Contacts of the helix formed by residues 826 - 832 (chain A) in PDB entry 3I5H
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 TRP 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A VAL* 3.8 7.5 + - + +
823A LEU* 3.1 22.2 + - + +
824A ARG 3.8 0.2 - - - -
825A ASN* 1.3 72.7 - - - +
827A GLU* 1.3 69.2 + - - +
828A TRP* 3.0 20.8 - + + +
829A TRP* 2.5 45.7 + - + +
830A ARG* 3.5 2.9 + - - -
60B GLU* 2.6 44.0 - - - -
73B LEU* 4.5 12.9 + - + -
74B PHE* 4.9 2.8 - - - -
76B GLU* 3.2 41.1 + - - +
77B LYS* 4.1 11.6 - - - +
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Residues in contact with GLU 827 (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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825A ASN 3.3 13.3 - - - +
826A TRP* 1.3 71.5 - - - +
828A TRP* 1.3 68.4 + - + +
830A ARG* 3.0 45.3 + - - +
831A LEU* 3.3 8.8 + - - +
53B GLU* 5.6 9.6 - - + +
57B MET* 4.4 29.6 - - + -
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Residues in contact with TRP 828 (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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826A TRP* 2.6 39.2 + + - +
827A GLU* 1.3 73.2 - - + +
829A TRP* 1.3 57.8 + - - +
831A LEU* 2.5 58.0 + - + +
832A PHE* 3.5 5.2 + - - -
25B ILE* 5.6 2.2 - - + -
33B ILE* 4.9 4.7 - - + -
38B LEU* 4.3 20.4 - - + -
57B MET* 3.1 62.7 - - + +
58B LEU* 5.8 2.7 - - + -
60B GLU* 3.3 25.1 + - - +
65B LEU* 4.7 11.2 - - + -
70B PHE* 4.7 14.8 - + - -
73B LEU* 3.9 15.5 - - + -
74B PHE* 4.2 23.1 - + + -
77B LYS* 4.6 2.2 - - - -
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Residues in contact with TRP 829 (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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820A TRP* 4.6 5.5 - + - -
823A LEU* 2.8 58.1 - - + +
824A ARG* 4.0 5.1 - - - +
826A TRP* 2.5 27.5 + - + +
828A TRP* 1.3 74.2 - - - +
830A ARG* 1.3 65.4 + - + +
831A LEU 3.3 0.2 + - - -
832A PHE* 3.5 31.1 + + - -
833A ASN* 2.9 42.4 + - - +
77B LYS* 3.6 33.6 - - + +
81B THR* 5.8 2.5 - - - -
146B LYS 3.1 27.1 + - - -
147B GLY* 3.3 20.2 - - - -
148B LYS* 3.9 18.8 - - - +
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Residues in contact with ARG 830 (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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823A LEU 5.0 2.7 - - - +
824A ARG 3.7 24.5 + - - +
825A ASN* 4.1 17.0 + - - +
826A TRP 4.2 3.4 - - - +
827A GLU* 3.1 40.7 + - - +
828A TRP 2.8 3.8 + - - -
829A TRP* 1.3 77.2 - - + +
831A LEU* 1.3 57.0 - - + +
833A ASN* 2.9 28.5 + - - +
834A LYS* 3.4 12.1 + - + +
148B LYS* 6.0 3.4 - - - +
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Residues in contact with LEU 831 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A GLU* 3.9 7.9 - - + +
828A TRP* 2.5 47.8 + - + +
830A ARG* 1.3 70.0 - - + +
832A PHE* 1.3 54.5 + - - +
833A ASN 2.8 4.5 - - - -
834A LYS* 2.6 29.7 + - - +
835A VAL* 2.7 23.1 + - + +
25B ILE* 5.7 6.5 - - + -
38B LEU* 5.1 6.5 - - + -
41B MET* 5.9 3.6 - - + -
42B PHE* 3.6 33.7 - - + -
45B LEU* 4.5 14.8 - - + -
57B MET* 3.7 18.8 - - + -
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Residues in contact with PHE 832 (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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828A TRP 3.5 5.6 + - - -
829A TRP* 3.5 35.2 - + - -
831A LEU* 1.3 75.8 - - + +
833A ASN* 1.3 64.8 + - - +
834A LYS 3.1 3.1 + - - -
835A VAL* 4.0 10.8 - - + -
836A LYS* 3.2 46.2 + - - +
837A PRO* 4.8 0.2 - - - +
17B GLU* 4.0 16.6 - - - -
18B LEU* 4.2 13.5 - - + -
21B ALA* 4.5 9.0 - - + -
70B PHE* 6.0 2.0 - - + -
74B PHE* 3.7 20.2 - + + -
77B LYS* 3.4 35.0 - - + -
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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