Contacts of the helix formed by residues 428 - 446 (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 GLY 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.8 15.9 - - - -
426A CYS* 3.2 11.4 - - - -
427A ALA* 1.3 79.5 - - - +
429A LYS* 1.3 64.6 + - - +
430A ASP 3.4 2.0 - - - -
431A PHE* 3.0 8.3 + - - +
432A VAL* 2.9 25.7 + - - +
600A HEM 3.7 21.0 - - - -
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Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A TRP* 3.7 26.2 - - + -
411A SER* 3.8 11.7 - - - +
415A GLU* 2.9 35.2 + - - +
416A THR 4.5 1.0 - - - -
417A GLU 2.6 32.0 + - - +
418A SER* 4.2 5.2 + - - +
419A PRO* 4.1 12.1 - - + -
425A GLN* 3.7 16.4 - - + +
426A CYS* 3.2 18.0 + - - +
427A ALA 3.3 2.4 + - - -
428A GLY* 1.3 77.5 - - - +
430A ASP* 1.3 90.1 + - - +
432A VAL* 3.4 3.5 + - - +
433A VAL* 3.2 22.4 + - - +
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Residues in contact with ASP 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER* 5.5 3.8 + - - -
419A PRO* 4.9 8.9 - - - +
427A ALA 5.3 0.4 + - - -
428A GLY 3.4 0.4 - - - -
429A LYS* 1.3 99.6 + - - +
431A PHE* 1.3 57.8 + - - +
433A VAL* 3.4 6.9 + - - +
434A LEU* 3.0 29.5 + - - +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.0 27.8 - - + +
133A SER* 4.4 4.5 - - - -
137A VAL* 4.0 28.7 - - + -
175A PHE* 4.0 14.8 - + - -
176A LEU* 4.2 9.0 - - + -
179A ALA* 4.9 2.9 - - + -
180A TYR* 3.5 35.2 - + - -
277A THR* 4.5 0.2 - - + -
428A GLY* 3.0 10.8 + - - +
430A ASP* 1.3 78.5 - - - +
432A VAL* 1.3 60.1 + - - +
434A LEU* 3.2 8.2 + - + +
435A ILE* 2.9 63.2 + - + +
600A HEM 3.8 19.1 - - + -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.8 2.9 - - + -
338A LEU* 5.2 2.7 - - + -
410A TRP* 3.0 42.0 - - + -
428A GLY 2.9 15.6 + - - +
429A LYS 3.6 0.2 - - - +
431A PHE* 1.3 76.4 - - - +
433A VAL* 1.3 67.1 + - + +
435A ILE* 3.4 12.4 - - + +
436A THR* 2.7 36.0 + - - +
600A HEM 3.4 56.1 - - + -
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 4.5 6.6 - - + +
335A TYR* 4.4 11.2 - - + +
338A LEU* 4.7 5.4 - - + -
410A TRP* 4.2 8.3 - - + +
415A GLU* 3.4 26.0 - - - +
429A LYS* 3.2 14.0 + - - +
430A ASP* 3.8 9.9 - - - +
431A PHE 3.3 0.2 - - - -
432A VAL* 1.3 88.3 - - + +
434A LEU* 1.3 64.7 + - - +
436A THR* 4.0 4.1 - - - -
437A ARG* 3.1 66.7 + - + +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.7 29.2 - - + -
138A ILE* 5.0 3.8 - - + -
321A LEU* 3.8 31.0 - - + -
324A ILE* 3.8 23.3 - - + -
430A ASP 3.0 18.5 + - - +
431A PHE* 3.6 8.5 - - + +
433A VAL* 1.3 78.9 - - - +
435A ILE* 1.3 59.5 + - - +
437A ARG* 3.2 8.6 + - - +
438A LEU* 2.9 42.6 + - + +
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Residues in contact with ILE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.2 10.1 - - + -
141A PHE* 3.6 14.8 - - + -
175A PHE* 3.8 33.9 - - + -
176A LEU* 5.4 1.3 - - + -
277A THR* 5.6 0.2 - - + -
281A VAL* 3.8 28.3 - - + -
285A PHE* 3.7 12.0 - - + -
431A PHE* 2.9 49.5 + - + +
432A VAL* 3.4 16.6 - - + +
434A LEU* 1.3 76.4 - - + +
436A THR* 1.3 62.0 + - - +
438A LEU* 3.2 9.2 + - - +
439A PHE* 2.9 26.5 + - - +
600A HEM 6.0 0.4 - - + -
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Residues in contact with THR 436 (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* 3.2 30.2 - - + +
285A PHE* 3.7 17.3 - - + -
288A THR* 4.0 25.6 - - + +
334A VAL* 3.6 30.5 - - + -
337A SER* 6.0 0.2 - - - -
338A LEU* 5.9 0.2 - - - -
432A VAL* 2.7 22.8 + - - +
433A VAL* 4.7 0.2 - - - -
435A ILE* 1.3 74.3 - - - +
437A ARG* 1.3 65.2 + - - +
439A PHE* 3.2 4.2 + - + +
440A VAL* 3.2 22.9 + - - +
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 3.9 28.1 - - + +
325A GLU* 4.0 18.6 + - - -
330A THR* 4.3 12.2 - - + +
331A LYS* 3.5 37.5 + - - +
334A VAL* 3.9 22.8 - - + +
335A TYR* 2.9 40.8 + - - -
433A VAL* 3.1 38.9 + - - +
434A LEU* 3.5 10.9 - - - +
436A THR* 1.3 76.8 - - - +
438A LEU* 1.3 56.5 + - - +
440A VAL* 3.3 2.9 + - - +
441A ILE* 2.9 36.7 + - + +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.1 23.1 - - + -
138A ILE* 4.2 18.2 - - + -
141A PHE* 3.4 35.9 - - + -
142A GLU* 6.0 1.8 - - + -
319A VAL* 3.8 28.0 - - + -
324A ILE* 3.9 15.3 - - + -
