Contacts of the strand formed by residues 117 - 124 (chain B) in PDB entry 3K0T
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 VAL 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.0 0.2 - - - -
35B PRO* 3.2 42.0 - - + +
47B ILE* 4.5 3.1 - - + -
50B GLN* 4.0 6.1 - - + -
51B ILE* 4.0 26.9 - - + +
54B VAL* 4.0 6.2 - - + +
77B ILE* 5.0 1.3 - - + -
78B PHE 3.3 12.6 - - - +
79B LEU* 3.7 18.4 - - + -
88B VAL* 4.7 2.7 - - + -
111B LEU* 3.4 3.1 - - - +
115B ALA* 3.4 4.5 - - - +
116B GLN* 1.3 83.2 - - - +
118B GLU* 1.3 71.4 + - - +
119B MSE 3.7 28.3 - - + -
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Residues in contact with GLU 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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104A ALA* 3.9 5.2 - - - +
105A ALA 2.7 41.4 + - - +
106A ILE* 4.4 5.8 - - - -
32B GLY* 3.6 12.0 - - - -
33B GLN 3.3 18.6 - - - +
34B ILE* 3.9 8.2 - - + +
54B VAL* 4.7 0.4 - - - -
78B PHE* 2.9 38.5 + - + +
111B LEU* 3.5 17.1 - - + +
112B PRO* 3.4 14.2 - - - +
117B VAL* 1.3 76.4 - - - +
119B MSE 1.3 69.3 + - - +
127B BGC 3.3 20.2 + - - +
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Residues in contact with MSE 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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32B GLY* 4.0 1.3 - - - -
33B GLN* 2.7 36.8 + - - +
51B ILE* 4.0 17.0 - - + +
54B VAL* 3.7 22.0 - - + +
55B PHE* 3.4 49.6 - - + -
58B LEU* 3.9 14.0 - - + +
75B LEU* 4.0 14.1 - - + -
76B ASN 3.2 15.9 - - - +
77B ILE* 4.1 12.1 - - - -
78B PHE* 4.5 1.1 - - - -
88B VAL* 4.2 9.4 - - + -
117B VAL* 3.7 22.7 - - + -
118B GLU* 1.3 82.9 - - - +
120B ASP* 1.3 60.1 + - - +
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Residues in contact with ASP 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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74A LYS* 2.9 27.6 + - - +
76A ASN* 4.1 1.9 + - - -
104A ALA* 3.5 13.7 - - + +
30B MSE 3.6 10.5 - - - +
31B SER 4.0 3.6 - - - -
32B GLY* 3.5 22.0 - - - +
58B LEU* 4.5 2.9 - - - -
75B LEU* 3.5 5.9 - - - +
76B ASN* 2.9 51.7 + - - +
78B PHE* 4.3 9.3 - - + -
119B MSE 1.3 74.8 - - - +
121B ALA* 1.3 67.5 + - - +
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Residues in contact with ALA 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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74A LYS* 5.5 1.2 + - - -
30B MSE 3.0 51.4 + - - +
58B LEU* 4.7 5.4 - - + +
72B ILE* 4.1 21.1 - - + -
74B LYS 3.2 14.4 - - - +
75B LEU* 4.2 8.7 - - + +
76B ASN* 5.7 0.4 - - - -
120B ASP* 1.3 82.4 + - - +
122B ILE* 1.3 66.4 + - - +
123B LEU 4.2 0.2 - - - -
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Residues in contact with ILE 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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74A LYS* 5.8 5.2 - - - +
122A ILE* 5.4 4.7 - - + -
27B THR* 3.7 28.3 - - + -
28B VAL 3.4 4.7 - - - +
29B TYR* 4.1 27.6 - - + -
72B ILE* 3.4 3.7 - - - +
73B VAL* 2.8 50.0 + - + +
74B LYS* 2.9 20.4 + - + +
76B ASN* 6.2 0.4 - - - +
121B ALA* 1.3 79.2 - - - +
123B LEU* 1.3 58.3 + - - +
29C TYR* 3.6 29.8 - - + +
122C ILE* 5.5 4.3 - - + -
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Residues in contact with LEU 123 (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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26B ASN 3.7 0.2 - - - +
27B THR* 3.5 2.6 - - - -
28B VAL* 2.7 57.0 + - + +
30B MSE 4.2 13.7 - - - -
62B ALA* 3.7 40.6 - - + +
65B ALA* 4.7 4.9 - - + -
68B SER 4.0 13.0 - - - +
71B ASP* 3.5 24.5 - - + +
72B ILE* 4.0 6.3 - - + +
121B ALA 4.2 0.2 - - - -
122B ILE* 1.3 75.8 - - - +
124B VAL* 1.3 63.3 + - - +
125B ILE* 3.4 34.3 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASN* 3.2 16.8 - - + +
27B THR* 4.0 19.7 - - + +
71B ASP* 2.9 25.6 + - - +
73B VAL* 3.8 31.1 - - + +
123B LEU* 1.3 80.5 - - - +
125B ILE* 1.3 72.2 + - - +
24C ALA* 4.0 22.4 - - + -
29C TYR* 4.6 5.8 - - + -
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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