Contacts of the helix formed by residues 425 - 443 (chain A) in PDB entry 3N9Z
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 425 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A CYS* 3.3 10.3 - - - -
424A LEU* 1.3 76.2 - - - +
426A ARG* 1.3 57.7 + - - +
427A ARG 3.4 2.7 - - - -
428A ILE* 3.2 10.8 + - - +
429A ALA* 2.8 32.3 + - - +
601A HEM 3.5 37.3 - - - +
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Residues in contact with ARG 426 (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 MET* 4.3 4.9 - - - -
413A ASN* 3.5 32.9 + - - +
416A PHE* 3.6 44.8 - - + +
417A GLY 4.1 11.7 + - - -
422A GLN* 3.0 31.4 - - - +
423A CYS* 3.4 21.8 + - + +
424A LEU 3.2 3.8 + - - -
425A GLY* 1.3 77.8 - - - +
427A ARG* 1.3 76.6 + - - +
429A ALA* 3.8 1.0 - - - +
430A GLU* 2.9 54.5 + - - +
76C ASP* 4.6 10.3 + - - +
77C MET* 3.6 18.3 - - - +
80C LEU* 6.0 1.8 - - - +
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL 3.8 4.2 + - - +
120A MET* 3.5 44.4 + - - +
125A THR* 3.7 24.7 - - + -
422A GLN* 5.2 1.4 - - - +
424A LEU 4.9 0.2 + - - -
425A GLY 3.4 0.2 - - - -
426A ARG* 1.3 106.4 - - - +
428A ILE* 1.3 65.7 + - - +
430A GLU* 2.9 31.2 + - - +
431A LEU* 3.0 36.3 + - + +
50C LEU* 3.4 27.0 + - - +
73C GLU* 4.1 35.2 + - - +
76C ASP* 5.6 3.0 + - - +
77C MET* 5.2 6.9 - - - +
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Residues in contact with ILE 428 (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 VAL* 4.2 13.7 + - + +
128A PHE* 3.6 27.6 - - + -
132A LEU* 4.3 9.6 - - + +
171A ILE* 4.0 25.8 - - + -
174A VAL* 4.4 10.1 - - + -
262A ILE* 4.1 25.8 - - + -
284A MET* 4.1 15.5 - - + -
425A GLY* 3.2 11.1 + - - +
427A ARG* 1.3 77.4 - - - +
429A ALA* 1.3 57.7 + - - +
431A LEU* 3.9 3.3 - - - +
432A GLU* 2.9 44.1 + - - +
601A HEM 4.5 12.3 - - + -
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Residues in contact with ALA 429 (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 THR* 3.6 28.9 - - + -
416A PHE* 3.9 9.9 - - + -
425A GLY 2.8 20.9 + - - +
426A ARG 3.8 3.4 - - - +
428A ILE* 1.3 72.0 - - - +
430A GLU* 1.3 59.0 + - - +
432A GLU* 3.4 2.3 + - - +
433A MET* 2.9 38.7 + - + +
601A HEM 3.8 23.6 - - + -
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Residues in contact with GLU 430 (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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339A LYS* 6.5 0.7 - - - -
342A ILE* 4.6 7.8 - - + +
416A PHE* 4.0 19.7 - - + -
426A ARG* 2.9 45.8 + - - +
427A ARG* 2.9 36.8 + - - +
429A ALA* 1.3 75.1 - - - +
431A LEU* 1.3 59.0 + - + +
433A MET* 3.8 8.2 - - + +
434A THR* 2.8 39.2 + - - +
73C GLU* 4.7 6.8 - - - +
76C ASP* 4.8 7.6 - - - +
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Residues in contact with LEU 431 (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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125A THR* 4.0 28.7 - - - +
128A PHE* 4.4 10.1 - - + -
129A LEU* 3.9 30.1 - - + -
132A LEU* 3.8 14.4 - - + -
332A LEU* 4.0 18.4 - - + -
339A LYS* 5.8 4.5 - - - +
427A ARG* 3.0 27.6 + - + +
428A ILE 3.9 0.2 - - - +
430A GLU* 1.3 75.8 - - + +
