Contacts of the helix formed by residues 551 - 561 (chain B) in PDB entry 5AM8
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 PRO 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ARG* 3.8 20.5 - - - +
203B ASN* 4.5 10.8 - - - +
549B SER 4.8 0.2 - - - +
550B ARG* 1.3 90.5 - - + +
552B TRP* 1.3 66.3 + - - +
553B GLN* 3.8 13.7 - - + +
554B GLU* 3.1 44.6 + - + +
555B VAL* 3.2 9.9 + - - +
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Residues in contact with TRP 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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90B ARG* 5.3 0.4 - - - +
201B TRP 4.8 1.1 - - - -
202B TYR* 2.7 38.4 + + + +
203B ASN* 4.7 5.2 - - + -
204B SER* 5.0 5.8 - - - -
207B PHE* 6.2 2.9 - + - -
383B ALA* 3.6 38.3 + - + +
384B ASN* 3.2 37.1 - - + +
387B PHE* 3.9 11.9 - + + -
507B LEU* 5.8 0.4 - - + -
550B ARG 3.4 2.2 + - - -
551B PRO* 1.3 71.9 - - - +
553B GLN* 1.3 89.2 + - + +
555B VAL* 3.1 2.7 + - - +
556B LEU* 2.8 55.8 + - + +
563B ASP 4.1 10.3 - - - -
564B ALA* 4.4 1.3 - - - -
565B LEU* 4.3 28.5 - - + -
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Residues in contact with GLN 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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202B TYR 3.8 0.8 + - - -
203B ASN* 3.2 42.4 + - - +
204B SER* 4.4 4.4 - - - -
551B PRO* 3.1 6.4 - - + +
552B TRP* 1.3 122.0 + - + +
554B GLU* 1.3 59.3 + - + +
556B LEU* 3.5 0.7 + - - +
557B LYS* 3.0 27.4 + - - +
563B ASP* 3.5 37.1 - - + +
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Residues in contact with GLU 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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550B ARG* 3.9 22.1 + - - +
551B PRO* 3.1 38.7 + - + +
553B GLN* 1.3 78.1 - - + +
555B VAL* 1.3 64.1 + - - +
557B LYS* 3.3 7.6 + - - +
558B ASP* 3.1 28.1 + - - +
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Residues in contact with VAL 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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383B ALA* 4.6 8.7 - - + -
387B PHE* 4.0 13.5 - - + -
542B LYS 5.5 0.4 - - - +
543B VAL* 3.9 35.3 - - + +
546B ALA* 4.5 11.2 - - + -
547B GLY 5.5 0.2 - - - +
550B ARG* 3.8 43.7 - - + +
551B PRO 3.2 13.1 + - - +
552B TRP* 3.1 9.7 + - - +
554B GLU* 1.3 76.8 - - - +
556B LEU* 1.3 63.7 + - - +
558B ASP* 3.5 3.8 + - + +
559B MET* 3.1 20.8 + - - +
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Residues in contact with LEU 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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387B PHE* 4.1 9.6 - - + -
507B LEU* 4.1 16.4 - - + -
510B GLN* 4.3 3.6 - - - +
511B PHE* 3.8 28.3 - - + -
552B TRP* 2.8 34.5 + - + +
553B GLN 3.8 4.5 - - - +
555B VAL* 1.3 78.7 - - - +
557B LYS* 1.3 56.5 + - - +
559B MET* 3.2 2.8 + - - -
560B VAL* 2.9 46.9 + - + -
562B LEU 3.3 10.8 - - - +
564B ALA 3.5 37.2 - - - +
565B LEU 4.1 1.1 - - - +
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Residues in contact with LYS 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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553B GLN 3.0 18.3 + - - +
554B GLU* 3.6 8.7 - - - +
556B LEU* 1.3 76.1 - - - +
558B ASP* 1.3 64.2 + - - +
561B GLY* 2.7 54.9 + - - +
562B LEU* 3.2 16.6 + - - +
563B ASP* 4.1 11.7 - - + +
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Residues in contact with ASP 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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539B LYS* 3.8 8.3 + - - -
542B LYS* 3.7 24.7 + - - -
550B ARG* 2.8 39.0 + - - +
554B GLU 3.1 12.7 + - - +
555B VAL 3.6 9.0 - - - +
557B LYS* 1.3 83.1 - - - +
559B MET* 1.3 61.0 + - - +
561B GLY* 4.5 0.7 + - - -
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Residues in contact with MET 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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387B PHE* 5.6 0.4 - - - -
511B PHE* 3.4 60.3 - - + -
514B ALA* 3.7 10.2 - - + +
515B LEU* 4.2 19.1 - - + -
539B LYS* 3.0 39.9 + - + +
540B LEU* 4.2 22.2 - - + -
543B VAL* 3.8 24.0 - - + -
555B VAL 3.1 14.5 + - - +
556B LEU* 3.8 4.0 - - - +
558B ASP* 1.3 81.0 - - - +
560B VAL* 1.3 63.4 + - + +
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Residues in contact with VAL 560 (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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510B GLN* 3.8 30.1 - - + +
511B PHE* 4.2 4.3 - - + -
514B ALA* 3.6 24.7 - - + -
556B LEU* 2.9 38.7 + - + +
559B MET* 1.3 95.5 - - - +
561B GLY* 1.3 60.6 + - - +
562B LEU* 3.5 17.0 + - + +
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Residues in contact with GLY 561 (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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557B LYS* 2.7 36.9 + - - +
558B ASP 4.5 0.8 + - - -
559B MET 3.7 0.6 - - - -
560B VAL* 1.3 77.6 - - - +
562B LEU* 1.3 61.1 + - - +
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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