Contacts of the helix formed by residues 326 - 341 (chain A) in PDB entry 3DDN
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 PRO 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLU 3.4 15.9 - - - +
323A GLU 3.6 7.2 - - - +
324A VAL 3.2 5.4 - - - +
325A ALA* 1.3 96.1 - - + +
327A TRP* 1.3 58.0 + - - +
328A LEU 3.2 0.6 + - - -
329A ASP* 4.0 8.0 + - + +
330A LEU 4.1 4.0 + - - -
431A LEU* 3.6 30.8 - - + +
436A LEU* 4.2 24.7 - - + -
438A GLN* 4.4 6.6 - - - +
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Residues in contact with TRP 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 GLU 3.4 24.9 + - - -
324A VAL* 2.7 18.6 + - - +
326A PRO* 1.3 74.4 - - + +
328A LEU* 1.3 62.3 + - - -
329A ASP 3.3 0.2 - - - -
330A LEU* 3.2 26.1 + - + +
331A VAL* 3.0 28.3 + - + +
357A LEU* 3.4 29.9 - - + +
365A LEU* 4.1 18.6 - - + -
411A SER* 3.8 33.2 - - - -
413A VAL* 3.8 19.5 - - + -
429A GLY 3.7 19.7 - - - -
430A THR* 3.8 7.9 - - + -
431A LEU* 3.4 44.6 - - + +
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Residues in contact with LEU 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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315A VAL* 4.3 31.4 - - + -
320A VAL* 4.7 6.1 - - + -
324A VAL* 4.1 9.9 - - + +
325A ALA* 3.2 24.2 + - + +
327A TRP* 1.3 77.9 - - - +
329A ASP* 1.3 58.8 + - + +
332A ARG* 3.0 25.1 + - - +
364A VAL* 3.7 21.8 - - + -
365A LEU* 3.4 23.8 - - + -
368A SER* 3.3 24.9 + - - +
383A THR* 5.7 7.0 - - + -
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Residues in contact with ASP 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 4.7 0.2 + - - -
326A PRO 4.0 5.4 + - - +
327A TRP 3.3 0.2 - - - -
328A LEU* 1.3 78.3 - - - +
330A LEU* 1.3 65.4 + - - +
332A ARG* 2.8 36.6 + - - +
333A LYS* 3.3 37.8 + - - +
438A GLN* 3.2 20.1 - - - +
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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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326A PRO 4.1 1.8 + - - +
327A TRP* 3.2 35.2 + - + +
329A ASP* 1.3 78.3 - - - +
331A VAL* 1.3 58.9 + - - +
333A LYS* 2.9 20.4 + - + +
334A LEU* 3.0 26.3 + - + +
429A GLY* 3.7 29.6 - - - +
430A THR 3.8 11.0 - - - +
431A LEU* 4.0 9.6 - - + -
438A GLN* 4.1 33.5 + - + +
439A LYS 4.0 16.8 - - - +
452A ALA* 4.2 13.2 - - + -
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Residues in contact with VAL 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 TRP* 3.0 23.8 + - + +
328A LEU 4.0 3.4 - - - +
330A LEU* 1.3 74.4 - - + +
332A ARG* 1.3 63.3 + - - +
334A LEU* 3.3 9.1 + - + +
335A GLY 3.1 17.7 + - - -
351A VAL* 4.8 2.0 - - + -
365A LEU* 3.4 40.4 - - + +
368A SER* 4.0 2.7 - - - -
369A ALA* 3.7 18.1 - - + +
413A VAL* 3.8 33.9 - - + -
415A VAL* 4.4 9.4 - - + -
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Residues in contact with ARG 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 LEU 3.0 17.6 + - - +
329A ASP* 2.8 33.4 + - - +
331A VAL* 1.3 76.3 - - - +
333A LYS* 1.3 81.0 + - - +
335A GLY 3.3 1.0 + - - -
336A VAL* 3.0 35.9 + - - +
368A SER* 3.3 18.1 - - - +
371A ARG* 4.1 26.4 - - + +
372A GLY* 3.1 29.5 - - - +
375A SER* 5.4 2.7 + - - +
527A ASP 5.9 0.2 + - - -
528A LEU* 5.5 2.6 + - - +
529A SER 3.2 26.4 + - - -
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Residues in contact with LYS 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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329A ASP* 3.3 16.5 + - - +
330A LEU* 2.9 9.5 + - + +
332A ARG* 1.3 104.7 - - - +
334A LEU* 1.3 59.5 + - + +
336A VAL* 3.3 10.0 + - + +
337A LEU* 3.0 34.3 + - + +
438A GLN* 2.6 34.3 - - - +
440A ILE* 5.8 0.4 - - + -
452A ALA* 2.8 31.7 + - + +
453A GLN* 4.7 2.2 - - - +
528A LEU* 3.2 36.8 + - + +
529A SER* 4.1 4.2 + - - +
