Contacts of the helix formed by residues 433 - 447 (chain B) in PDB entry 5IJ7
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 SER 433 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B SER* 5.2 0.4 - - - -
431B GLU 4.4 0.2 + - - -
432B TRP* 1.3 75.4 - - - +
434B GLY* 1.3 65.9 + - - +
435B ALA* 3.9 6.7 + - - +
436B GLU* 2.7 41.8 + - - +
437B ALA* 2.9 22.7 + - - +
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Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ALA 3.3 20.9 + - - -
270B LYS* 3.2 7.2 - - - +
271B SER* 3.4 23.8 - - - -
433B SER* 1.3 72.2 - - - +
435B ALA* 1.4 54.7 + - - +
438B SER* 3.0 34.5 + - - -
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.3 43.3 - - + +
269B ALA* 4.0 13.4 + - + +
270B LYS 5.1 0.2 - - - -
433B SER* 3.2 7.5 + - - +
434B GLY* 1.4 73.3 - - - +
436B GLU* 1.4 60.5 + - + +
439B MET* 3.2 28.2 + - - +
654T ARG* 4.2 13.9 - - - +
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU 4.3 0.5 - - - +
432B TRP* 3.6 20.4 - - + -
433B SER* 2.7 43.6 + - - +
435B ALA* 1.4 74.6 - - + +
437B ALA* 1.3 60.5 + - - +
439B MET* 3.5 3.8 + - - +
440B PHE* 3.0 28.1 + - - +
458B ILE* 4.0 15.3 - - + +
460B THR* 2.7 37.0 + - + +
461B LYS* 2.9 33.4 + - - +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 3.2 16.8 - - - +
432B TRP* 4.1 12.9 - - + +
433B SER 2.9 15.9 + - - +
436B GLU* 1.3 73.8 - - - +
438B SER* 1.4 64.6 + - - +
440B PHE* 3.0 16.7 + - - +
441B ARG* 3.0 42.6 + - - +
469B PHE* 4.4 8.3 - - + -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.8 15.0 - - - -
270B LYS 2.8 15.7 + - - -
271B SER* 4.5 0.2 - - - +
272B VAL* 2.8 43.7 + - - +
273B GLN 4.4 0.7 - - - +
277B SER* 3.7 15.5 - - - -
434B GLY 3.0 10.0 + - - -
435B ALA* 4.6 0.2 - - - -
437B ALA* 1.4 76.4 - - - +
439B MET* 1.4 56.1 + - - +
441B ARG* 3.5 4.5 - - - +
442B VAL* 3.1 32.2 + - - +
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Residues in contact with MET 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.8 20.3 - - + +
435B ALA 3.2 19.1 + - - +
436B GLU* 3.7 4.7 - - - +
437B ALA 3.2 0.6 - - - -
438B SER* 1.4 75.7 - - - +
440B PHE* 1.4 59.2 + - - +
442B VAL* 3.8 6.6 - - - +
443B LEU* 2.9 53.8 + - + +
458B ILE* 4.1 11.9 - - + -
654T ARG* 3.6 39.0 - - + +
657T MET* 3.4 35.0 - - + -
658T LEU* 4.0 16.8 - - + -
661T VAL* 5.8 0.2 - - - -
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Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 4.1 12.1 - + + -
436B GLU 3.0 13.4 + - - +
437B ALA 3.0 10.0 + - - +
439B MET* 1.4 73.4 - - - +
441B ARG* 1.3 66.0 + - + +
443B LEU* 3.2 4.1 + - - +
444B ILE* 2.9 69.4 + - + +
451B PHE* 4.6 1.6 - + - -
454B ILE* 4.4 4.0 - - + -
458B ILE* 3.9 13.2 - - + +
466B VAL* 3.5 42.2 - - + -
469B PHE* 3.7 27.1 - + + -
470B ARG* 3.7 34.1 - - + -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 2.8 27.5 + - - -
272B VAL* 3.2 29.1 + - - +
273B GLN* 3.9 9.2 - - - +
274B ARG* 3.4 21.1 - - + +
437B ALA* 3.0 37.0 + - - +
438B SER 3.5 10.3 - - - +
440B PHE* 1.3 79.7 - - + +
442B VAL* 1.4 58.8 + - - +
444B ILE* 2.9 33.6 - - + +
445B GLY 3.8 2.3 + - - -
469B PHE* 3.9 21.8 - - - -
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 2.8 59.4 + - + +
277B SER* 3.8 17.0 - - - -
278B LEU* 4.2 5.4 - - + -
438B SER 3.1 20.5 + - - +
439B MET* 3.8 10.1 - - - +
440B PHE 3.3 0.2 - - - -
441B ARG* 1.4 73.2 - - - +
443B LEU* 1.3 63.7 + - + +
445B GLY 3.1 5.4 + - - -
658T LEU* 3.8 22.7 - - + -
661T VAL* 3.7 34.8 - - + -
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B MET* 2.9 35.7 + - + +
440B PHE 3.8 3.1 - - - +
442B VAL* 1.3 73.3 - - + +
444B ILE* 1.4 51.0 + - - +
446B THR* 3.4 3.9 + - - +
447B TYR* 2.8 54.1 + - + +
454B ILE* 3.8 21.7 - - + +
457B LEU* 3.6 33.9 - - + -
458B ILE* 3.6 18.6 - - + -
657T MET* 3.6 28.5 - - + -
661T VAL* 5.1 11.9 - - + -
674T ILE* 5.8 0.7 - - + -
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B PHE* 2.9 58.6 + - + +
441B ARG* 2.9 36.3 - - + +
443B LEU* 1.4 70.1 - - - +
445B GLY* 1.3 58.9 + - - +
447B TYR 2.7 19.7 - - - +
448B TYR* 3.5 27.5 - - - +
451B PHE* 5.0 3.8 - - + -
454B ILE* 4.3 13.9 - - + -
470B ARG* 5.7 4.7 - - - -
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Residues in contact with GLY 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.4 29.4 + - - -
441B ARG 3.8 1.4 + - - -
442B VAL 3.1 5.4 + - - -
444B ILE* 1.3 81.9 - - - +
446B THR* 1.4 55.6 + - - +
448B TYR* 3.3 27.0 + - - -
665T ASP* 5.5 1.3 - - - +
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 2.8 23.5 + - - +
442B VAL 4.1 1.7 + - - -
443B LEU* 3.4 6.8 + - - -
444B ILE 3.3 0.2 - - - -
445B GLY* 1.4 75.9 - - - +
447B TYR* 1.3 81.8 + - + +
448B TYR* 3.3 21.5 - - - -
661T VAL* 3.8 15.5 - - + +
664T HIS* 3.6 31.7 + - + +
665T ASP* 4.2 5.9 + - - -
671T ILE* 4.5 8.9 - - + +
674T ILE* 4.1 14.4 - - + -
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Residues in contact with TYR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LEU* 2.8 37.9 + - + +
444B ILE* 2.7 17.8 - - - +
446B THR* 1.3 86.3 - - + +
448B TYR* 1.3 62.7 + - - +
450B ASN* 4.3 14.6 - - + +
453B ALA* 3.9 21.5 - - + -
454B ILE* 3.7 20.1 - - + +
457B LEU* 3.4 22.1 - - + +
671T ILE* 3.5 31.1 + - + -
674T ILE* 3.6 18.1 - - + +
675T ASP* 2.7 34.1 + - - -
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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