Contacts of the helix formed by residues 327 - 341 (chain A) in PDB entry 3DAN
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 MET 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A GLU* 3.3 24.0 - - + +
307A ILE* 3.8 25.1 - - + +
310A ALA* 3.7 24.9 - - + -
311A ILE* 3.9 14.8 - - + -
319A VAL* 5.6 1.3 - - + -
323A ALA* 3.6 22.9 - - + +
324A ILE* 3.0 16.9 + - + +
325A GLU 3.3 1.0 - - - -
326A GLN* 1.3 78.3 - - - +
328A PRO* 1.3 64.9 - - - +
330A THR* 3.3 9.7 + - + +
331A LYS* 3.1 26.1 + - + +
441A ILE* 3.6 36.6 - - + -
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Residues in contact with PRO 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU* 3.1 17.0 - - + +
325A GLU 5.0 1.6 - - - +
326A GLN* 3.2 12.3 - - - +
327A MET* 1.3 87.6 - - - +
329A LEU* 1.3 59.4 + - - +
331A LYS* 3.4 13.5 + - + +
332A SER* 3.1 22.9 + - - -
398A VAL* 3.8 23.9 - - + +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.9 15.0 - - + -
302A GLN* 3.7 37.9 - - + +
303A LEU* 3.7 19.5 - - + -
306A GLU* 2.7 24.5 + - - +
328A PRO* 1.3 70.6 - - - +
330A THR* 1.3 59.3 + - - +
332A SER* 3.1 1.9 + - - -
333A VAL* 2.8 32.1 + - + +
394A PRO* 4.0 21.1 - - + +
395A ASP* 4.0 20.2 - - + -
398A VAL* 4.3 6.7 - - + +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 3.7 10.7 - - - +
306A GLU* 2.8 21.6 + - - -
307A ILE* 3.3 24.8 - - - +
324A ILE* 6.0 0.9 - - + -
327A MET* 3.3 13.5 + - + +
329A LEU* 1.3 73.5 - - - +
331A LYS* 1.3 63.1 + - + +
333A VAL* 3.3 4.3 + - - +
334A VAL* 3.2 22.7 + - - +
437A ARG* 4.3 26.5 - - + +
440A VAL* 4.1 21.3 - - + -
441A ILE* 4.3 11.9 - - + -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 3.8 15.9 - - + +
325A GLU* 3.4 36.1 + - - +
327A MET* 3.1 21.2 + - + +
328A PRO* 3.6 10.4 - - + +
330A THR* 1.3 77.0 - - - +
332A SER* 1.3 61.3 + - - +
334A VAL* 3.4 4.8 + - - +
335A TYR* 3.1 35.8 + - + -
437A ARG* 3.5 50.8 + - - +
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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
----------------------------------------------------------
328A PRO 3.1 6.3 + - - -
329A LEU 3.1 6.0 + - - -
331A LYS* 1.3 73.5 - - - +
333A VAL* 1.3 60.2 + - - +
335A TYR* 3.2 2.7 + - - +
336A GLU* 2.8 31.2 + - - +
394A PRO 2.7 22.0 + - - -
395A ASP* 3.4 2.3 - - - -
396A ARG 3.4 0.3 + - - -
397A PHE* 3.0 40.1 + - - -
398A VAL* 3.6 24.0 - - - -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 5.1 2.0 - - + -
292A ILE* 3.1 37.0 - - + -
299A LEU* 4.3 13.2 - - + -
303A LEU* 4.1 22.0 - - + -
329A LEU* 2.8 21.0 + - + +
330A THR* 3.6 7.2 - - - +
332A SER* 1.3 76.3 - - - +
334A VAL* 1.3 67.2 + - - +
336A GLU* 3.4 0.8 + - - -
337A SER* 3.1 15.6 + - - -
392A TYR* 2.9 23.5 + - - +
394A PRO* 3.9 14.6 - - + +
440A VAL* 4.6 14.4 - - + -
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 5.5 1.6 - - + -
330A THR* 3.2 14.2 + - + +
331A LYS 3.7 6.5 - - - +
333A VAL* 1.3 75.4 - - - +
335A TYR* 1.3 66.9 + - + +
337A SER* 3.2 8.4 + - - -
338A LEU* 3.1 34.5 + - + +
433A VAL* 4.5 15.0 - - + +
436A THR* 3.6 35.2 - - + +
437A ARG* 3.9 33.4 - - + +
440A VAL* 4.2 12.8 - - + -
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Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS* 3.1 31.1 + - + -
332A SER* 3.2 4.7 + - - +
334A VAL* 1.3 76.2 - - + +
336A GLU* 1.3 57.2 + - - +
