Contacts of the helix formed by residues 402 - 420 (chain A) in PDB entry 4DTZ
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 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PHE* 4.1 9.4 - - - -
400A CYS* 3.1 9.9 - - - -
401A ILE* 1.3 80.5 - - - +
403A GLN* 1.3 55.0 + - - +
404A GLN 3.3 2.7 - - - -
405A PHE* 3.1 5.5 + - - +
406A ALA* 2.7 34.5 + - - +
500A HEM 3.6 31.7 - - - +
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PHE* 3.4 58.7 - - + +
399A ALA* 5.7 2.8 - - - +
400A CYS* 3.4 17.1 + - - +
401A ILE 3.3 3.6 - - - -
402A GLY* 1.3 77.3 - - - +
404A GLN* 1.3 83.9 + - + +
406A ALA* 3.4 1.4 + - - +
407A LEU* 3.0 37.6 + - + +
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Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.2 24.5 + - - +
108A SER* 4.3 3.1 - - - -
109A GLN* 3.7 44.5 - - + +
112A MET* 4.0 5.4 - - + +
400A CYS 5.4 0.5 - - - +
401A ILE 4.3 6.2 - - - +
402A GLY 3.3 0.6 - - - -
403A GLN* 1.3 100.1 + - + +
405A PHE* 1.3 56.9 + - - +
407A LEU* 4.2 4.2 - - - +
408A HIS* 2.9 32.6 + - - +
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Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 4.3 15.9 + + + -
112A MET* 3.5 27.6 - - + +
115A TYR* 4.1 13.9 - + - -
119A MET* 3.5 26.9 - - + +
152A THR* 4.2 15.3 - - + -
153A ILE* 4.0 24.0 - - + -
156A CYS* 3.6 35.2 - - + -
233A LEU* 5.1 6.1 - - + -
269A THR* 6.3 0.4 - - + -
402A GLY* 3.1 16.9 + - - +
404A GLN* 1.3 74.2 - - - +
406A ALA* 1.3 66.5 + - - +
408A HIS 3.4 0.2 + - - -
409A GLU* 2.9 33.7 + - + +
500A HEM 3.9 17.9 - - + -
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Residues in contact with ALA 406 (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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269A THR* 3.7 19.8 - - + +
272A LEU* 5.1 0.6 - - - +
393A PHE* 4.3 6.1 - - + -
402A GLY 2.7 18.9 + - - +
403A GLN 3.8 3.6 - - - +
405A PHE* 1.3 75.0 - - - +
407A LEU* 1.3 60.6 + - - +
409A GLU* 3.6 2.2 - - - +
410A ALA* 2.9 31.9 + - - +
500A HEM 3.7 41.5 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 4.2 20.2 - - + -
309A LYS* 5.5 0.7 - - - -
318A LEU* 4.7 15.0 - - + -
319A ASN* 4.7 14.1 - - - +
322A LEU* 4.3 8.3 - - + -
393A PHE* 4.0 21.1 - - + -
403A GLN* 3.0 43.4 + - + +
404A GLN* 4.2 4.0 - - - +
406A ALA* 1.3 77.5 - - - +
408A HIS* 1.3 58.3 + - - +
410A ALA* 4.2 1.3 - - - +
411A THR* 2.7 39.8 + - - +
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Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A MET* 4.1 18.6 - - + +
116A HIS* 2.8 34.1 + + + +
119A MET* 3.7 22.2 - - + -
305A TYR* 3.4 29.7 - + - -
308A VAL* 3.6 17.3 - - + +
309A LYS* 2.7 37.1 + - - +
404A GLN 2.9 23.4 + - - +
405A PHE 3.9 2.5 - - - +
407A LEU* 1.3 70.9 - - - +
409A GLU* 1.4 59.5 + - - +
411A THR* 3.9 2.7 - - - -
412A LEU* 2.9 36.0 + - + +
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Residues in contact with GLU 409 (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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119A MET* 3.8 24.3 - - + +
148A LEU* 3.3 23.7 - - + +
149A THR* 3.9 9.0 - - + -
152A THR* 3.1 40.7 + - - +
269A THR* 4.1 18.8 - - + -
273A LEU* 4.8 1.3 - - + -
405A PHE* 2.9 23.8 + - + +
406A ALA* 3.6 4.5 - - - +
408A HIS* 1.4 77.5 - - - +
410A ALA* 1.3 58.7 + - - +
412A LEU* 3.7 3.1 - - - +
413A VAL* 2.9 44.4 + - + +
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Residues in contact with ALA 410 (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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269A THR* 4.9 3.4 - - + -
272A LEU* 4.1 13.5 - - + -
273A LEU* 3.6 24.7 - - + +
318A LEU* 3.8 26.6 - - + +
406A ALA 2.9 18.3 + - - +
407A LEU* 4.2 1.6 - - - +
409A GLU* 1.3 77.5 - - - +
411A THR* 1.4 57.6 + - - +
414A LEU* 2.9 33.3 + - - +
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Residues in contact with THR 411 (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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308A VAL* 3.6 31.2 - - + +
309A LYS* 6.0 0.7 - - - +
311A LEU* 3.8 24.9 - - + +
314A VAL* 4.0 11.4 - - + +
315A GLY* 4.6 6.4 - - - +
318A LEU* 3.3 17.7 - - - +
407A LEU* 2.7 23.8 + - - +
408A HIS* 3.9 2.5 - - - -
410A ALA* 1.4 73.6 - - - +
412A LEU* 1.3 61.3 + - - +
415A GLY* 2.9 27.7 + - - -
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Residues in contact with LEU 412 (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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116A HIS* 4.2 9.6 - - + +
119A MET* 3.8 43.7 - - + +
120A VAL* 4.0 12.3 - - + +
