Contacts of the helix formed by residues 611 - 617 (chain A) in PDB entry 1D0N
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 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A TYR* 4.4 21.3 - - + -
603A VAL* 6.0 5.6 - - + -
605A VAL* 4.2 11.7 - - + -
609A SER 4.5 1.6 - - - +
610A GLU* 1.3 89.0 - - + +
612A ASP* 1.3 62.5 + - - +
613A SER* 2.9 19.9 + - - +
614A PHE* 2.9 20.3 + - + +
615A TRP* 3.5 3.5 + - - -
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Residues in contact with ASP 612 (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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610A GLU 3.6 1.6 + - - -
611A PRO* 1.3 73.0 - - - +
613A SER* 1.3 64.0 + - - +
614A PHE 3.2 0.4 - - - -
615A TRP* 3.7 19.8 - - + +
616A GLU* 3.2 35.5 + - + +
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Residues in contact with SER 613 (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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576A TYR* 3.1 25.6 + - - -
611A PRO* 2.9 11.5 + - - +
612A ASP* 1.3 83.8 + - - +
614A PHE* 1.3 61.5 + - - +
616A GLU* 3.5 8.8 + - - +
617A ALA* 3.5 18.9 + - - +
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Residues in contact with PHE 614 (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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538A LEU* 6.4 1.3 - - + -
561A LEU* 4.0 10.8 - - + -
569A LEU* 4.0 15.8 - - + +
576A TYR* 3.3 44.9 - + + -
578A TRP* 3.4 47.3 - + + -
605A VAL* 4.6 3.6 - - + -
610A GLU* 4.3 11.0 - - + -
611A PRO* 2.9 15.1 + - + +
613A SER* 1.3 79.4 - - - +
615A TRP* 1.3 104.7 + + - +
617A ALA* 3.1 23.2 + - - +
618A LEU* 3.6 20.3 - - + +
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Residues in contact with TRP 615 (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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558A ALA* 3.9 20.0 - - + -
561A LEU* 4.0 13.9 - - + -
610A GLU* 3.0 53.9 + - - -
611A PRO 3.5 1.6 + - - -
612A ASP* 3.8 19.5 - - + +
613A SER 3.4 0.4 - - - -
614A PHE* 1.3 102.3 - + - +
616A GLU* 1.3 60.8 + - + +
618A LEU* 3.5 14.6 + - + +
620A GLY* 2.6 41.8 + - - +
621A LYS* 3.1 52.7 - - + +
622A ALA 5.6 1.6 - - - -
624A TYR* 4.2 16.2 - + - -
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Residues in contact with GLU 616 (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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612A ASP* 3.2 26.2 + - + +
613A SER* 3.8 9.0 - - - +
614A PHE 3.2 0.8 - - - -
615A TRP* 1.3 71.8 - - + +
617A ALA* 1.3 52.2 + - - +
618A LEU 2.7 18.1 + - - -
619A GLY* 3.2 11.1 + - - +
620A GLY* 4.7 3.8 - - - +
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Residues in contact with ALA 617 (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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536A THR* 3.7 20.9 - - + +
556A PRO* 4.5 0.9 - - - +
569A LEU* 3.3 32.0 - - + +
571A THR* 4.9 11.2 - - - +
576A TYR* 5.7 4.0 - - + -
613A SER 3.5 8.7 + - - +
614A PHE* 3.1 6.4 + - - +
616A GLU* 1.3 76.6 - - - +
618A LEU* 1.3 72.5 + - - +
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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