Contacts of the helix formed by residues 547 - 559 (chain B) in PDB entry 1XJP
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 547 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B VAL* 3.2 11.9 - - - +
532B ALA 3.4 15.4 + - - -
533B ALA* 3.5 17.3 - - - -
544B ILE 3.2 14.4 + - - -
545B SER 3.1 4.7 + - - -
546B ASN* 1.3 77.0 - - - +
548B THR* 1.3 56.8 + - - +
549B GLU* 3.6 3.9 + - - +
550B ALA* 3.1 25.3 + - - +
551B GLY 3.0 20.6 + - - -
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Residues in contact with THR 548 (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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316B VAL 5.5 0.4 - - - +
317B SER 4.3 7.4 - - - +
318B VAL 3.3 23.8 - - - +
319B GLY* 4.0 9.6 - - - +
546B ASN 3.3 6.1 + - - +
547B SER* 1.3 71.0 - - - +
549B GLU* 1.3 63.8 + - - +
550B ALA 3.2 0.2 - - - -
551B GLY 3.8 0.2 - - - -
552B GLN* 2.9 30.3 + - - +
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Residues in contact with GLU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA* 3.5 27.1 - - + +
547B SER* 3.1 2.8 - - - +
548B THR* 1.3 86.1 + - - +
550B ALA* 1.3 61.2 + - - +
552B GLN* 3.6 11.7 + - - +
553B LYS* 3.3 32.3 + - + +
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Residues in contact with ALA 550 (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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318B VAL* 5.1 0.2 - - + -
529B LEU* 3.5 40.5 - - + +
532B ALA* 4.2 9.6 + - - -
544B ILE* 4.4 15.3 - - + +
547B SER* 3.1 29.4 + - - +
549B GLU* 1.3 77.4 - - - +
551B GLY* 1.3 59.2 + - - +
552B GLN 3.2 0.3 + - - -
553B LYS 3.2 1.7 + - - -
554B LEU* 2.9 26.2 + - - +
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Residues in contact with GLY 551 (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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318B VAL* 3.1 33.6 - - - +
319B GLY* 5.8 1.3 - - - -
320B LEU* 4.4 8.6 - - - +
544B ILE* 5.9 0.6 - - - +
547B SER 3.0 11.3 + - - -
548B THR 3.8 0.4 - - - -
549B GLU 3.4 0.2 - - - -
550B ALA* 1.3 77.1 - - - +
552B GLN* 1.3 56.7 + - - +
554B LEU* 3.8 9.2 - - - +
555B PHE* 2.9 30.0 + - - +
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Residues in contact with GLN 552 (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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548B THR 2.9 19.0 + - - +
549B GLU* 3.8 14.6 - - - +
550B ALA 3.1 0.2 - - - -
551B GLY* 1.3 75.4 - - - +
553B LYS* 1.3 67.7 + - + +
555B PHE* 3.2 13.4 + - - -
556B ASN* 2.6 58.6 + - - +
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Residues in contact with LYS 553 (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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528B ALA* 4.9 6.5 - - - +
529B LEU* 4.1 7.4 - - + -
532B ALA* 3.9 23.1 - - + -
549B GLU* 3.3 16.7 + - + +
550B ALA 3.2 7.5 + - - +
552B GLN* 1.3 81.2 - - + +
554B LEU* 1.3 64.6 + - - +
556B ASN* 3.4 18.7 + - - +
571B GLU 5.3 0.8 + - - -
572B ASN 3.2 22.7 + - - +
573B VAL* 3.0 43.2 + - - +
574B VAL 5.8 0.2 - - - -
575B GLY 5.6 1.2 - - - +
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Residues in contact with LEU 554 (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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318B VAL* 6.0 1.6 - - + -
320B LEU* 4.8 12.8 - - + -
404B VAL* 4.8 7.2 - - + -
407B ILE* 6.0 0.9 - - + -
408B MET* 3.7 29.2 - - + -
525B PHE* 5.5 4.7 - - + -
529B LEU* 4.1 26.8 - - + +
544B ILE* 5.1 8.7 - - + -
550B ALA 2.9 17.2 + - - +
551B GLY* 3.8 8.1 - - - +
553B LYS* 1.3 77.1 - - - +
555B PHE* 1.3 62.0 + - - +
557B MET* 3.2 23.0 + - + +
558B LEU* 3.1 48.4 + - + +
573B VAL* 4.4 7.4 - - + -
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Residues in contact with PHE 555 (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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320B LEU* 4.0 22.4 - - + -
321B PRO* 5.5 7.9 - - + -
384B ALA* 3.9 28.9 - - + -
551B GLY 2.9 19.5 + - - +
552B GLN* 3.2 13.2 + - - +
554B LEU* 1.3 77.6 - - - +
556B ASN* 1.3 71.2 + - - +
557B MET 3.2 0.2 - - - -
558B LEU* 3.7 7.9 - - + -
559B ARG* 3.1 48.2 + - + +
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Residues in contact with ASN 556 (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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552B GLN* 2.6 48.9 + - - +
553B LYS* 3.7 14.7 + - - +
554B LEU 3.2 1.0 + - - -
555B PHE* 1.3 81.5 - - - +
557B MET* 1.3 58.3 + - - +
559B ARG* 4.0 11.2 + - - +
560B LEU* 3.0 24.5 - - - +
572B ASN* 3.9 21.4 + - + +
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Residues in contact with MET 557 (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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381B TYR* 3.9 10.0 + - - +
396B ALA* 6.1 0.2 - - - +
400B PHE* 3.8 31.4 - - + -
404B VAL* 3.6 21.1 - - + -
525B PHE* 4.1 13.2 - - + -
553B LYS 3.9 0.8 + - - -
554B LEU* 3.2 13.1 + - + +
555B PHE 3.2 0.2 - - - -
556B ASN* 1.3 78.0 - - - +
558B LEU* 1.3 91.2 + - + +
559B ARG 3.4 0.4 - - - -
560B LEU* 3.2 24.9 + - + +
561B GLY 4.0 2.8 + - - +
569B ALA* 3.3 30.8 - - - +
572B ASN* 4.3 1.8 - - + -
573B VAL* 3.2 26.0 - - + -
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Residues in contact with LEU 558 (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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320B LEU* 4.6 13.2 - - + -
380B GLN* 4.6 8.1 - - + +
381B TYR* 3.4 53.3 - - + +
384B ALA* 3.7 16.3 - - + +
385B TYR* 3.5 8.3 - - - +
404B VAL* 4.0 11.9 - - + -
408B MET* 6.3 0.2 - - + -
554B LEU* 3.1 40.3 + - + +
555B PHE* 3.3 11.6 + - - +
557B MET* 1.3 103.9 - - + +
559B ARG* 1.3 61.0 + - - +
560B LEU 3.1 1.2 + - - -
561B GLY 3.3 9.7 + - - -
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Residues in contact with ARG 559 (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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384B ALA* 3.1 24.3 - - - +
385B TYR* 3.6 4.6 - - - +
388B GLN* 3.1 44.9 + - - +
555B PHE* 3.1 43.5 + - + +
556B ASN* 4.0 12.4 + - - +
558B LEU* 1.3 75.8 - - - +
560B LEU* 1.3 82.4 + - - +
561B GLY 3.3 0.8 + - - -
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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