338A LEU* 3.2 15.1 + - + +
339A ARG* 2.9 27.9 + - - +
397A PHE* 3.6 24.4 - - + -
405A LEU* 3.5 39.7 - - + +
408A VAL* 4.4 7.4 - - + +
415A GLU* 3.6 35.6 + - + +
433A VAL* 4.4 11.2 - - + +
437A ARG* 2.9 31.8 + - - -
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A SER 2.8 21.2 + - - +
333A VAL* 3.8 2.5 - - - +
335A TYR* 1.3 70.6 - - - +
337A SER* 1.3 65.1 + - - +
339A ARG* 2.8 36.9 + - - -
340A ILE* 3.0 24.6 + - - +
391A GLU 3.3 0.9 - - - +
392A TYR* 3.3 30.2 - - + -
393A VAL 2.8 39.1 + - - +
396A ARG* 2.9 28.3 + - - -
397A PHE* 3.4 7.8 - - + -
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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
----------------------------------------------------------
284A LEU* 4.0 8.3 - - - +
287A ASN* 4.3 1.9 - - - +
288A THR* 2.9 43.9 + - - -
291A TRP* 4.1 6.7 + - - -
333A VAL 3.1 14.1 + - - -
334A VAL* 3.2 10.5 + - - -
336A GLU* 1.3 77.9 - - - +
338A LEU* 1.3 61.1 + - - +
340A ILE* 3.7 5.7 - - - +
341A GLU* 3.2 26.9 + - - +
392A TYR* 3.7 12.5 - - - -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.6 37.5 - - + -
334A VAL* 3.1 31.0 + - + +
335A TYR* 3.2 17.9 + - + +
337A SER* 1.3 78.3 - - - +
339A ARG* 1.3 58.4 + - - +
341A GLU 4.7 3.1 - - - -
342A PRO* 3.5 24.3 - - - +
343A PRO* 4.1 8.5 - - + -
376A GLN* 4.8 1.4 + - - -
408A VAL* 4.5 4.2 - - + +
410A TRP* 3.7 60.1 + - + +
432A VAL* 5.2 2.5 - - + -
433A VAL* 4.7 7.4 - - + -
436A THR* 5.7 0.2 - - - +
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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
----------------------------------------------------------
335A TYR 2.9 16.1 + - - +
336A GLU* 2.8 42.5 + - - +
337A SER 3.3 0.2 - - - -
338A LEU* 1.3 78.6 - - - +
340A ILE* 1.3 80.0 + - - +
341A GLU 3.3 0.7 + - - -
342A PRO* 3.6 2.4 - - - +
380A THR* 2.9 60.0 + - + +
381A LYS* 4.0 6.9 - - - +
386A PHE* 3.5 40.6 - - + -
389A PRO* 3.0 35.1 + - - +
391A GLU 3.2 12.3 + - - -
396A ARG* 3.5 10.9 - - - +
397A PHE* 4.0 8.1 - - + -
407A TYR 5.3 0.2 - - - +
408A VAL* 4.5 11.8 - - + +
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Residues in contact with ILE 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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291A TRP* 3.6 51.2 - - + +
336A GLU 3.0 18.7 + - - +
337A SER 3.7 3.8 - - - +
339A ARG* 1.3 97.8 - - - +
341A GLU* 1.3 64.0 + - - +
342A PRO* 3.8 3.0 - - - +
377A PRO* 5.6 0.9 - - - +
381A LYS* 3.3 33.0 + - - +
389A PRO 4.5 1.1 - - - +
390A GLU 3.9 10.5 - - - +
391A GLU 3.7 9.2 - - - +
392A TYR* 3.7 36.8 - - + +
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Residues in contact with GLU 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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284A LEU* 5.5 1.4 - - - +
287A ASN* 3.4 33.4 + - + +
290A LYS* 3.0 30.4 + - - -
291A TRP* 3.0 26.4 + - + +
337A SER 3.2 13.0 + - - +
338A LEU 3.9 0.4 - - - -
339A ARG 3.2 0.2 - - - -
340A ILE* 1.3 83.4 - - + +
342A PRO* 1.3 72.7 - - - +
343A PRO* 3.1 9.4 - - - +
377A PRO* 6.1 0.2 - - - -
460A GLY* 5.8 2.4 - - - -
461A ALA* 5.4 1.0 - - - +
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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
------------------------------------------------------------
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