Contacts of the helix formed by residues 552 - 561 (chain A) in PDB entry 1DIY
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 GLY 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A GLU* 5.4 1.8 - - - -
320A HIS* 4.3 9.4 + - - -
547A ALA* 2.7 33.6 + - - +
548A SER* 4.5 2.0 - - - +
550A PHE 3.9 0.3 - - - +
551A GLY* 1.3 75.3 - - - -
553A GLU* 1.3 64.9 + - - -
554A VAL* 3.2 7.2 - - - -
555A GLY 3.7 4.9 + - - -
556A PHE 3.8 4.5 + - - -
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Residues in contact with GLU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ALA* 4.0 19.8 - - - +
552A GLY* 1.3 71.6 - - - -
554A VAL* 1.3 63.0 + - - +
555A GLY 3.2 0.7 - - - -
556A PHE* 3.4 10.6 + - - +
557A ASN* 2.7 51.7 + - - +
560A LYS* 4.8 6.9 + - - -
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 5.8 15.3 - - + +
316A LEU* 5.2 6.3 - - + +
319A GLU* 3.9 39.3 - - + +
551A GLY 4.2 9.4 - - - +
552A GLY* 4.3 0.7 - - - -
553A GLU* 1.3 83.2 - - - +
555A GLY* 1.3 66.8 + - - +
557A ASN* 3.8 6.1 + - - +
558A LEU* 3.1 30.7 + - + +
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Residues in contact with GLY 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU* 5.2 1.1 - - - -
335A ILE* 3.7 19.2 - - - +
550A PHE* 3.4 27.2 + - - -
552A GLY 3.7 3.2 + - - -
553A GLU 3.2 0.8 - - - -
554A VAL* 1.3 82.8 - - - +
556A PHE* 1.3 55.1 + - - +
558A LEU* 2.8 27.1 + - - +
559A VAL* 3.1 13.2 + - - +
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Residues in contact with PHE 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A TRP* 3.3 70.9 - + - -
546A LYS* 3.3 22.7 - - - -
547A ALA* 3.2 33.9 - - + -
550A PHE* 3.7 17.9 - + - +
552A GLY 3.8 2.2 + - - +
553A GLU* 3.4 16.0 + - - +
555A GLY* 1.3 73.6 - - - +
557A ASN* 1.3 58.1 + - - +
559A VAL* 3.0 6.7 + - + +
560A LYS* 2.7 64.8 + - + +
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Residues in contact with ASN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A GLU* 2.7 50.2 + - - +
554A VAL* 4.1 6.5 - - - +
556A PHE* 1.3 75.7 - - - +
558A LEU* 1.3 58.5 + - - +
560A LYS* 4.2 15.4 + - - +
561A THR* 2.6 41.8 + - + +
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ARG* 3.7 25.4 - - - +
312A VAL* 4.0 13.0 - - + -
315A LEU* 4.0 25.1 - - + -
316A LEU* 6.3 0.2 - - + -
335A ILE* 3.9 31.6 - - + -
339A GLU* 3.4 26.0 - - - +
554A VAL* 3.1 25.0 + - + +
555A GLY* 2.8 14.7 + - - +
557A ASN* 1.3 72.8 - - + +
559A VAL* 1.3 59.9 + - - +
561A THR* 4.1 2.3 - - - -
562A ALA* 3.5 12.3 + - - -
566A LYS* 6.0 3.8 - - - +
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Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ILE* 3.7 21.1 - - + +
338A GLY* 3.4 25.4 - - - +
339A GLU* 4.2 5.8 - - - +
342A LYS* 3.1 26.0 - - - +
361A PHE* 4.4 4.3 - - + -
545A TRP* 3.6 30.1 - - + -
550A PHE* 3.5 34.5 - - + -
555A GLY 3.7 6.5 - - - +
556A PHE* 3.0 9.1 + - + +
558A LEU* 1.3 79.8 - - - +
560A LYS* 1.3 56.7 + - - +
562A ALA* 4.1 0.9 + - - +
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Residues in contact with LYS 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LYS* 3.2 21.9 + - - +
361A PHE* 6.1 1.8 - - - -
545A TRP* 4.6 13.7 - - + +
553A GLU* 4.8 7.1 + - - -
556A PHE* 2.7 70.5 + - + +
557A ASN* 3.2 15.8 + - - +
559A VAL* 1.3 74.3 - - - +
561A THR* 1.3 64.6 + - + +
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LYS* 3.8 3.1 - - - +
557A ASN* 2.6 28.5 + - + +
558A LEU* 4.1 4.3 - - - +
560A LYS* 1.3 86.4 - - + +
562A ALA* 1.3 68.5 + - - +
563A THR* 3.4 2.1 + - - -
566A LYS* 3.4 33.4 + - - +
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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