Contacts of the helix formed by residues 542 - 551 (chain B) in PDB entry 2PA5
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 ASN 542 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLY* 5.7 4.1 - - - +
284B HIS* 3.7 37.5 - - - +
285B ALA* 3.8 8.8 - - + +
286B MET* 5.7 4.4 - - - +
531B CYS* 4.4 2.5 - - - +
534B GLN* 4.5 9.6 + - - +
541B LEU* 1.3 78.1 - - - +
543B VAL* 1.3 54.2 + - - +
544B PHE* 3.3 11.4 + - - +
545B GLN* 2.8 49.2 + - + +
546B THR* 2.7 37.0 + - - +
549B ARG* 6.2 0.2 - - - +
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B MET* 5.8 2.4 - - - +
291B LEU* 5.2 0.2 - - + -
527B SER* 6.1 0.9 - - - -
531B CYS* 4.1 11.9 - - - -
541B LEU* 3.9 11.6 - - + +
542B ASN* 1.3 68.7 + - - +
544B PHE* 1.3 66.2 + - - +
546B THR* 3.2 1.5 + - - -
547B VAL* 2.9 30.0 + - + +
564B TYR* 3.7 21.5 - - + -
567B CYS* 4.1 19.3 - - + -
568B TYR* 3.8 41.5 + - + +
571B ILE* 3.9 27.8 - - + -
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Residues in contact with PHE 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B TYR* 5.9 0.7 - - - +
306B GLU* 3.8 28.7 - - + +
309B ASP* 4.7 12.3 - - + -
310B ILE* 3.6 23.2 - - + +
542B ASN* 3.3 8.0 + - - +
543B VAL* 1.3 78.6 - - - +
545B GLN* 1.3 70.0 + - + +
547B VAL* 4.1 0.3 - - - -
548B SER* 2.7 49.0 + - - -
564B TYR* 3.2 23.8 + - - +
568B TYR* 4.3 3.2 + - - +
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Residues in contact with GLN 545 (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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542B ASN* 2.8 40.2 + - + +
544B PHE* 1.3 82.9 - - + +
546B THR* 1.3 60.5 + - - +
548B SER* 4.3 4.0 - - - -
549B ARG* 2.9 68.3 + - - +
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Residues in contact with THR 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B HIS* 3.3 16.6 + - + -
527B SER* 3.9 28.0 - - - +
530B ILE* 3.6 43.3 - - + +
531B CYS* 3.8 12.3 - - - -
534B GLN* 5.3 3.1 + - - -
542B ASN* 2.7 25.8 + - - +
543B VAL 3.6 3.4 - - - -
545B GLN* 1.3 76.3 - - - +
547B VAL* 1.3 58.6 + - - +
549B ARG* 5.4 0.6 - - - +
550B MET* 2.9 27.9 + - + +
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 5.4 1.6 - - + -
310B ILE* 4.1 13.9 - - + -
527B SER* 3.7 23.1 - - - +
543B VAL* 2.9 26.6 + - + +
544B PHE 4.2 1.1 - - - +
546B THR* 1.3 71.8 - - - +
548B SER* 1.3 66.9 + - - +
550B MET* 3.2 7.5 + - + +
551B ARG* 3.0 41.0 + - - +
557B SER 4.1 0.7 - - - +
558B ILE* 3.7 30.7 - - + -
564B TYR* 3.9 20.9 - - + -
567B CYS* 5.1 2.7 - - - -
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Residues in contact with SER 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.7 23.9 - - - +
544B PHE* 2.7 41.7 + - - -
545B GLN* 3.8 5.6 - - - -
547B VAL* 1.3 79.4 - - - +
549B ARG* 1.3 65.3 + - - +
551B ARG* 3.4 11.8 + - - +
552B THR* 3.6 13.5 - - - +
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Residues in contact with ARG 549 (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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278B VAL* 3.2 38.5 + - + +
279B HIS* 3.6 21.9 + - + +
280B VAL* 3.0 35.7 + - - +
281B PRO 5.3 1.0 + - - -
282B GLY* 5.4 5.5 - - - +
542B ASN* 6.2 0.2 - - - +
545B GLN* 2.9 46.1 + - + +
546B THR 5.4 0.2 - - - +
548B SER* 1.3 76.6 - - - +
550B MET* 1.3 63.9 + - - +
552B THR* 2.6 31.2 + - - -
553B GLN* 3.8 5.7 + - - +
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Residues in contact with MET 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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279B HIS* 3.8 7.9 - - + +
363B MET* 3.6 31.6 - - + -
364B ASP 5.4 0.7 - - - +
523B GLY* 3.6 19.5 - - - +
526B CYS* 3.7 7.4 - - + -
527B SER* 3.2 41.3 - - - +
530B ILE* 3.6 26.0 - - + -
546B THR* 2.9 16.9 + - + +
547B VAL* 3.2 6.9 + - - +
549B ARG* 1.3 76.6 - - - +
551B ARG* 1.3 53.7 + - - +
553B GLN* 2.9 10.0 + - - +
554B ARG 2.8 32.4 + - - +
557B SER* 3.7 13.5 - - - +
558B ILE* 5.5 0.7 - - - -
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Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 3.7 8.7 + - - -
310B ILE* 3.5 34.2 + - - +
311B ARG* 4.1 27.5 + - - +
313B GLU 5.6 2.2 + - - -
315B PRO* 5.7 4.9 - - - +
339B LEU* 4.5 1.2 - - - +
547B VAL* 3.0 21.8 + - - +
548B SER* 3.7 6.5 - - - +
549B ARG 3.2 0.6 - - - -
550B MET* 1.3 74.5 - - - +
552B THR* 1.3 58.2 + - - +
553B GLN 3.3 1.8 - - - -
554B ARG 3.6 9.0 - - - -
555B ALA* 3.5 18.2 - - - +
556B PHE* 3.5 29.7 + - - +
557B SER* 2.8 51.0 + - - +
558B ILE 3.0 16.8 + - - -
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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