Contacts of the helix formed by residues 795 - 801 (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 MET 795 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.7 27.4 - - + -
234A LYS* 5.0 0.2 - - - -
237A MET* 3.6 32.8 - - - +
471A TRP* 3.7 31.6 - - + -
472A GLY* 3.6 14.1 - - - +
782A HIS 2.8 14.1 + - - +
783A ALA* 3.4 11.4 + - + -
794A PRO* 1.3 82.5 - - + +
796A ARG* 1.3 64.6 + - - +
797A TRP 3.2 2.9 - - - -
798A HIS* 3.0 18.9 + - + +
799A PHE 3.2 9.0 + - - -
805A PHE* 3.5 32.8 - - + -
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Residues in contact with ARG 796 (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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472A GLY 3.7 13.7 - - - +
783A ALA 3.0 2.0 + - - -
784A ASN* 2.8 37.3 + - - +
785A GLU* 2.6 31.6 + - - -
793A TYR* 3.3 27.8 - - + +
794A PRO 3.3 3.8 + - - -
795A MET* 1.3 77.8 - - - +
797A TRP* 1.3 74.5 + - - +
800A ASP* 2.8 76.4 + - - +
801A ASP* 4.3 10.1 + - - -
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Residues in contact with TRP 797 (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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526A ASP* 5.5 0.9 - - - -
779A ARG* 3.6 27.4 - - + -
780A TYR* 4.0 12.3 - + - -
783A ALA* 2.9 36.5 + - + +
784A ASN* 3.6 25.7 - - - +
785A GLU* 3.0 28.8 + - + -
796A ARG* 1.3 95.6 - - - +
798A HIS* 1.3 61.4 + - - +
801A ASP* 3.0 26.1 - - + +
802A LYS 3.0 8.1 + - - -
803A LYS* 2.9 60.4 + - + -
1983A ACT 5.9 2.7 - - + -
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Residues in contact with HIS 798 (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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234A LYS* 2.9 32.0 + - - -
328A GLN* 3.0 21.1 + - - +
374A LEU* 3.8 1.0 - - - +
471A TRP* 5.0 0.7 - - - +
527A GLU* 3.9 9.2 - - - -
783A ALA* 3.4 22.8 - - + +
795A MET* 3.0 21.5 + - + +
797A TRP* 1.3 78.6 - - - +
799A PHE* 1.3 56.6 + - - +
802A LYS* 3.1 21.0 - - - -
803A LYS* 2.7 32.3 + - + +
804A VAL 3.3 20.3 + - - -
805A PHE* 3.5 40.6 - + + -
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Residues in contact with PHE 799 (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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324A PHE* 3.9 26.2 - + - -
327A GLU* 4.2 4.9 - - - -
328A GLN* 3.7 7.6 - - - +
471A TRP* 4.2 6.1 - - + +
472A GLY* 3.7 34.3 - - - +
473A LYS* 3.6 33.7 - - + -
795A MET 3.2 2.0 + - - -
796A ARG 3.2 2.2 + - - +
798A HIS* 1.3 77.4 - - - +
800A ASP* 1.3 78.3 + - - +
802A LYS* 2.6 49.0 + - - +
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Residues in contact with ASP 800 (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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472A GLY 5.3 0.2 - - - -
793A TYR* 5.0 0.5 + - - -
796A ARG* 2.8 63.2 + - - +
799A PHE* 1.3 94.9 - - - +
801A ASP* 1.3 63.9 + - - +
802A LYS* 4.2 8.2 - - - +
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Residues in contact with ASP 801 (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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373A THR* 4.8 1.6 + - - -
796A ARG* 4.3 9.0 + - - -
797A TRP* 3.0 41.6 + - + +
800A ASP* 1.3 88.5 - - - +
802A LYS* 1.3 72.2 + - - +
803A LYS* 3.3 5.1 + - + +
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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