432A GLU* 1.3 61.2 + - - +
434A THR* 4.7 2.9 - - - -
435A ILE* 2.9 39.6 + - + +
73C GLU* 6.0 3.1 - - - +
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Residues in contact with GLU 432 (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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132A LEU* 3.9 19.0 - - + +
136A SER* 4.5 0.7 + - - -
166A PHE* 3.4 31.7 - - + -
167A ALA* 3.8 10.3 - - - +
170A SER* 3.5 27.1 - - - +
171A ILE* 4.7 3.1 + - - +
288A GLY 4.8 2.3 - - - +
292A THR* 2.8 35.4 + - - +
296A LEU* 4.7 0.2 - - - +
428A ILE* 2.9 30.0 + - - +
429A ALA 3.8 3.6 - - - +
431A LEU* 1.3 75.5 - - - +
433A MET* 1.3 58.5 + - + +
435A ILE* 4.2 0.9 - - - +
436A PHE* 3.0 29.6 + - - +
601A HEM 5.5 1.0 - - - +
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Residues in contact with MET 433 (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 THR* 4.1 16.6 - - - +
295A THR* 3.7 33.0 - - + -
296A LEU* 3.8 28.5 - - + -
342A ILE* 4.0 34.1 - - + -
346A LEU* 4.9 0.4 - - + -
416A PHE* 4.1 11.0 - - + -
429A ALA 2.9 29.0 + - - +
430A GLU* 4.0 4.0 - - - +
432A GLU* 1.3 76.2 - - - +
434A THR* 1.3 63.8 + - - +
436A PHE* 3.5 1.3 + - - +
437A LEU* 3.1 30.5 + - + +
601A HEM 4.0 20.4 - - + -
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Residues in contact with THR 434 (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 LEU* 3.7 24.9 - - + -
335A VAL* 4.1 13.0 - - + -
338A LEU* 3.8 24.4 - - + +
339A LYS* 4.5 16.5 + - + +
342A ILE* 3.3 18.3 - - - +
430A GLU* 2.8 25.0 + - - +
431A LEU* 4.2 3.1 - - - -
433A MET* 1.3 74.4 - - - +
435A ILE* 1.3 58.1 + - - +
437A LEU* 3.3 1.4 + - - -
438A ILE* 3.0 30.7 + - + +
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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
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129A LEU* 3.9 41.1 - - + +
132A LEU* 4.0 15.3 - - + +
133A ASP* 3.5 38.1 - - + +
136A SER* 4.1 5.4 - - - +
328A MET* 4.1 22.4 - - + -
332A LEU* 4.2 9.9 - - + -
431A LEU 2.9 24.5 + - - +
432A GLU* 4.2 3.1 - - - +
434A THR* 1.3 72.1 - - - +
436A PHE* 1.3 64.9 + - - +
438A ILE* 3.5 7.8 + - - +
439A ASN* 2.9 32.1 + - - +
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Residues in contact with PHE 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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136A SER* 3.3 16.9 + - - +
139A PHE* 3.6 36.6 - + + -
163A LEU* 3.9 24.2 - - + -
166A PHE* 3.5 26.9 - + + -
296A LEU* 3.4 34.8 - - + -
300A LEU* 4.4 12.8 - - + -
432A GLU 3.0 20.3 + - - +
433A MET 3.7 3.6 - - - +
435A ILE* 1.3 76.3 - - - +
437A LEU* 1.3 69.5 + - + +
439A ASN* 3.3 4.3 + - - +
440A MET* 3.0 57.7 + - + +
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Residues in contact with LEU 437 (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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296A LEU* 3.9 16.2 - - + -
299A HIS* 3.6 50.9 - - + +
300A LEU* 4.5 7.4 - - + -
303A MET* 4.3 11.7 - - + -
338A LEU* 4.0 21.5 - - + -
342A ILE* 4.1 14.4 - - + -
433A MET* 3.1 21.6 + - + +
434A THR 4.0 1.6 - - - +
436A PHE* 1.3 92.1 - - + +
438A ILE* 1.3 58.6 + - - +
