Contacts of the strand formed by residues 115 - 122 (chain B) in PDB entry 4X61
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 ILE 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B LEU* 4.1 16.6 - - + +
59B TRP 4.6 0.9 - - - +
60B LEU* 4.5 7.6 - - + +
75B ALA* 3.8 12.3 - - + +
76B GLY* 3.8 32.7 + - - +
77B VAL* 3.5 39.1 - - + +
94B ILE* 4.1 20.2 - - + -
106B TRP* 3.7 26.0 - - + -
107B GLU 3.9 6.7 - - - +
108B LEU* 3.8 15.9 - - + +
114B LEU* 1.3 84.2 - - - +
116B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 116 (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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106B TRP* 3.4 6.6 - - - -
107B GLU* 2.6 62.8 + - + +
108B LEU 5.6 2.0 - - - -
109B ASP* 5.7 3.1 - - - +
114B LEU* 5.4 12.3 - - + -
115B ILE* 1.3 73.8 - - - +
117B SER* 1.3 70.1 + - - +
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Residues in contact with SER 117 (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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104B GLU* 5.1 1.2 + - - +
105B LEU 3.9 3.3 + - - -
106B TRP* 3.3 34.4 - - - -
107B GLU* 5.4 0.2 - - - -
116B VAL* 1.3 86.7 - - - +
118B LYS* 1.3 66.9 + - - +
119B PHE 4.2 10.9 + - - -
120B CYS* 4.6 7.4 - - - +
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Residues in contact with LYS 118 (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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105B LEU* 2.7 41.2 + - + +
107B GLU* 4.1 36.0 + - + +
116B VAL 3.6 0.6 + - - -
117B SER* 1.3 75.8 + - - +
119B PHE* 1.3 61.1 + - + +
157B GLN* 3.6 23.8 + - - +
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Residues in contact with PHE 119 (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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95B LEU* 4.5 5.8 - - + -
103B VAL* 3.7 25.8 - - + -
104B GLU* 3.2 5.2 - - - +
105B LEU* 2.9 69.7 + - + +
117B SER* 4.2 5.3 + - - -
118B LYS* 1.3 79.1 - - + +
120B CYS* 1.3 63.2 + - - +
121B LYS* 3.7 23.3 - - + -
152B TRP* 4.4 13.7 - + - -
153B ASP 5.5 0.2 - - - -
154B LEU* 4.0 31.2 - - + -
157B GLN* 3.5 45.1 - - + +
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Residues in contact with CYS 120 (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 GLU* 4.1 3.6 - - - -
102B ALA* 4.4 5.4 - - - -
104B GLU* 3.7 36.8 - - + +
117B SER* 4.6 7.9 - - - +
119B PHE* 1.3 77.6 - - - +
121B LYS* 1.3 66.7 + - - +
122B TYR* 3.8 38.7 + - - -
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Residues in contact with LYS 121 (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* 3.4 2.8 - - - -
103B VAL 3.0 31.1 + - - +
119B PHE* 3.7 20.6 - - + -
120B CYS* 1.3 77.8 - - - +
122B TYR* 1.3 60.8 + - - +
123B GLU* 3.1 15.2 + - + -
152B TRP* 3.8 26.2 - - + -
157B GLN* 3.4 46.7 + - - +
158B VAL* 6.1 0.6 - - - +
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Residues in contact with TYR 122 (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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269A THR* 3.8 26.8 + - + -
270A ASN 4.2 12.1 - - - +
271A HIS* 4.4 1.9 - - - -
80B GLU* 2.6 39.0 + - - -
100B SER* 3.7 27.6 - - - -
101B GLY 4.2 2.5 - - - -
102B ALA* 3.5 15.3 - - + -
120B CYS* 3.8 25.3 - - - -
121B LYS* 1.3 68.2 - - - +
123B GLU* 1.3 66.3 + - - +
124B HIS 3.9 0.4 - - - -
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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