434A LEU* 2.9 26.2 + - + +
435A ILE* 3.5 11.4 - - - +
436A THR 3.2 0.2 - - - -
437A ARG* 1.3 75.3 - - - +
439A PHE* 1.3 59.7 + - - +
441A ILE* 4.1 6.3 - - + -
442A GLU* 2.8 38.1 + - + +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.4 9.8 - - + -
145A TYR* 3.9 23.6 - + - -
149A PHE* 4.3 15.7 - + - -
164A PHE* 3.7 37.2 - + - -
285A PHE* 3.6 51.1 - + + -
288A THR* 4.7 12.1 - - + -
289A LEU* 4.3 25.6 - - + -
435A ILE 2.9 13.2 + - - +
436A THR* 3.3 11.2 - - + +
437A ARG 3.2 0.2 - - - -
438A LEU* 1.3 77.0 - - - +
440A VAL* 1.3 64.4 + - + +
442A GLU* 4.0 1.4 - - - +
443A LEU* 3.1 29.1 + - + +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 4.1 24.7 - - + -
292A ILE* 5.1 4.3 - - + -
303A LEU* 4.3 11.2 - - + -
307A ILE* 4.2 5.6 - - + -
330A THR* 4.1 17.7 - - + -
333A VAL* 4.6 9.6 - - + -
334A VAL* 4.2 11.9 - - + -
436A THR 3.2 13.3 + - - +
437A ARG 3.3 6.3 + - - +
439A PHE* 1.3 79.2 - - + +
441A ILE* 1.3 63.9 + - - +
443A LEU* 3.3 8.2 + - + +
444A PHE* 3.1 44.1 + - + -
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Residues in contact with ILE 441 (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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307A ILE* 3.9 21.9 - - + +
311A ILE* 4.3 2.5 - - + -
319A VAL* 4.1 17.9 - - + -
324A ILE* 3.7 31.0 - - + -
327A MET* 3.6 32.1 - - + -
330A THR* 4.3 8.5 - - + -
437A ARG* 2.9 27.0 + - + +
438A LEU* 3.6 9.9 - - + +
440A VAL* 1.3 75.9 - - - +
442A GLU* 1.3 66.4 + - + +
444A PHE 3.3 2.4 + - - -
445A ARG* 3.0 42.9 + - - +
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Residues in contact with GLU 442 (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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141A PHE* 3.8 24.0 - - + -
142A GLU* 3.7 37.0 - - + +
145A TYR* 4.6 2.7 - - + -
146A THR* 3.9 14.6 + - - -
149A PHE* 3.7 21.1 - - + -
319A VAL* 4.2 5.0 - - - +
438A LEU* 2.8 26.1 + - + +
439A PHE 4.0 2.2 - - - +
441A ILE* 1.3 73.7 - - + +
443A LEU* 1.3 64.1 + - - +
445A ARG* 3.5 29.3 + - - +
446A ARG* 3.4 21.3 + - - +
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Residues in contact with LEU 443 (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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149A PHE* 3.8 28.0 - - + -
289A LEU* 3.9 22.9 - - + -
292A ILE* 5.2 2.9 - - + -
439A PHE* 3.1 20.6 + - + +
440A VAL* 3.4 13.2 - - + +
442A GLU* 1.3 78.2 - - - +
444A PHE* 1.3 72.5 + - + +
447A TYR* 2.9 52.3 + - + +
450A PHE* 3.5 37.0 - - + -
465A LEU* 6.3 2.5 - - + -
468A LEU* 5.4 4.0 - - + -
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Residues in contact with PHE 444 (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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292A ILE* 3.8 25.8 - - + -
300A HIS* 3.8 43.7 - + + -
303A LEU* 3.6 28.9 - - + -
304A ALA* 4.1 9.8 - - + +
307A ILE* 3.8 15.9 - - + -
308A ARG* 2.8 33.6 + - - +
440A VAL* 3.1 34.5 + - + +
441A ILE 3.7 0.4 - - - -
443A LEU* 1.3 87.9 - - + +
445A ARG* 1.3 61.3 + - - +
446A ARG 3.2 1.3 - - - -
447A TYR* 3.5 16.6 - - + -
448A ASP 4.0 7.6 - - - -
450A PHE* 4.0 14.8 - + - -
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Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 3.0 27.5 + - - -
307A ILE* 4.1 4.7 - - + -
308A ARG* 4.3 11.6 + - + +
311A ILE* 3.4 34.0 - - + +
317A GLY 4.0 17.8 + - - -
318A ASN* 5.2 1.0 - - - +
319A VAL* 3.2 12.1 - - - +
441A ILE* 3.0 27.4 + - + +
442A GLU* 3.5 25.7 + - - +
443A LEU 3.4 0.6 - - - -
444A PHE* 1.3 79.1 - - - +
446A ARG* 1.3 60.8 + - + +
471A ALA* 4.0 10.9 - - - +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 4.2 18.1 + - - +
149A PHE* 3.7 19.7 - - + +
150A GLU* 3.3 33.0 + - - +
153A GLU* 2.9 26.4 + - - +
442A GLU 3.4 13.9 + - - +
443A LEU 4.0 1.8 - - - +
445A ARG* 1.3 83.1 - - + +
447A TYR* 1.3 90.2 + - + +
470A ARG* 3.8 22.2 + - - +
471A ALA* 2.9 24.1 + - - +
472A SER 4.7 0.3 + - - -
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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
------------------------------------------------------------
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