Contacts of the helix formed by residues 695 - 707 (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 GLU 695 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647A ASN* 4.0 20.0 - - + +
691A GLU 3.0 25.4 - - - +
692A GLU 3.3 7.7 + - - +
693A LYS 3.3 0.4 - - - -
694A THR* 1.3 96.4 - - - +
696A ALA* 1.3 52.5 + - - +
697A LEU 3.4 2.0 - - - -
698A THR* 3.0 29.0 + - - +
699A SER* 2.7 38.3 + - - +
702A ARG* 4.6 6.4 + - - +
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Residues in contact with ALA 696 (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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671A VAL* 5.2 1.6 - - - -
682A VAL* 3.9 28.7 - - + +
684A VAL* 4.2 12.1 - - + -
692A GLU 3.2 8.5 + - - +
693A LYS 3.3 18.2 - - - +
694A THR 3.2 2.2 - - - -
695A GLU* 1.3 76.9 - - - +
697A LEU* 1.3 64.7 + - - +
699A SER* 3.0 13.8 + - - -
700A ALA* 3.1 12.8 + - - +
719A VAL* 4.2 14.8 - - + -
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Residues in contact with LEU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ALA* 6.1 5.4 - - + -
496A GLN* 3.9 25.4 - - + +
498A ARG* 4.1 27.8 - - + +
694A THR 4.7 3.2 + - - +
695A GLU 3.4 0.6 - - - -
696A ALA* 1.3 78.8 - - - +
698A THR* 1.3 63.5 + - - +
700A ALA* 3.1 8.1 + - - +
701A LYS* 3.0 37.2 + - - +
717A ILE* 3.4 35.2 - - + +
719A VAL* 4.0 16.4 - - + +
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Residues in contact with THR 698 (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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694A THR 5.0 1.6 + - - -
695A GLU* 3.0 30.9 + - - +
697A LEU* 1.3 79.0 - - - +
699A SER* 1.3 57.4 + - - +
701A LYS* 3.3 13.6 + - + +
702A ARG* 2.9 60.4 + - + +
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Residues in contact with SER 699 (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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645A CYS* 4.2 17.4 - - - +
647A ASN* 3.6 18.2 + - - -
652A PHE* 3.7 21.1 - - - -
671A VAL* 5.3 4.2 - - - +
673A LEU* 4.9 4.0 - - - -
692A GLU 4.7 2.6 + - - -
695A GLU* 2.7 27.5 + - - +
696A ALA* 3.0 10.4 + - - -
698A THR* 1.3 70.9 - - - +
700A ALA* 1.3 55.0 + - - +
702A ARG* 3.1 7.2 + - - +
703A TYR* 2.7 35.6 + - - +
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Residues in contact with ALA 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LEU* 4.5 13.1 - - + +
680A VAL* 4.4 13.7 - - + -
682A VAL* 5.0 2.5 - - + -
696A ALA 3.1 7.5 + - - +
697A LEU 3.1 5.6 + - - +
699A SER* 1.3 79.8 - - - +
701A LYS* 1.3 56.4 + - - +
703A TYR* 3.0 10.2 + - - +
704A ILE* 2.8 31.4 + - - +
717A ILE* 3.3 39.3 - - + -
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Residues in contact with LYS 701 (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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467A GLN* 5.9 0.2 + - - -
498A ARG* 3.7 38.3 - - - +
697A LEU* 3.0 29.0 + - - +
698A THR* 3.6 14.3 + - + +
699A SER 3.3 0.2 - - - -
700A ALA* 1.3 74.1 - - - +
702A ARG* 1.3 55.9 + - - +
704A ILE* 3.0 5.7 + - - +
705A ASP* 2.7 50.3 + - - +
713A ARG 6.1 0.9 - - - +
717A ILE* 3.8 13.7 - - + -
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Residues in contact with ARG 702 (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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267A ASN* 5.9 4.9 - - - +
647A ASN* 3.0 33.8 + - - +
652A PHE* 3.6 36.0 - - + +
695A GLU* 4.6 7.3 + - - +
698A THR* 2.9 48.4 + - + +
699A SER* 3.4 12.4 - - - +
701A LYS* 1.3 76.0 - - + +
703A TYR* 1.3 63.9 + - - +
705A ASP* 3.3 6.0 + - - +
706A THR* 3.0 30.5 + - - +
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Residues in contact with TYR 703 (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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641A ARG* 5.2 2.6 + - - -
643A PHE* 3.3 40.3 - + - -
652A PHE* 3.9 10.7 - - + -
654A ILE* 4.1 28.3 - - + -
673A LEU* 3.6 28.0 - - + -
675A ASP* 2.5 39.5 + - + -
680A VAL* 4.4 10.3 - - + -
699A SER 2.7 16.5 + - - +
700A ALA 3.2 7.6 - - - +
702A ARG* 1.3 75.2 - - - +
704A ILE* 1.3 73.9 + - + +
706A THR* 3.3 5.1 + - + +
707A ASP* 3.2 28.2 + - + +
711A ARG* 4.1 8.9 + - - -
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Residues in contact with ILE 704 (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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269A LYS* 5.4 0.3 + - - -
680A VAL* 3.6 32.1 - - + -
700A ALA 2.8 22.4 + - - +
701A LYS* 3.7 4.5 - - - +
703A TYR* 1.3 76.9 - - + +
705A ASP* 1.3 64.1 + - - +
706A THR 3.1 5.3 + - - -
707A ASP* 3.4 18.4 + - - +
710A HIS* 5.9 0.2 - - - -
711A ARG* 4.3 25.1 + - + +
712A ASP 4.1 18.8 - - - +
713A ARG* 4.4 14.3 - - + +
715A THR* 3.8 22.7 - - + +
717A ILE* 4.1 22.2 - - + -
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Residues in contact with ASP 705 (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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267A ASN* 5.6 3.2 + - - +
269A LYS* 3.0 31.3 + - - +
701A LYS* 2.7 33.8 + - - +
702A ARG* 4.0 5.4 - - - +
704A ILE* 1.3 73.0 - - - +
706A THR* 1.3 57.7 + - - +
707A ASP 3.5 0.4 - - - -
713A ARG* 3.0 51.5 + - - +
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Residues in contact with THR 706 (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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266A ALA 3.8 19.6 + - - +
267A ASN* 3.1 28.1 + - - +
268A ARG 3.9 18.6 - - - +
269A LYS* 2.9 19.7 - - - +
652A PHE* 5.1 5.2 - - + -
654A ILE* 5.8 8.7 - - + -
702A ARG 3.0 18.8 + - - -
703A TYR* 3.7 5.4 - - - +
705A ASP* 1.3 77.3 - - - +
707A ASP* 1.3 66.6 + - - +
708A PRO* 3.2 4.4 - - + +
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Residues in contact with ASP 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS* 3.7 11.6 + - - -
364A GLN* 3.7 6.0 - - - +
641A ARG* 5.8 1.9 + - - -
677A TRP* 4.7 1.7 - - - -
703A TYR* 3.2 22.3 + - + +
704A ILE* 3.4 13.0 + - - +
706A THR* 1.3 77.2 - - - +
708A PRO* 1.3 76.1 - - - +
709A ALA* 2.6 34.6 + - - +
710A HIS* 3.1 10.4 + - - -
711A ARG* 2.9 49.1 + - + +
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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