Contacts of the strand formed by residues 115 - 119 (chain I) in PDB entry 4R2G
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 115 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113I ALA 4.3 4.2 + - - -
114I PRO* 1.3 70.7 - - - +
116I VAL* 1.3 61.9 + - - +
117I THR* 4.0 4.8 + - - -
136I LEU 3.3 5.9 - - - +
138I SER* 2.8 42.5 + - - -
139I ASP* 4.7 10.2 + - - +
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Residues in contact with VAL 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I PRO* 3.8 4.6 + - + -
115I SER* 1.3 73.2 - - - +
117I THR* 1.3 70.8 + - - +
135I CYS* 3.5 25.8 - - - -
136I LEU 3.3 2.0 - - - +
137I ILE* 3.8 16.4 - - + -
194I CYS 4.7 1.6 - - - +
196I VAL* 3.5 26.9 - - + -
203I VAL* 3.5 29.5 - - + +
205I LYS* 3.4 44.0 + - + +
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Residues in contact with THR 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I SER* 4.0 5.9 + - - -
116I VAL* 1.3 82.2 + - - +
118I LEU* 1.3 62.3 + - - +
119I PHE* 3.5 28.3 - - + -
134I VAL 3.5 2.9 - - - +
136I LEU* 2.9 39.2 + - - +
205I LYS* 4.8 4.3 - - - +
155J ALA* 3.6 23.8 - - + -
199J VAL* 5.9 3.6 - - + -
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I VAL* 4.2 1.2 - - - +
117I THR* 1.3 75.1 - - - +
119I PHE* 1.3 83.4 + - - +
120I PRO* 4.5 1.9 - - - +
133I LEU* 4.4 3.6 - - + -
134I VAL 3.2 22.0 - - - +
135I CYS* 3.9 4.0 - - + +
149I TRP* 3.8 22.9 - - + -
192I TYR 4.0 4.5 - - - +
194I CYS* 3.6 25.6 - - + +
205I LYS* 3.6 41.6 - - + +
207I VAL* 3.7 34.4 - - + +
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Residues in contact with PHE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I THR* 3.5 32.3 - - + -
118I LEU* 1.3 85.2 - - - +
120I PRO* 1.3 70.1 - - + +
133I LEU* 3.8 4.0 - - - +
134I VAL* 2.8 36.7 + - + +
136I LEU* 5.3 1.1 - - + -
207I VAL* 4.3 4.0 - - - -
142J LEU* 3.4 67.3 - - + -
143J ALA 4.1 10.1 - - - -
144J PRO* 5.2 0.7 - - + -
155J ALA* 3.4 32.5 - - + -
157J GLY 4.1 1.6 - - - -
199J VAL* 4.3 23.1 - - + -
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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