.2 - - - -
27A GLN* 3.1 18.8 + - - +
175A ARG* 4.1 0.3 + - - -
332A LEU* 1.3 76.6 - - - +
334A SER* 1.3 63.2 + - - +
335A ALA* 4.0 2.5 - - - -
336A TYR* 3.0 18.0 + - - +
337A ILE* 3.0 23.9 + - - +
702A EDO 4.3 0.7 - - - -
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 2.9 20.3 + - - -
332A LEU 3.8 0.4 + - - -
333A SER* 1.3 70.9 - - - +
335A ALA* 1.3 64.0 + - - +
337A ILE* 4.0 8.3 - - - -
338A GLN* 3.0 43.4 + - - +
702A EDO 3.9 10.9 - - - -
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO 3.8 21.0 + - - +
24A GLU* 4.2 4.9 - - + -
26A ASP* 5.2 0.2 + - - -
168A ASP* 3.5 29.5 - - - +
169A PHE* 3.9 4.9 - - + -
333A SER* 3.2 7.0 - - - +
334A SER* 1.3 78.6 - - - +
336A TYR* 1.3 62.5 + - - +
338A GLN* 4.3 2.3 - - - +
339A ARG* 3.2 24.3 + - - +
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Residues in contact with TYR 336 (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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24A GLU* 3.9 2.2 - - - +
169A PHE* 3.6 24.2 - + + -
175A ARG* 3.3 43.8 - - - +
302A GLU* 4.0 8.7 + - - -
304A PHE* 3.7 28.4 - - - +
305A LEU* 4.5 10.4 + - + +
325A TYR* 4.8 7.8 + - - -
327A ASP* 5.2 2.2 + - - -
332A LEU* 3.8 40.8 - - + -
333A SER* 3.0 22.4 + - - +
335A ALA* 1.3 75.2 - - - +
337A ILE* 1.3 62.5 + - - +
339A ARG* 3.2 1.6 + - - +
340A VAL* 2.8 54.3 + - + +
378A PHE* 4.8 4.5 - + - -
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Residues in contact with ILE 337 (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 GLU* 3.5 31.9 - - + -
332A LEU* 4.2 12.6 - - + -
333A SER 3.0 15.2 + - - +
334A SER* 3.5 15.9 - - - +
336A TYR* 1.3 82.3 - - - +
338A GLN* 1.3 69.9 + - + +
341A ASN* 3.0 24.3 + - - +
378A PHE* 3.4 42.1 - - + -
415A VAL* 4.1 23.8 - - + -
416A PHE* 3.8 10.0 - - + -
702A EDO 4.2 8.5 - - - -
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Residues in contact with GLN 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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334A SER* 3.0 32.3 + - - +
335A ALA* 4.3 3.1 - - - +
337A ILE* 1.3 78.5 - - + +
339A ARG* 1.3 64.1 + - - +
341A ASN* 3.2 9.1 + - - +
342A THR* 3.0 24.2 + - - -
415A VAL* 3.6 31.1 + - - +
416A PHE* 3.7 18.2 - - - -
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Residues in contact with ARG 339 (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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52A ALA* 3.5 16.3 - - + +
53A LEU 2.9 24.4 + - - +
55A GLN* 3.3 29.3 + - - +
118A ASP* 3.0 27.1 + - - +
119A PHE* 3.3 19.6 - - + -
168A ASP* 3.0 21.9 + - + +
169A PHE* 3.7 26.0 - - + -
305A LEU* 6.1 0.4 - - + -
335A ALA 3.2 18.4 + - - +
336A TYR 3.2 0.4 + - - +
338A GLN* 1.3 77.3 - - - +
340A VAL* 1.3 66.2 + - + +
342A THR* 3.0 5.5 + - - -
343A GLU* 2.8 50.8 + - + +
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Residues in contact with VAL 340 (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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169A PHE* 5.4 0.4 - - + -
304A PHE* 4.0 15.5 - - + -
305A LEU* 5.0 4.5 - - + -
308A LEU* 4.0 27.4 - - + -
336A TYR* 2.8 60.3 + - + +
339A ARG* 1.3 72.1 - - + +
341A ASN* 1.3 63.3 + - - +
343A GLU* 3.0 4.6 + - - +
344A LEU* 3.0 30.5 + - + +
378A PHE* 3.6 28.7 - - + -
379A PRO* 4.7 0.7 - - + -
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Residues in contact with ASN 341 (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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337A ILE 3.0 19.4 + - - +
338A GLN* 3.4 8.7 + - - +
339A ARG 3.2 0.2 - - - -
340A VAL* 1.3 76.7 - - - +
342A THR* 1.3 57.3 + - - +
344A LEU* 3.2 12.2 + - - +
345A MET* 2.9 29.4 + - - +
378A PHE* 4.2 2.2 - - + -
382A SER* 2.7 28.4 + - - -
383A PRO* 3.2 12.1 - - - +
384A TYR* 3.5 22.2 - - - -
416A PHE* 3.5 30.8 - - + -
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Residues in contact with THR 342 (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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55A GLN* 3.5 33.4 + - - +
58A VAL* 4.0 31.0 - - + +
61A LEU* 4.4 12.8 - - + -
89A VAL* 6.0 0.7 - - + -
338A GLN 3.0 14.4 + - - -
339A ARG* 3.0 10.8 + - - -
341A ASN* 1.3 73.5 + - - +
343A GLU* 1.3 60.6 + - - +
345A MET* 3.1 11.5 + - + +
346A LYS* 2.8 27.6 + - + +
