Contacts of the helix formed by residues 818 - 824 (chain A) in PDB entry 2IVF
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 HIS 818 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LYS* 4.3 2.0 - - - +
586A TRP* 3.7 16.2 - + - -
816A LEU 3.2 1.0 - - - -
817A ASP* 1.3 79.9 + - - +
819A ASP* 1.3 68.4 + - + +
820A TRP* 3.2 52.5 + + + +
821A TYR* 3.0 12.3 + - + -
822A LEU* 3.0 19.4 + - - +
946A ALA* 3.9 9.2 - - + +
947A GLY 2.6 29.2 + - - -
948A GLY 4.0 6.5 - - - -
949A TYR* 3.9 21.0 - + + -
952A PHE* 3.7 32.8 - + + -
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Residues in contact with ASP 819 (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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341A LYS* 2.8 32.7 + - - +
817A ASP 3.7 0.4 + - - -
818A HIS* 1.3 75.4 + - + +
820A TRP* 1.3 65.5 + - + +
822A LEU* 3.4 8.7 + - - +
823A GLU* 2.9 43.5 + - - +
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Residues in contact with TRP 820 (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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577A TYR* 3.5 55.2 + + + -
580A GLU* 2.9 42.2 + - + -
581A ALA* 4.1 3.6 - - + -
584A LYS* 4.4 2.4 - - - +
586A TRP* 3.5 28.7 - + - -
818A HIS* 3.1 21.2 + + - +
819A ASP* 1.3 83.9 - - + +
821A TYR* 1.3 62.1 + - + +
823A GLU* 3.9 7.4 - - - +
824A ALA* 2.9 31.0 + - - +
942A PRO 3.5 17.0 - - - -
943A LEU* 3.9 20.5 - - + +
945A LEU* 3.8 7.4 - - + -
946A ALA* 3.5 24.7 - - + -
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Residues in contact with TYR 821 (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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230A HIS* 3.6 14.3 + - - -
455A ASP* 4.4 4.9 + - - -
459A ARG* 4.5 4.0 - - - -
816A LEU* 3.5 41.7 - - + +
818A HIS* 3.0 8.7 + - + +
820A TRP* 1.3 82.3 - - + +
822A LEU* 1.3 63.9 + - - +
824A ALA* 3.4 4.2 + - - -
825A GLY 3.1 3.3 + - - -
826A GLU* 2.8 60.6 + - + -
827A SER 3.3 3.5 + - - -
943A LEU* 3.7 29.1 + - + +
944A HIS* 3.7 12.8 + - - -
946A ALA* 4.3 3.8 - - + -
952A PHE* 3.4 33.0 - + - -
1981A GOL 3.0 20.6 + - - -
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Residues in contact with LEU 822 (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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339A THR 4.2 13.2 - - - +
340A GLY* 4.1 8.3 - - - +
341A LYS* 3.8 19.5 - - - +
815A TYR* 3.6 24.5 - - + +
816A LEU 4.4 0.2 + - - -
817A ASP* 3.4 24.5 - - - +
818A HIS 3.0 12.1 + - - +
819A ASP* 3.6 13.2 - - - +
821A TYR* 1.3 79.1 - - - +
823A GLU* 1.3 62.9 + - + +
825A GLY* 3.3 10.2 + - - -
827A SER* 3.7 21.1 + - - +
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Residues in contact with GLU 823 (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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569A ALA 4.3 6.3 - - - +
571A LYS* 2.8 44.6 + - + +
577A TYR* 6.1 0.9 - - - +
819A ASP* 2.9 27.7 + - - +
820A TRP* 4.0 5.9 - - - +
822A LEU* 1.3 79.3 - - + +
824A ALA* 1.3 60.1 + - - +
825A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 824 (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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569A ALA* 3.7 20.0 - - - +
570A LEU* 3.7 27.1 - - + +
577A TYR* 5.2 2.4 + - - +
820A TRP 2.9 20.2 + - - +
821A TYR 3.9 2.9 - - - +
822A LEU 3.4 0.2 - - - -
823A GLU* 1.3 74.1 - - - +
825A GLY* 1.3 58.0 + - - +
826A GLU 4.3 1.1 - - - +
832A LYS* 2.8 29.8 + - - +
943A LEU* 3.8 18.6 - - + -
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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