Contacts of the helix formed by residues 552 - 562 (chain L) in PDB entry 6PSS
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 THR 552 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550L GLY 5.7 0.4 - - - +
551L LEU* 1.3 81.4 - - - +
553L ALA* 1.3 67.5 + - - +
554L ARG* 3.5 3.3 + - - +
555L GLU* 2.9 37.0 + - - +
556L ALA* 3.4 19.1 + - - +
597L LYS* 6.0 0.7 - - - +
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Residues in contact with ALA 553 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552L THR* 1.3 81.3 + - - +
554L ARG* 1.3 64.2 + - + +
556L ALA* 4.7 0.5 - - - +
557L LYS* 3.3 25.5 + - - +
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Residues in contact with ARG 554 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552L THR* 3.5 3.2 + - - +
553L ALA* 1.3 80.9 - - + +
555L GLU* 1.3 72.9 + - - +
557L LYS* 3.1 5.7 + - - +
558L VAL* 3.1 25.6 + - - +
580L PHE* 5.4 21.9 - - + -
586L ARG* 5.2 3.6 - - - +
587L ILE* 6.3 0.4 - - - +
590L ILE* 4.4 22.9 - - + +
24O C 4.0 3.0 + - - -
25O A 2.4 36.7 + - - -
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Residues in contact with GLU 555 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551L LEU* 3.9 17.4 - - + +
552L THR* 2.9 48.3 + - - +
554L ARG* 1.3 80.8 - - - +
556L ALA* 1.3 64.9 + - - +
558L VAL* 3.3 20.9 - - - +
559L LEU* 3.3 16.8 + - - +
590L ILE* 4.5 21.7 - - + +
593L LYS* 6.1 3.8 - - + -
594L ALA* 4.0 18.6 - - + -
597L LYS* 3.9 19.8 + - - +
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Residues in contact with ALA 556 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548L LEU* 4.0 22.1 - - + +
551L LEU* 3.7 22.2 - - + +
552L THR 3.4 17.8 + - - +
553L ALA 4.7 0.4 - - - +
554L ARG 3.3 0.4 - - - -
555L GLU* 1.3 81.7 - - - +
557L LYS* 1.3 58.0 + - - +
559L LEU* 3.3 5.4 + - - +
560L ARG* 2.8 40.7 + - - +
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Residues in contact with LYS 557 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553L ALA 3.3 18.9 + - - +
554L ARG* 3.1 5.9 + - - +
556L ALA* 1.3 78.4 - - - +
558L VAL* 1.3 65.7 + - - +
560L ARG* 3.2 13.0 + - + +
561L MET* 3.1 43.6 + - + +
579L GLN* 4.8 4.8 + - - -
580L PHE* 4.8 24.3 - - + -
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Residues in contact with VAL 558 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554L ARG 3.1 18.6 + - - +
555L GLU* 3.3 18.4 - - - +
557L LYS* 1.3 75.5 - - - +
559L LEU* 1.3 58.8 + - + +
561L MET* 3.0 7.7 + - - -
562L ARG* 2.5 50.5 + - + +
576L VAL* 3.7 24.0 - - + -
580L PHE* 5.2 6.8 - - + -
587L ILE* 4.0 22.4 - - + +
590L ILE* 4.1 19.5 - - + +
591L GLU* 4.9 4.9 - - + -
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Residues in contact with LEU 559 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901I LEU* 3.7 23.1 - - + +
548L LEU* 4.6 8.3 - - + -
551L LEU* 4.6 5.2 - - + -
555L GLU 3.3 18.4 + - - +
556L ALA* 3.5 7.0 - - - +
557L LYS 3.3 0.2 - - - -
558L VAL* 1.3 82.0 - - + +
560L ARG* 1.3 58.9 + - - +
562L ARG* 4.7 0.4 - - + -
563L PHE* 3.1 39.3 - - + -
565L ILE* 3.4 9.5 - - - +
591L GLU* 3.8 43.3 - - + +
594L ALA* 4.1 21.3 - - + -
595L LEU* 4.8 5.2 - - + +
598L LEU* 4.4 14.1 - - + -
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Residues in contact with ARG 560 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545L HIS* 3.1 38.8 + - - +
548L LEU* 3.5 45.1 + - + +
556L ALA* 2.8 26.3 + - - +
557L LYS* 3.7 12.3 - - + +
558L VAL 3.1 0.6 - - - -
559L LEU* 1.3 77.0 - - - +
561L MET* 1.3 58.2 + - - +
563L PHE 3.0 12.5 - - - +
565L ILE* 3.3 35.5 + - + +
566L ASP* 3.4 24.3 + - - -
567L MET* 3.3 20.9 - - + +
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Residues in contact with MET 561 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557L LYS* 3.1 34.3 + - + +
558L VAL 3.0 3.5 + - - +
560L ARG* 1.3 79.6 - - - +
562L ARG* 1.3 60.1 + - - +
563L PHE 3.3 4.7 - - - -
567L MET* 3.6 17.0 - - + -
571L TYR* 3.0 50.0 + - + +
576L VAL* 3.7 34.9 - - + +
579L GLN* 3.3 43.7 - - - +
580L PHE* 5.3 2.9 - - + -
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Residues in contact with ARG 562 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558L VAL* 2.5 40.6 + - + +
559L LEU* 4.7 1.8 - - - -
561L MET* 1.3 73.4 - - - +
563L PHE* 1.3 79.1 - - + +
570L ASP* 3.3 24.9 + - - +
571L TYR 3.1 28.2 + - - +
572L THR* 3.7 12.3 - - - +
573L LEU* 3.4 31.4 - - + +
576L VAL* 4.1 11.9 - - + -
591L GLU* 4.1 26.4 + - + +
56P G 3.8 34.7 + - - -
57P T 5.9 0.2 + - - -
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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