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Residues in contact with GLU 343 (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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55A GLN* 2.9 15.6 + - - -
119A PHE* 3.5 22.2 - - + -
308A LEU* 3.3 46.5 - - + +
311A LEU* 5.8 1.2 - - - +
312A SER* 3.7 5.2 + - - -
339A ARG* 2.8 42.8 + - + +
340A VAL 3.0 3.0 + - - +
342A THR* 1.3 75.6 - - - +
344A LEU* 1.3 63.3 + - - +
346A LYS* 2.8 32.6 + - - +
347A ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 344 (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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304A PHE* 5.2 0.7 - - + -
307A TRP* 5.3 0.2 - - + -
308A LEU* 4.0 17.3 - - + -
340A VAL* 3.0 27.3 + - + +
341A ASN* 3.2 9.6 + - - +
343A GLU* 1.3 73.9 - - - +
345A MET* 1.3 58.8 + - - +
347A ALA* 3.3 6.5 + - - +
348A ALA* 3.0 27.9 + - - +
354A LEU* 3.5 27.4 - - + +
356A PHE* 4.3 11.0 - - + -
378A PHE* 4.6 1.1 - - + -
379A PRO* 4.0 15.0 - - + -
382A SER* 3.5 29.2 - - - +
384A TYR* 4.2 18.0 - - + +
385A VAL* 3.8 16.8 - - + -
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Residues in contact with MET 345 (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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58A VAL* 3.6 20.2 - - + +
61A LEU* 3.2 35.0 - - + -
62A SER* 3.5 23.6 - - - +
65A VAL* 3.4 11.9 - - + +
341A ASN* 2.9 18.3 + - - +
342A THR* 3.1 13.0 + - + +
344A LEU* 1.3 73.7 - - - +
346A LYS* 1.3 60.1 + - - +
348A ALA* 3.1 6.5 + - - -
349A ALA* 2.9 25.3 + - - +
384A TYR* 3.2 51.1 - - + +
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Residues in contact with LYS 346 (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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55A GLN* 3.7 16.8 - - - +
61A LEU* 3.7 19.9 - - + +
82A LEU* 5.9 0.2 - - - -
85A VAL* 3.9 27.1 - - + +
89A VAL* 4.4 5.2 - - + -
116A THR* 3.3 11.8 + - - -
118A ASP* 2.7 27.1 + - - +
119A PHE* 4.6 0.4 - - - -
312A SER* 3.0 24.4 + - - +
342A THR* 2.8 15.5 + - + +
343A GLU* 2.8 37.3 + - - +
345A MET* 1.3 76.5 - - - +
347A ALA* 1.3 60.5 + - - +
349A ALA* 3.3 11.7 + - - +
350A ARG* 3.2 26.0 + - - +
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Residues in contact with ALA 347 (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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311A LEU* 4.9 9.0 - - + -
343A GLU 3.1 12.7 + - - +
344A LEU 3.5 9.2 - - - +
345A MET 3.2 0.2 - - - -
346A LYS* 1.3 75.4 - - - +
348A ALA* 1.3 61.6 + - - +
350A ARG* 3.1 12.6 + - - +
352A LEU* 3.1 47.7 + - + +
354A LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 348 (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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65A VAL* 3.8 18.6 - - + +
68A VAL* 4.3 5.0 - - - +
69A SER* 5.8 0.2 - - - -
79A TYR* 4.3 6.2 - - - -
344A LEU 3.0 13.3 + - - +
345A MET* 3.1 10.5 + - - +
347A ALA* 1.3 76.8 - - - +
349A ALA* 1.3 62.2 + - - +
351A GLY* 3.1 13.3 + - - -
352A LEU 4.3 6.3 - - - -
384A TYR* 4.7 7.9 - - + +
502A PHE* 3.7 35.7 - - + +
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Residues in contact with ALA 349 (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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61A LEU* 3.6 24.9 - - + -
64A LEU* 5.6 0.4 - - + -
65A VAL* 3.8 12.5 - - + +
68A VAL* 4.3 7.7 - - - +
79A TYR* 3.4 10.4 - - - +
80A LEU* 2.9 35.1 + - + +
85A VAL* 4.4 9.9 - - + -
345A MET 2.9 13.1 + - - +
346A LYS 3.5 9.9 - - - +
347A ALA 3.3 0.2 - - - -
348A ALA* 1.3 77.2 - - - +
350A ARG* 1.3 57.3 + - - +
351A GLY 3.3 0.4 - - - -
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Residues in contact with ARG 350 (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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79A TYR* 3.6 7.1 - - - +
80A LEU 3.4 16.4 - - - +
82A LEU* 3.7 31.2 - - - +
85A VAL* 3.7 23.8 - - + -
311A LEU* 2.9 29.1 + - - +
312A SER* 4.2 2.8 + - - +
314A GLU 3.0 24.2 + - - -
315A SER* 3.2 20.8 + - - +
317A LEU* 3.4 17.5 - - - +
346A LYS* 3.2 20.0 - - - +
347A ALA* 3.1 11.5 + - - +
348A ALA 3.1 0.8 - - - -
349A ALA* 1.3 77.5 - - - +
351A GLY* 1.3 60.5 + - - +
352A LEU* 3.7 14.5 + - + +
704A EDO 2.8 23.0 + - - -
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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