Contacts of the helix formed by residues 89 - 94 (chain B) in PDB entry 3HN3
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 ASP 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B PHE* 4.9 3.5 - - - -
84B ASN 5.3 0.7 - - - +
87B SER* 3.2 18.8 + - - +
88B GLN* 1.3 74.4 - - - +
90B TRP* 1.3 65.4 + - - +
91B ARG* 2.9 49.0 + - - +
92B LEU* 3.0 27.2 + - + +
93B ARG* 3.2 12.3 + - - +
553D PRO* 4.2 3.4 - - - +
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Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN 3.6 16.5 + - - -
89B ASP* 1.3 74.2 + - - +
91B ARG* 1.3 68.0 + - + +
92B LEU 3.5 0.3 + - - -
93B ARG* 3.5 6.9 + - - +
94B HIS* 3.4 26.3 + - + +
514D LEU* 3.9 22.7 - - + -
552D ASP* 4.8 7.9 + - - -
553D PRO* 3.6 26.9 - - + +
554D PRO* 3.4 39.0 - - + -
564D SER* 4.6 6.7 - - - -
375E TRP* 6.2 0.2 - - - +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.6 46.5 - - + +
89B ASP* 2.9 32.1 + - - +
90B TRP* 1.3 79.5 - - + +
92B LEU* 1.3 60.3 + - - +
94B HIS* 3.9 3.3 + - - +
95B PHE* 3.2 26.2 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.9 21.5 - - + -
49B ALA* 3.8 29.2 - - + -
51B PHE* 4.3 6.5 - - + -
75B VAL* 5.8 3.1 - - + -
77B MET* 4.7 5.8 - - + -
83B PHE* 3.5 40.8 - - + +
84B ASN 4.9 1.3 - - - +
87B SER* 3.8 20.4 - - - +
89B ASP* 3.0 25.6 + - + +
91B ARG* 1.3 78.5 - - - +
93B ARG* 1.3 65.6 + - - +
94B HIS 3.2 0.2 - - - -
95B PHE* 3.2 20.4 + - + +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 2.9 53.0 + - + +
85B ASP* 3.1 22.9 + - - +
89B ASP 3.2 8.4 + - - +
90B TRP* 3.5 10.7 + - - +
91B ARG 3.4 0.2 - - - -
92B LEU* 1.3 78.3 - - - +
94B HIS* 1.3 90.4 + - + +
209B PHE* 3.6 28.0 - - + -
211B TYR* 4.6 0.8 + - - -
593B MET* 3.4 40.2 - - - +
594B THR 4.5 2.6 + - - -
595B GLU* 5.6 0.4 + - - -
596B GLN* 4.8 4.0 - - - +
551D GLN* 5.2 3.0 - - - +
553D PRO* 5.3 17.5 - - + -
555D LEU* 3.5 30.8 - - - +
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Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 3.4 19.6 + - + +
91B ARG* 3.9 3.8 - - - +
92B LEU 3.2 0.4 - - - -
93B ARG* 1.3 118.4 + - + +
95B PHE* 1.3 65.4 + - - +
96B VAL* 3.6 12.9 + - - +
209B PHE* 4.1 16.1 - + - -
595B GLU* 4.4 12.3 + - - -
596B GLN* 3.9 21.2 + - - -
513D HIS* 6.3 3.8 - + + -
553D PRO* 6.3 2.0 - - + -
554D PRO 5.8 1.1 - - - -
555D LEU* 4.6 4.3 - - + -
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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