Contacts of the helix formed by residues 84 - 93 (chain B) in PDB entry 4RG7
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 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR* 5.8 3.8 - - + +
79B CYS* 2.9 26.0 + - + +
80B VAL* 4.6 0.4 + - - +
82B LEU* 4.4 7.9 - - + +
83B SER* 1.3 76.0 - - - +
85B LEU* 1.3 58.6 + - - +
86B ALA* 3.2 3.1 - - - -
87B GLU* 3.1 20.9 + - + +
88B GLY 3.0 22.5 + - - -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 5.4 5.6 - - - +
83B SER* 3.5 5.0 + - - +
84B LYS* 1.3 72.9 - - - +
86B ALA* 1.3 64.3 + - - +
88B GLY* 3.4 2.8 + - - +
89B GLU* 3.0 24.9 + - - +
124B VAL* 3.7 26.9 - - + +
127B LYS* 5.7 6.5 - - + -
128B THR* 4.9 13.2 - - + -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LYS 3.2 0.6 - - - -
85B LEU* 1.3 75.5 - - - +
87B GLU* 1.3 66.6 + - - +
89B GLU* 3.4 5.3 + - - +
90B GLN* 2.9 25.1 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 4.3 17.9 + - - +
79B CYS* 3.5 20.5 - - - -
84B LYS* 3.1 19.9 + - + +
86B ALA* 1.3 78.8 - - - +
88B GLY* 1.3 58.6 + - - +
90B GLN* 2.9 9.4 + - - +
91B ILE* 2.8 53.3 + - - +
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.3 17.9 - - - +
79B CYS* 3.7 16.5 - - - +
80B VAL* 5.1 2.5 - - - -
84B LYS 3.0 8.2 + - - -
85B LEU* 3.4 4.5 + - - -
86B ALA 3.4 0.4 - - - -
87B GLU* 1.3 79.1 - - - +
89B GLU* 1.3 61.1 + - - +
91B ILE* 3.3 8.1 + - - +
92B LEU* 3.3 15.6 + - - +
120B LEU* 6.4 0.4 - - - -
121B LEU* 4.8 1.8 - - - +
124B VAL* 5.1 9.2 - - - -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 3.0 17.2 + - - +
86B ALA* 3.6 6.5 - - - +
88B GLY* 1.3 72.2 - - - +
90B GLN* 1.3 67.9 + - - +
91B ILE 3.0 1.2 + - - -
93B SER* 3.0 33.7 + - - +
121B LEU* 4.2 15.5 - - + -
124B VAL* 4.2 13.9 - - + +
125B TYR* 5.4 7.4 - - + -
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Residues in contact with GLN 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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86B ALA 2.9 16.7 + - - +
87B GLU* 2.9 10.8 + - - +
89B GLU* 1.3 75.1 - - - +
91B ILE* 1.3 56.7 + - + +
93B SER* 4.9 0.2 - - - -
94B GLY* 2.5 38.4 - - - +
95B GLY 5.1 0.2 - - - -
96B VAL* 5.9 4.8 - - + +
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Residues in contact with ILE 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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66B CYS* 6.0 4.7 - - - -
72B LYS* 3.5 41.2 - - + +
75B LEU* 5.1 7.9 - - + -
76B ALA* 4.4 9.4 - - + +
79B CYS* 4.9 6.3 - - - -
87B GLU* 2.8 38.1 + - - +
88B GLY* 3.8 6.5 - - - +
89B GLU 3.0 0.4 - - - -
90B GLN* 1.3 83.4 - - + +
92B LEU* 1.3 68.0 + - - +
94B GLY 3.6 6.8 - - - +
109B GLU* 5.7 0.7 - - - +
110B PHE* 5.1 2.3 - - - -
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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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72B LYS 6.0 0.2 - - - +
76B ALA* 5.2 8.7 - - + -
88B GLY 3.3 10.2 + - - +
91B ILE* 1.3 82.5 - - - +
93B SER* 1.3 64.3 + - - +
94B GLY 5.0 0.3 - - - +
101B LYS* 4.9 1.0 - - - +
106B ILE* 4.1 12.4 - - + +
109B GLU* 4.5 5.4 - - - +
110B PHE* 4.1 20.7 - - + -
117B THR* 3.5 25.1 - - - +
121B LEU* 4.0 19.5 - - + -
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 3.0 17.9 + - - +
90B GLN* 4.9 0.2 - - - -
92B LEU* 1.3 79.1 - - - +
94B GLY* 1.3 64.0 + - - +
95B GLY 3.8 1.9 + - - -
98B ASN* 5.8 0.2 - - - +
99B LYS 4.0 1.0 - - - +
100B GLN* 3.1 29.3 + - - -
101B LYS* 3.1 31.0 + - - +
106B ILE* 4.2 13.7 - - - -
121B LEU* 3.9 13.4 - - - +
125B TYR* 3.9 15.6 + - - -
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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