Contacts of the helix formed by residues 552 - 559 (chain D) in PDB entry 1S77
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 ASP 552 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D SER* 2.8 23.8 + - - -
550D LEU* 3.0 6.4 - - + +
551D ARG* 1.3 76.4 - - - +
553D GLU* 1.3 56.6 + - - +
554D VAL* 2.5 29.2 + - - +
555D GLY* 2.6 19.3 + - - -
556D GLY* 2.8 26.9 + - - -
690D VAL* 5.0 4.3 + - - +
691D ALA* 3.1 38.1 + - + +
692D ALA 4.8 0.5 + - - -
868D GLY* 4.6 4.5 - - - -
870D LEU* 3.7 2.7 - - - +
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Residues in contact with GLU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ARG 3.2 5.3 + - - -
552D ASP* 1.3 70.7 + - - +
554D VAL* 1.3 69.7 + - + +
556D GLY 4.3 0.4 - - - +
557D ARG* 2.9 24.3 + - + +
562D LEU* 3.8 24.7 - - + +
868D GLY* 5.2 0.4 - - - -
869D ASN* 3.6 27.3 - - + +
870D LEU* 3.6 23.3 - - - +
871D ASN 5.0 0.5 + - - -
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Residues in contact with VAL 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552D ASP* 2.5 18.8 + - - +
553D GLU* 1.3 76.7 - - + +
555D GLY* 1.3 64.2 + - - +
557D ARG* 3.4 9.4 + - - +
558D ALA* 3.5 9.2 + - - +
688D THR* 4.7 13.5 - - + +
690D VAL* 6.0 8.3 - - + -
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Residues in contact with GLY 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D ILE* 4.7 7.4 - - - -
547D SER* 3.5 11.7 - - - -
552D ASP* 2.6 25.2 + - - -
554D VAL* 1.3 71.9 - - - +
556D GLY* 1.3 66.6 + - - +
558D ALA* 2.8 21.1 + - - +
559D VAL* 3.2 11.3 + - - +
570D ILE* 6.2 0.2 - - - -
688D THR* 5.1 8.7 + - - -
689D VAL* 6.4 0.4 - - - -
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Residues in contact with GLY 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D SER* 3.3 12.2 + - - -
552D ASP 2.8 19.4 + - - -
553D GLU* 3.8 1.6 - - - -
554D VAL 3.3 0.2 - - - -
555D GLY* 1.3 73.5 - - - +
557D ARG* 1.3 63.6 + - - +
559D VAL* 3.0 9.1 + - - -
561D LEU* 2.8 44.6 + - - -
562D LEU* 4.8 1.3 - - - -
870D LEU* 4.6 4.0 - - - -
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Residues in contact with ARG 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D GLU* 2.9 19.8 + - + +
554D VAL* 3.6 6.1 - - - +
556D GLY* 1.3 76.5 - - - +
558D ALA* 1.3 65.7 + - - +
559D VAL 3.1 0.5 + - - -
560D ASN* 3.1 10.0 + - - -
562D LEU* 4.6 25.8 - - + +
564D SER* 6.3 1.0 - - - -
568D GLN* 3.3 33.9 + - + +
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Residues in contact with ALA 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D VAL 3.5 6.5 + - - +
555D GLY* 2.8 17.8 + - - +
557D ARG* 1.3 75.8 - - - +
559D VAL* 1.3 57.6 + - - +
560D ASN 3.4 0.2 - - - -
568D GLN* 3.4 21.4 - - - +
570D ILE* 3.6 45.5 + - + -
573D ILE* 4.2 15.5 - - + -
688D THR* 5.0 7.9 - - + -
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Residues in contact with VAL 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D SER* 3.6 18.4 - - - +
540D CYS* 4.1 10.1 - - + -
543D ILE* 3.6 27.6 - - + -
544D GLN* 2.9 46.9 + - + +
547D SER* 4.1 3.1 - - - +
555D GLY 3.2 8.7 + - - +
556D GLY* 3.0 13.9 + - - +
558D ALA* 1.3 78.8 - - - +
560D ASN* 1.3 71.4 + - - +
561D LEU* 3.1 7.0 + - + +
570D ILE* 4.2 13.5 - - + -
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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