Contacts of the strand formed by residues 117 - 124 (chain B) in PDB entry 2B33
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.0 0.5 - - - -
34B PRO* 3.3 24.2 - - + +
47B ILE* 4.0 11.7 - - + -
50B LYS* 3.9 31.4 - - + -
51B THR* 4.3 9.9 - - - +
54B VAL* 3.9 16.5 - - + +
77B VAL* 3.4 33.0 - - + -
78B PHE 3.5 4.7 - - - +
79B THR* 3.4 13.9 - - + -
88B VAL* 4.2 17.5 - - + -
111B LEU* 3.7 2.8 - - - +
115B VAL* 3.5 4.9 - - - +
116B GLU* 1.3 81.2 - - - +
118B GLU* 1.3 65.3 + - - +
119B ILE* 4.2 14.8 - - + -
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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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31B GLY* 3.5 27.4 - - - +
32B GLN 3.2 13.7 - - - +
33B ILE* 3.8 14.0 - - + +
77B VAL* 3.6 0.2 - - - -
78B PHE* 2.7 54.1 + - + +
111B LEU* 3.6 20.8 - - + +
112B PRO* 3.2 32.5 - - - +
117B ILE* 1.3 76.8 - - - +
119B ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 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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30B SER 3.9 1.4 - - - +
31B GLY* 3.9 1.1 - - - -
32B GLN* 2.8 39.8 + - - +
51B THR* 4.7 6.7 - - + -
54B VAL* 3.6 23.3 - - + -
55B LEU* 3.9 22.4 - - + -
58B LEU* 4.5 17.6 - - + +
75B VAL* 3.4 31.2 - - + -
76B THR 3.4 4.7 - - - +
77B VAL* 4.1 22.9 - - + -
88B VAL* 5.1 1.1 - - + -
92B TYR* 4.6 6.1 - - + -
117B ILE* 4.2 14.6 - - + -
118B GLU* 1.3 80.3 - - - +
120B GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 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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29B VAL* 3.7 14.5 - - - +
30B SER* 4.2 1.7 - - - -
31B GLY* 3.8 18.6 + - - +
58B LEU* 5.2 1.1 - - - -
75B VAL* 3.5 0.7 - - - +
76B THR* 3.1 50.6 + - - +
78B PHE* 4.0 23.3 - - + -
119B ILE* 1.3 80.9 - - - +
121B ALA* 1.3 67.3 + - - +
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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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27B MET 4.8 0.2 - - - -
28B PHE 3.8 0.2 - - - -
29B VAL* 2.9 36.1 + - + +
58B LEU* 4.0 24.9 - - + -
62B LEU* 6.0 0.2 - - + -
72B VAL* 4.2 19.3 - - + -
74B LYS 3.3 12.8 - - - +
75B VAL* 4.2 5.6 - - + +
120B GLU* 1.3 81.4 - - - +
122B ILE* 1.3 68.3 + - - +
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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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26B MET* 4.0 25.8 - - + -
27B MET 3.4 10.3 - - - +
28B PHE* 3.8 28.5 - - + -
29B VAL* 6.1 0.2 - - - -
72B VAL* 3.7 2.8 - - - +
73B VAL* 3.0 35.8 + - + +
74B LYS* 2.8 28.3 + - + +
121B ALA* 1.3 79.0 - - - +
123B ALA* 1.3 65.4 + - - +
124B VAL* 4.6 0.2 - - + -
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Residues in contact with ALA 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 MET* 3.4 1.9 - - - +
27B MET* 2.8 36.5 + - + +
29B VAL* 5.7 0.7 - - + -
62B LEU* 3.8 28.7 - - + -
67B PHE* 3.9 14.1 - - + -
71B ASP* 3.4 19.7 - - + +
72B VAL* 3.8 3.4 - - + -
73B VAL 4.1 0.7 - - - +
121B ALA* 6.1 0.4 - - + -
122B ILE* 1.3 76.0 - - - +
124B VAL* 1.3 68.3 + - - +
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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
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25B ASN* 3.5 32.1 - - - +
26B MET* 4.1 22.9 - - + -
67B PHE* 4.4 0.4 - - - -
71B ASP* 2.8 26.8 + - - +
73B VAL* 4.0 28.3 - - + +
122B ILE* 4.6 0.7 - - + -
123B ALA* 1.3 80.1 - - - +
125B LYS* 1.3 67.7 + - - +
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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