123A ALA* 4.4 4.3 - - + -
298A LEU* 5.2 1.0 - - - +
303A PRO* 3.7 25.4 - - + -
308A VAL* 3.8 22.3 - - + +
311A LEU* 5.1 1.3 - - - -
408A HIS* 2.9 19.7 + - + +
409A GLU* 3.7 7.2 - - - +
411A THR* 1.3 77.9 - - - +
413A VAL* 1.3 57.1 + - - +
415A GLY* 3.4 1.0 + - - -
416A MET* 3.0 54.4 + - - +
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Residues in contact with VAL 413 (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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123A ALA* 4.0 15.3 - - + -
126A LEU* 3.8 20.9 - - + -
145A MET* 4.7 1.1 - - - -
148A LEU* 3.8 23.3 - - + -
273A LEU* 4.2 18.2 - - + -
409A GLU* 2.9 37.8 + - - +
412A LEU* 1.3 76.7 - - + +
414A LEU* 1.3 61.1 + - - +
416A MET* 3.2 6.3 + - - +
417A MET* 2.9 51.2 + - + +
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Residues in contact with LEU 414 (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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273A LEU* 4.0 10.2 - - + +
276A ALA* 3.9 24.5 - - + -
277A LEU* 4.7 12.1 - - + +
280A LEU* 4.3 12.6 - - + -
314A VAL* 4.0 18.6 - - + -
317A VAL* 4.0 15.9 - - + -
318A LEU* 4.0 11.7 - - + -
410A ALA 2.9 19.7 + - - +
413A VAL* 1.3 76.6 - - - +
415A GLY* 1.4 63.6 + - - +
417A MET* 3.4 27.1 + - + +
418A LEU* 2.9 46.4 + - + +
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Residues in contact with GLY 415 (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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294A ALA* 3.5 16.3 - - - +
298A LEU* 3.5 15.4 - - - +
311A LEU* 4.1 8.7 - - - -
314A VAL* 4.4 6.8 - - - +
411A THR 2.9 19.5 + - - -
412A LEU 3.7 1.3 - - - -
414A LEU* 1.4 77.9 - - - +
416A MET* 1.4 55.7 + - - +
418A LEU* 3.3 1.9 + - - -
419A LYS* 2.9 26.2 + - - +
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Residues in contact with MET 416 (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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120A VAL* 5.2 1.8 - - + -
123A ALA* 3.7 21.5 - - + -
124A VAL* 4.0 17.5 - - + -
127A VAL* 4.2 20.6 - - + -
298A LEU* 4.4 2.2 - - + -
303A PRO* 3.7 34.3 - - + -
412A LEU* 3.0 38.2 + - - +
413A VAL* 3.7 4.9 - - + +
415A GLY* 1.4 71.7 - - - +
417A MET* 1.3 67.7 + - - +
419A LYS* 3.2 5.4 + - + -
420A HIS* 3.0 39.2 + - + +
455A LEU* 4.0 26.0 - - + -
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Residues in contact with MET 417 (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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126A LEU* 4.5 5.2 - - + -
127A VAL* 5.0 4.5 - - + +
130A TRP* 3.8 32.1 - - + -
145A MET* 4.3 13.5 - - + +
273A LEU* 4.9 2.7 - - - +
277A LEU* 3.8 35.4 - - + -
413A VAL* 2.9 40.5 + - + +
414A LEU* 3.6 26.2 - - + +
416A MET* 1.3 78.7 - - + +
418A LEU* 1.4 62.0 + - - +
421A PHE* 3.2 30.5 + - - -
423A PHE* 3.5 17.6 - - + -
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Residues in contact with LEU 418 (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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277A LEU* 5.1 2.0 - - + -
280A LEU* 4.0 13.7 - - + -
287A LEU* 3.2 31.4 - - + -
290A ALA* 3.4 39.0 - - + +
291A ALA* 4.0 23.4 - - + +
294A ALA* 4.0 10.5 - - + -
314A VAL* 4.6 7.9 - - + -
414A LEU* 2.9 35.3 + - + +
415A GLY 3.8 2.9 - - - +
417A MET* 1.4 74.7 - - - +
419A LYS* 1.4 65.6 + - - +
421A PHE 3.8 10.8 - - - +
423A PHE* 4.2 16.2 - - + -
451A LYS* 4.4 6.4 + - - +
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Residues in contact with LYS 419 (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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294A ALA* 3.9 16.5 - - + +
295A ALA* 5.1 8.1 - - - +
298A LEU* 2.8 37.7 + - + +
299A VAL 4.5 1.0 - - - -
300A ASP 2.8 31.5 + - - +
301A PRO* 4.4 6.3 + - - +
303A PRO* 6.1 2.3 - - + +
415A GLY 2.9 17.3 + - - +
416A MET* 3.2 7.2 + - + +
418A LEU* 1.4 76.1 - - - +
420A HIS* 1.3 79.6 + - + +
451A LYS* 3.5 11.3 - - - +
453A ILE* 3.4 46.8 - - + +
454A PRO 5.1 0.6 + - - -
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Residues in contact with HIS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 4.0 12.8 - - + +
131A GLU* 4.1 8.1 + - - +
301A PRO 4.8 1.2 + - - -
416A MET* 3.0 36.5 + - + +
418A LEU 3.3 0.2 - - - -
419A LYS* 1.3 102.8 + - + +
421A PHE* 1.3 87.1 + - + +
450A SER* 3.7 4.0 + - - -
451A LYS* 2.9 24.9 + - - +
452A LYS 4.5 0.7 + - - -
453A ILE* 3.2 43.1 + - + +
454A PRO 3.8 12.1 - - - -
455A LEU* 3.8 22.6 - - + +
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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