440A MET* 3.9 3.8 - - + +
441A LEU* 2.8 39.6 + - + +
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Residues in contact with ILE 438 (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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317A VAL* 3.9 15.9 - - + +
321A ARG* 3.7 25.6 - - - +
328A MET* 3.9 24.5 - - + -
331A MET* 3.7 32.8 - - + -
332A LEU* 4.0 17.0 - - + -
335A VAL* 4.7 6.7 - - + -
338A LEU* 3.8 14.1 - - + +
434A THR* 3.0 24.8 + - + +
435A ILE* 3.7 5.2 - - - +
437A LEU* 1.3 76.8 - - - +
439A ASN* 1.3 62.9 + - - +
442A GLU* 3.0 29.2 + - - +
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Residues in contact with ASN 439 (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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133A ASP* 3.0 25.0 + - - +
136A SER* 3.5 19.3 - - - +
137A ARG* 3.6 22.1 + - - +
140A VAL* 3.8 17.4 - - + +
321A ARG* 4.3 12.6 + - - -
328A MET* 4.6 4.2 - - - +
435A ILE* 2.9 22.4 + - - +
436A PHE 3.3 6.5 + - - +
438A ILE* 1.3 79.1 - - - +
440A MET* 1.3 62.3 + - - +
442A GLU* 3.6 6.4 + - - +
443A ASN* 2.8 35.5 + - - +
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Residues in contact with MET 440 (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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139A PHE* 4.0 17.3 - - + -
140A VAL* 4.4 6.7 - - + -
143A LEU* 3.6 23.1 - - + -
300A LEU* 4.3 15.9 - - + -
303A MET* 6.0 1.3 - - + -
436A PHE* 3.0 49.9 + - + +
437A LEU* 3.9 7.4 - - + +
439A ASN* 1.3 76.2 - - - +
441A LEU* 1.3 58.7 + - + +
443A ASN 3.2 0.5 + - - -
444A PHE* 2.9 49.0 + - + +
446A VAL* 5.1 4.7 - - + +
472A PHE* 3.5 35.2 - - + -
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Residues in contact with LEU 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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303A MET* 3.8 35.0 - - + -
310A GLN* 4.1 13.2 - - + +
313A LEU* 3.8 24.0 - - + -
314A ARG* 2.8 64.0 + - - +
317A VAL* 4.0 22.0 - - + -
338A LEU* 4.3 15.0 - - + -
437A LEU* 2.8 24.2 + - + +
438A ILE 4.1 2.2 - - - +
440A MET* 1.3 73.4 - - - +
442A GLU* 1.3 62.1 + - - +
443A ASN 3.4 0.2 + - - -
444A PHE 3.9 3.6 + - - +
446A VAL* 6.2 0.7 - - + -
475A PHE* 4.4 0.2 - - - -
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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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317A VAL* 3.8 14.4 - - + +
318A LEU* 4.2 22.1 - - + +
321A ARG* 2.7 62.6 + - - +
438A ILE* 3.0 27.4 + - - +
439A ASN* 3.9 9.9 - - - +
440A MET 3.3 0.2 - - - -
441A LEU* 1.3 76.6 - - - +
443A ASN* 1.3 66.9 + - - +
475A PHE* 3.5 20.7 - - - +
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Residues in contact with ASN 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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140A VAL* 3.6 18.9 - - + +
144A HIS* 3.2 21.6 + - - +
439A ASN* 2.8 29.3 + - - +
440A MET 3.2 2.2 + - - -
442A GLU* 1.3 91.3 + - - +
444A PHE* 1.3 89.5 + - + +
474A PRO* 3.5 2.4 - - - +
475A PHE* 2.9 24.1 + - - +
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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