Contacts of the helix formed by residues 78 - 88 (chain B) in PDB entry 3HI7
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 LYS 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B PRO* 1.3 75.1 - - - +
79B LYS* 1.3 65.4 + - - +
80B TYR* 4.3 8.7 - - + +
81B HIS* 3.0 34.9 + - + +
82B VAL* 2.9 19.1 + - - +
629B GLU* 3.6 33.9 - - + +
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Residues in contact with LYS 79 (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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77B PRO 3.5 2.6 + - - -
78B LYS* 1.3 72.0 - - - +
80B TYR* 1.3 63.7 + - - +
82B VAL* 3.8 0.2 - - - +
83B LEU* 2.9 44.3 + - + +
348B TYR* 3.7 41.5 - - + +
519B ASP* 2.9 21.4 + - - -
521B ASP* 2.9 33.2 + - - -
525B THR* 4.2 0.9 - - - -
627B TYR* 3.3 38.9 + - + +
629B GLU* 3.0 8.1 + - - +
664B ASP* 2.8 27.4 + - - +
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Residues in contact with TYR 80 (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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78B LYS* 3.2 9.8 - - + +
79B LYS* 1.3 80.4 - - - +
81B HIS* 1.3 88.2 + + + +
83B LEU* 3.6 4.8 + - - +
84B ARG* 3.2 51.8 + - + +
629B GLU* 4.7 1.0 + - - -
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Residues in contact with HIS 81 (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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77B PRO* 5.1 0.7 - - + -
78B LYS* 3.0 39.5 + - + +
80B TYR* 1.3 102.3 - + - +
82B VAL* 1.3 67.6 + - - +
84B ARG* 3.4 7.9 + - - +
85B PHE* 3.1 22.7 + - - +
91B ARG 4.7 1.9 - - - +
93B PRO* 3.9 22.1 - - + +
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Residues in contact with VAL 82 (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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32B VAL* 4.2 15.5 - - + -
33B PHE* 3.8 13.7 - - + -
76B LEU* 5.2 0.9 - - + -
77B PRO* 3.8 32.8 - - + +
78B LYS 2.9 19.8 + - - +
79B LYS 3.8 1.6 - - - +
81B HIS* 1.3 76.3 - - - +
83B LEU* 1.3 57.6 + - - +
85B PHE* 3.1 5.5 + - + +
86B LEU* 2.9 47.5 + - + +
93B PRO* 4.1 6.1 - - + -
348B TYR* 3.1 30.3 - - + +
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Residues in contact with LEU 83 (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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79B LYS* 2.9 45.5 + - + +
80B TYR* 4.1 4.5 - - - +
82B VAL* 1.3 74.4 - - - +
84B ARG* 1.3 58.1 + - + +
86B LEU* 4.3 4.7 - - + +
87B ASP* 2.7 44.2 + - + +
88B LYS* 4.9 1.5 - - - +
345B ARG* 3.6 37.7 - - - +
348B TYR* 3.9 20.4 - - + -
521B ASP* 4.8 1.1 - - - +
525B THR* 3.9 22.4 - - + +
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Residues in contact with ARG 84 (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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80B TYR* 3.2 63.9 + - + +
81B HIS* 3.9 8.7 - - - +
82B VAL 3.3 0.2 - - - -
83B LEU* 1.3 74.8 - - - +
85B PHE* 1.3 57.9 + - - +
88B LYS* 3.0 44.8 + - + +
89B GLY 3.2 0.2 + - - -
90B GLU* 3.1 44.7 + - + +
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Residues in contact with PHE 85 (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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29B LYS* 2.8 77.3 + - + -
32B VAL* 4.1 10.3 - - + -
81B HIS 3.1 13.5 + - - +
82B VAL 3.3 7.9 - - - +
84B ARG* 1.3 77.9 - - - +
86B LEU* 1.3 68.8 + - + +
89B GLY* 4.1 4.5 + - - -
90B GLU* 3.4 25.5 - - - +
91B ARG 3.6 10.1 + - - +
92B HIS* 3.5 44.2 - + + -
93B PRO* 3.8 14.8 - - + -
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Residues in contact with LEU 86 (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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29B LYS* 3.5 50.8 + - + +
30B ALA 5.3 0.2 - - - +
32B VAL* 4.6 4.0 - - + -
33B PHE* 3.9 9.0 - - + -
82B VAL* 2.9 38.5 + - + +
83B LEU* 4.0 7.0 - - + +
85B PHE* 1.3 89.1 - - + +
87B ASP* 1.3 70.8 + - - +
338B ASN* 3.7 37.7 - - - +
345B ARG* 4.0 6.1 - - - +
348B TYR* 4.7 0.9 - - + -
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Residues in contact with ASP 87 (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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83B LEU* 2.7 31.4 + - + +
86B LEU* 1.3 79.7 - - - +
88B LYS* 1.3 68.8 + - + +
89B GLY 3.6 1.6 - - - -
340B HIS* 5.6 0.5 + - - -
345B ARG* 2.9 44.0 + - - -
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Residues in contact with LYS 88 (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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83B LEU 3.7 1.5 + - - +
84B ARG* 3.0 36.8 + - + +
87B ASP* 1.3 85.9 - - + +
89B GLY* 1.3 64.1 + - - +
90B GLU* 3.3 16.6 + - + +
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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