Contacts of the strand formed by residues 117 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.9 0.5 - - - -
34A PRO* 3.3 24.1 - - + +
47A ILE* 4.2 11.7 - - + -
50A LYS* 3.8 32.1 - - + -
51A THR* 4.3 10.1 - - - +
54A VAL* 3.9 18.4 - - + -
77A VAL* 3.4 33.0 - - + -
78A PHE 3.5 4.7 - - - +
79A THR* 3.4 13.7 - - + -
88A VAL* 4.2 17.7 - - + -
111A LEU* 3.5 3.7 - - - +
115A VAL* 3.5 5.2 - - - +
116A GLU* 1.3 81.4 - - - +
118A GLU* 1.3 64.1 + - - +
119A ILE* 4.2 14.8 - - + -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 3.5 27.6 - - - +
32A GLN 3.2 13.7 - - - +
33A ILE* 3.8 14.8 - - + +
78A PHE* 2.7 53.2 + - + +
111A LEU* 3.4 20.9 - - + +
112A PRO* 3.1 32.2 - - - +
117A ILE* 1.3 76.8 - - - +
119A ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER 3.9 1.6 - - - +
31A GLY* 3.9 1.1 - - - -
32A GLN* 2.8 37.3 + - - +
51A THR* 4.6 8.1 - - + -
54A VAL* 3.6 22.9 - - + -
55A LEU* 3.9 22.4 - - + -
58A LEU* 4.5 18.1 - - + +
75A VAL* 3.4 31.6 - - + -
76A THR 3.5 4.7 - - - +
77A VAL* 4.1 22.4 - - + -
88A VAL* 5.1 1.1 - - + -
92A TYR* 4.7 5.2 - - + -
117A ILE* 4.2 13.7 - - + -
118A GLU* 1.3 80.3 - - - +
120A GLU* 1.3 64.2 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.7 14.4 - - - +
30A SER 4.2 1.8 - - - -
31A GLY* 3.8 18.5 + - - +
58A LEU* 5.2 1.1 - - - -
75A VAL* 3.5 6.9 - - - +
76A THR* 3.1 52.2 + - - +
78A PHE* 4.0 21.6 - - + -
119A ILE* 1.3 74.4 - - - +
121A ALA* 1.3 67.4 + - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.9 0.2 - - - -
29A VAL* 2.9 36.5 + - + +
58A LEU* 4.0 25.1 - - + -
62A LEU* 6.0 0.2 - - + -
72A VAL* 4.1 19.1 - - + -
74A LYS 3.3 12.8 - - - +
75A VAL* 4.2 5.8 - - + +
76A THR 5.0 0.2 - - - +
120A GLU* 1.3 80.8 - - - +
122A ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A MET* 4.0 25.8 - - + -
27A MET 3.4 9.4 - - - +
28A PHE* 3.8 27.8 - - + -
72A VAL* 3.7 3.6 - - - +
73A VAL* 3.0 34.9 + - + -
74A LYS* 2.8 28.7 + - + +
121A ALA* 1.3 78.9 - - - +
123A ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.4 1.7 - - - +
27A MET* 2.8 35.8 + - + +
29A VAL* 5.7 0.7 - - + -
62A LEU* 3.8 27.8 - - + -
67A PHE* 3.9 14.8 - - + -
71A ASP* 3.3 20.6 - - + +
72A VAL* 3.8 3.1 - - + -
73A VAL 4.1 1.1 - - - +
122A ILE* 1.3 74.7 - - - +
124A VAL* 1.3 68.9 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.5 33.7 - - - +
26A MET* 4.1 23.3 - - + -
67A PHE* 4.3 0.4 - - - -
71A ASP* 2.8 27.0 + - - +
73A VAL* 4.0 28.2 - - + +
122A ILE* 4.6 0.7 - - + -
123A ALA* 1.3 80.4 - - - +
125A LYS* 1.3 67.6 + - - +
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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