Contacts of the helix formed by residues 408 - 423 (chain A) in PDB entry 1R9J
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 ARG 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 3.4 48.5 + - + +
168A SER* 3.1 26.1 + - - -
169A LEU* 3.8 20.1 - - + +
172A HIS* 5.5 0.2 - - - +
375A ALA* 4.3 1.5 - - - +
405A PHE* 2.6 43.6 + - + +
406A GLY* 2.8 16.0 + - - -
407A VAL* 1.3 81.7 - - - +
409A GLU* 1.3 64.6 + - - +
410A HIS 3.3 2.9 + - - -
411A ALA* 3.4 3.7 + - + -
412A MET* 2.9 24.0 + - - +
159B MET* 3.8 24.0 + - + +
196B SER 2.8 30.3 + - - -
197B PHE* 3.7 18.4 - - - +
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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
----------------------------------------------------------
165A GLU* 4.1 0.2 + - - -
375A ALA* 4.2 12.9 - - + +
407A VAL* 4.0 3.3 - - - +
408A ARG* 1.3 74.4 - - - +
410A HIS* 1.3 62.1 + - - +
412A MET* 3.3 11.8 + - + +
413A CYS* 3.1 27.9 + - - -
431A THR* 3.6 25.6 + - + +
435A PHE* 3.7 25.1 - - + +
436A ILE* 6.3 0.2 - - + -
438A TYR* 3.9 9.5 - - + -
439A ALA* 3.9 4.9 - - + -
160B GLU* 2.6 29.5 + - - +
2671B TPP 2.6 37.8 + - - -
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Residues in contact with HIS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.1 22.6 + - - -
162A VAL* 3.6 27.2 + - + +
165A GLU* 3.6 15.1 + - - +
408A ARG 3.4 0.8 - - - -
409A GLU* 1.3 78.3 + - - +
411A ALA* 1.3 63.2 + - - +
413A CYS* 3.2 3.5 + - - +
414A ALA* 3.0 19.1 + - - +
438A TYR* 3.5 23.4 + - + +
439A ALA* 3.6 17.2 - - - +
441A GLY* 3.7 5.8 + - - -
442A ALA* 3.5 19.4 + - + -
160B GLU* 5.6 0.2 + - - -
438B TYR* 4.0 34.0 + + - -
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 4.8 0.7 - - - -
162A VAL* 3.8 14.3 - - - +
165A GLU* 2.9 42.5 + - + +
166A ALA* 3.7 19.7 - - + +
169A LEU* 6.0 0.9 - - + -
408A ARG* 4.1 5.6 - - + +
410A HIS* 1.3 70.5 - - - +
412A MET* 1.3 61.6 + - - +
414A ALA* 3.9 2.5 - - - +
415A ILE* 2.8 40.7 + - + +
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Residues in contact with MET 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA* 3.9 11.9 - - + -
405A PHE* 3.6 51.9 - - + -
408A ARG* 2.9 19.6 + - - +
409A GLU* 3.4 15.0 - - - +
410A HIS 3.1 0.2 - - - -
411A ALA* 1.3 76.5 - - - +
413A CYS* 1.3 67.5 + - - +
415A ILE* 3.1 4.3 + - - +
416A LEU* 2.9 39.7 + - + +
429A GLY* 3.9 7.2 - - - +
430A GLY 3.5 44.2 - - - +
431A THR* 4.1 16.4 - - + -
436A ILE* 5.5 1.3 - - + -
455A TYR* 5.8 0.9 - - + -
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Residues in contact with CYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLU* 3.1 14.6 + - - +
410A HIS 3.7 4.5 - - - +
412A MET* 1.3 93.1 - - - +
414A ALA* 1.3 60.0 + - - +
416A LEU* 3.3 10.9 + - - +
417A ASN* 3.3 25.1 + - - +
436A ILE* 4.7 6.5 - - - -
439A ALA* 3.6 18.4 - - + +
442A ALA* 3.6 17.7 - - + -
443A VAL* 4.4 5.2 - - + +
455A TYR* 3.5 35.6 + - + +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.5 23.3 - - - +
121A ALA* 3.2 29.8 - - + -
122A ASN* 2.8 24.9 + - - +
162A VAL* 4.2 3.8 - - + -
410A HIS 3.0 16.3 + - - +
411A ALA 3.9 0.7 - - - +
413A CYS* 1.3 75.5 - - - +
415A ILE* 1.3 62.2 + - - +
417A ASN* 3.3 6.7 + - - +
418A GLY 3.2 8.1 + - - -
442A ALA* 3.5 7.1 - - + +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 3.6 24.0 - - + +
124A VAL* 4.0 16.8 - - + -
125A GLY* 3.7 17.2 - - - -
128A ILE* 4.0 13.5 - - + -
166A ALA* 4.9 2.9 - - - -
169A LEU* 3.7 31.2 - - + -
405A PHE* 4.0 17.0 - - + -
411A ALA* 2.8 35.6 + - + +
412A MET 3.4 4.5 - - - +
414A ALA* 1.3 74.5 - - - +
416A LEU* 1.3 66.3 + - - +
418A GLY* 3.0 3.0 + - - +
419A LEU* 2.9 30.2 + - + +
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Residues in contact with LEU 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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371A MET 5.4 0.4 - - - +
372A GLY* 5.9 0.2 - - - -
405A PHE* 4.0 18.8 - - + -
412A MET* 2.9 24.5 + - + +
413A CYS* 3.5 9.4 - - - +
414A ALA 3.3 0.4 - - - -
415A ILE* 1.3 76.2 - - - +
