Contacts of the helix formed by residues 101 - 107 (chain B) in PDB entry 3I58
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 SER 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LYS* 2.9 30.0 + - - -
96B TRP 4.2 0.3 + - - -
98B ASP* 3.0 18.2 + - - +
100B ASN* 1.3 84.6 - - - +
102B ALA* 1.3 62.8 + - - +
103B VAL 3.7 1.9 + - - -
104B GLY 3.2 11.8 + - - -
105B ARG* 3.1 21.0 + - - +
142B LEU* 4.0 0.2 - - - -
145B SER* 3.6 16.4 - - - -
149B LEU* 4.0 13.0 - - - +
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Residues in contact with ALA 102 (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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101B SER* 1.3 74.3 - - - +
103B VAL* 1.3 59.6 + - - +
105B ARG* 4.0 3.8 - - - +
106B GLY* 3.0 23.2 + - - -
132B PHE* 3.8 13.9 - - + -
136B LEU* 4.1 9.9 - - + -
142B LEU* 3.7 18.2 - - + +
145B SER* 3.0 13.7 + - - +
146B PHE* 3.7 39.0 - - + -
149B LEU* 4.2 1.2 - - - +
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Residues in contact with VAL 103 (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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11A ARG* 5.2 2.2 - - - +
96B TRP* 3.7 29.3 - - + +
101B SER* 3.3 1.6 + - - -
102B ALA* 1.3 76.2 - - - +
104B GLY* 1.3 64.6 + - - +
105B ARG 3.2 1.3 - - - -
106B GLY 3.8 0.2 - - - -
107B ASP* 3.1 31.3 + - - +
146B PHE* 4.2 16.2 - - + -
149B LEU* 3.6 23.7 - - + +
150B MET* 4.8 0.2 - - + -
289B ARG* 4.7 0.2 - - - +
293B TYR* 3.2 10.3 + - + +
402B 7NA 3.4 43.1 - - + +
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Residues in contact with GLY 104 (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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23B ARG* 4.2 9.2 + - - -
96B TRP 3.5 12.9 + - - -
97B LEU 3.9 7.0 - - - -
98B ASP 3.2 21.5 - - - -
99B MET* 3.9 9.7 - - - +
101B SER* 3.2 9.7 + - - -
103B VAL* 1.3 78.3 - - - +
105B ARG* 1.3 58.8 + - - +
108B LEU* 3.5 22.7 + - - +
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Residues in contact with ARG 105 (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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99B MET 3.6 15.9 + - - +
100B ASN 4.9 0.9 - - - +
101B SER 3.1 16.4 + - - +
102B ALA* 4.0 3.4 - - - +
104B GLY* 1.3 77.9 - - - +
106B GLY* 1.3 64.3 + - - +
107B ASP 3.3 0.2 - - - -
108B LEU* 3.3 12.6 + - - +
124B TYR* 2.9 22.7 + - - -
128B TYR* 2.6 62.9 + - + +
132B PHE* 6.2 0.2 - - - -
135B ASP* 2.9 24.0 + - - -
142B LEU* 3.8 30.2 - - - +
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Residues in contact with GLY 106 (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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102B ALA 3.0 15.4 + - - -
103B VAL 3.7 0.2 + - - -
105B ARG* 1.3 78.9 - - - +
107B ASP* 1.3 51.5 + - - +
109B GLY* 2.8 28.4 + - - -
110B PHE 4.3 0.3 + - - -
124B TYR* 3.6 25.2 - - - -
292B THR* 5.0 0.7 + - - -
293B TYR* 3.3 29.0 - - - -
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Residues in contact with ASP 107 (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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11A ARG* 5.7 1.9 + - - -
16A LEU* 3.9 5.8 - - + +
23B ARG* 3.1 41.1 + - - +
96B TRP 5.4 0.3 - - - +
103B VAL* 3.1 18.8 + - - +
104B GLY 4.5 0.4 - - - +
105B ARG 3.3 0.2 - - - -
106B GLY* 1.3 69.6 - - - +
108B LEU* 1.3 57.2 + - - +
109B GLY 2.8 5.4 - - - -
110B PHE* 2.8 43.8 + - + +
289B ARG* 2.4 37.2 + - - -
293B TYR* 2.7 31.4 + - - -
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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