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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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330A LEU* 3.0 26.0 + - + +
331A VAL* 3.3 15.4 + - - +
333A LYS* 1.3 76.1 - - + +
335A GLY* 1.3 56.8 + - - +
337A LEU* 3.2 4.4 + - + +
338A ALA* 2.8 32.9 + - - +
413A VAL* 3.5 43.3 - - + +
415A VAL* 3.7 17.3 - - + -
427A VAL* 4.0 18.4 - - + +
428A SER* 3.6 23.6 - - - +
429A GLY* 3.6 12.1 - - - +
440A ILE* 4.5 10.5 - - + -
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Residues in contact with GLY 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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331A VAL 3.1 11.7 + - - -
332A ARG 3.3 2.8 + - - -
334A LEU* 1.3 72.4 - - - +
336A VAL* 1.3 64.5 + - - +
338A ALA* 3.6 1.9 + - - +
339A GLY* 3.1 17.0 + - - -
349A LEU* 4.9 1.3 - - - -
369A ALA* 3.5 25.1 - - - -
373A LEU* 3.4 21.4 - - - +
415A VAL* 4.5 11.2 - - - +
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Residues in contact with VAL 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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332A ARG* 3.0 31.2 + - - +
333A LYS* 3.5 11.9 - - - +
335A GLY* 1.3 76.5 - - - +
337A LEU* 1.3 57.4 + - - +
339A GLY* 3.6 1.6 - - - -
340A VAL* 3.0 31.3 + - + +
372A GLY* 3.5 21.7 - - - +
373A LEU* 4.6 0.4 - - - +
375A SER* 3.7 12.3 - - - +
526A VAL* 3.5 29.6 - - + -
527A ASP 4.9 3.8 - - - +
528A LEU* 4.3 7.6 - - + -
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Residues in contact with LEU 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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333A LYS 3.0 17.9 + - - +
334A LEU* 3.4 5.6 - - - +
336A VAL* 1.3 76.7 - - - +
338A ALA* 1.3 60.5 + - - +
340A VAL* 3.1 4.5 + - + +
341A LEU* 2.8 42.3 + - + +
427A VAL* 4.0 21.1 - - + -
440A ILE* 3.4 39.0 - - + -
443A ILE* 5.2 4.5 - - + -
456A ASN* 5.9 0.4 - - + -
458A ILE* 4.3 14.6 - - + -
499A LEU* 5.7 2.5 - - + -
526A VAL* 3.8 27.8 - - + -
528A LEU* 3.8 14.6 - - + -
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Residues in contact with ALA 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 LEU 2.8 19.3 + - - +
335A GLY* 4.1 3.6 - - - +
337A LEU* 1.3 73.3 - - - +
339A GLY* 1.3 57.7 + - - +
342A SER* 2.8 29.3 + - - -
349A LEU* 4.9 2.5 - - + -
373A LEU* 5.0 0.2 - - - -
415A VAL* 4.0 21.8 - - + +
417A ALA* 3.8 23.7 - - + +
425A VAL* 4.0 7.7 - - + +
427A VAL* 3.9 17.6 - - + +
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Residues in contact with GLY 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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335A GLY 3.1 10.7 + - - -
336A VAL 3.6 3.6 - - - -
338A ALA* 1.3 74.1 - - - +
340A VAL* 1.3 65.0 + - - +
342A SER* 3.4 20.5 + - - +
344A GLU 5.8 1.0 - - - -
346A PRO* 5.1 1.7 - - - +
373A LEU* 3.5 28.9 - - - +
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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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336A VAL* 3.0 21.7 + - + +
337A LEU* 3.7 6.5 - - + +
339A GLY* 1.3 78.9 - - - +
341A LEU* 1.3 59.2 + - + +
342A SER 3.2 2.5 + - - +
458A ILE* 4.6 11.7 - - + -
522A LYS* 3.1 22.3 + - - -
524A GLU* 3.6 36.3 - - + +
525A VAL 5.6 0.7 - - - +
526A VAL* 3.9 33.4 - - + -
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Residues in contact with LEU 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 LEU* 2.8 19.5 + - + +
338A ALA 4.1 0.2 - - - -
340A VAL* 1.3 76.3 - - + +
342A SER* 1.3 59.2 + - - +
343A ASP* 3.9 2.4 + - - +
425A VAL* 3.7 25.2 - - + +
427A VAL* 3.5 31.9 - - + -
443A ILE* 3.6 32.5 - - + -
444A ASN* 5.3 2.7 - - - +
458A ILE* 3.7 40.6 - - + -
460A HIS* 4.1 18.2 + - + +
522A LYS* 3.5 17.5 - - - +
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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