417A ASN* 1.3 63.1 + - - +
419A LEU* 3.2 8.7 + - + -
420A ASP 3.0 18.4 + - - -
427A PRO* 3.5 24.0 - - + +
428A PHE* 3.7 22.4 - - - +
429A GLY* 3.5 25.4 - - - +
453A VAL* 3.6 18.7 - - + +
454A ILE 4.2 7.6 - - - +
455A TYR* 4.2 22.7 - - + -
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Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 5.2 0.2 - - - -
118A GLN* 4.9 1.6 - - - +
122A ASN* 3.8 11.1 - - - +
413A CYS 3.3 14.5 + - - +
414A ALA* 3.4 13.0 - - - +
415A ILE 3.1 0.4 - - - -
416A LEU* 1.3 78.5 - - - +
418A GLY* 1.3 58.3 + - - +
420A ASP* 3.3 1.7 + - - +
421A ALA* 3.0 23.6 + - - +
442A ALA* 3.1 28.1 + - - +
445A LEU* 4.4 6.3 - - - +
446A ALA* 3.2 27.7 - - - +
451A HIS* 3.5 33.8 - - + +
453A VAL* 3.7 13.2 - - - +
455A TYR* 4.4 0.9 + - - -
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 3.4 31.2 - - - +
125A GLY 3.9 6.7 - - - -
126A LEU* 3.2 14.4 + - - +
414A ALA 3.2 4.6 + - - -
415A ILE 3.0 7.3 + - - -
417A ASN* 1.3 77.9 - - - +
419A LEU* 1.3 63.8 + - - +
421A ALA* 3.3 5.7 + - - -
422A HIS* 3.2 18.0 + - - +
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Residues in contact with LEU 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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125A GLY* 3.3 22.6 - - - +
128A ILE* 3.8 14.4 - - + -
129A ALA* 3.8 22.2 - - + +
371A MET* 4.5 7.4 - - + +
403A ILE* 4.2 22.4 - - + -
415A ILE* 2.9 23.4 + - + +
416A LEU* 3.5 15.9 - - + +
418A GLY* 1.3 75.6 - - - +
420A ASP* 1.3 62.3 + - - +
422A HIS* 3.3 15.2 + - - +
423A ASP 3.9 2.6 + - - -
425A ILE* 3.8 29.5 - - + +
427A PRO* 3.8 25.8 - - + -
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Residues in contact with ASP 420 (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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103A ARG* 3.8 11.4 + - - -
416A LEU 3.0 12.6 + - - +
417A ASN 3.6 7.2 - - - +
418A GLY 3.2 0.2 - - - -
419A LEU* 1.3 78.9 - - - +
421A ALA* 1.3 60.2 + - - +
422A HIS 3.3 0.7 + - - -
423A ASP* 3.6 13.3 + - - +
425A ILE 4.6 9.1 - - - +
427A PRO* 4.0 8.6 - - + +
450A HIS 4.5 0.3 - - - +
451A HIS* 2.6 36.1 + - - +
452A ARG* 3.2 40.6 + - - +
453A VAL* 4.2 4.3 - - + -
508A ILE 5.4 0.5 - - - +
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Residues in contact with ALA 421 (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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57A ARG* 5.0 2.3 + - - -
103A ARG* 4.1 14.4 + - - +
110A GLU* 3.7 22.6 - - - +
111A VAL* 3.5 28.3 - - + -
126A LEU* 4.0 6.7 - - + -
417A ASN 3.0 17.0 + - - +
418A GLY 3.7 5.6 - - - +
419A LEU 3.3 0.2 - - - -
420A ASP* 1.3 76.8 + - - +
422A HIS* 1.3 63.6 + - - +
423A ASP* 4.4 6.1 - - - +
451A HIS* 3.8 6.3 - - + -
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Residues in contact with HIS 422 (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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55A VAL 4.8 1.1 - - - -
57A ARG* 5.0 0.3 + - - -
59A ARG* 3.0 48.7 + - - +
126A LEU* 3.5 37.4 - - + +
129A ALA* 3.6 15.5 - - + +
130A GLU* 4.0 6.0 - - - +
133A LEU* 3.6 23.3 - - + +
145A VAL* 5.8 0.4 - - + -
147A HIS* 2.9 36.5 + + - -
331A MET* 4.6 6.3 - - + -
418A GLY 3.2 5.9 + - - +
419A LEU 3.6 10.5 - - - +
420A ASP 3.2 0.8 - - - -
421A ALA* 1.3 78.3 - - - +
423A ASP* 1.3 90.1 + - - +
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Residues in contact with ASP 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 5.6 1.6 - - - +
55A VAL* 5.7 3.6 - - - +
57A ARG* 4.9 8.0 + - - -
59A ARG* 4.6 3.6 + - - -
103A ARG* 5.6 2.4 + - - -
133A LEU* 3.6 4.5 - - - +
331A MET* 3.5 35.8 - - + +
419A LEU 3.9 2.0 + - - -
420A ASP 3.6 13.3 + - - +
421A ALA 3.5 5.8 - - - +
422A HIS* 1.3 104.9 + - - +
424A GLY* 1.3 63.3 + - - +
425A ILE* 3.3 6.0 + - - +
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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
------------------------------------------------------------
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