Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 1SOI
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.7 23.3 - - + -
31A GLN 3.6 2.2 - - - -
33A LYS* 3.3 6.3 + - - -
46A HIS* 5.4 3.1 - - - +
69A GLU* 3.7 51.6 - - + +
111A ALA* 3.4 24.7 - - + +
112A PHE* 3.5 2.8 - - - -
113A THR* 3.0 35.1 + - + +
115A GLU* 1.3 86.2 - - + +
117A ALA* 1.3 62.6 + - - +
118A GLU* 3.7 17.7 - - - +
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Residues in contact with ALA 117 (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 GLN* 2.8 22.5 + - - +
32A GLU 3.6 20.4 - - - +
33A LYS* 3.5 24.8 + - + +
112A PHE* 3.0 18.7 - - - +
116A ILE* 1.3 73.3 - - - +
118A GLU* 1.3 71.5 + - + +
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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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30A VAL* 3.6 1.2 - - - -
31A GLN* 2.8 47.1 + - - +
45A TRP* 4.3 10.8 - - + -
110A PRO* 4.0 5.6 - - + -
112A PHE* 3.9 19.5 - - + -
116A ILE* 3.5 8.2 - - - +
117A ALA* 1.3 85.9 - - - +
119A ALA* 1.3 67.6 + - - +
120A SER* 4.6 8.0 + - - -
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Residues in contact with ALA 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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28A LEU* 4.6 0.7 - - + -
29A LEU 3.2 13.9 - - - +
30A VAL* 4.1 6.7 - - + -
45A TRP* 4.5 1.3 - - - -
69A GLU 4.5 2.9 - - - +
70A THR* 4.1 26.2 - - + -
108A LEU* 3.4 14.4 - - + +
110A PRO* 3.4 25.7 - - + +
118A GLU* 1.3 81.5 - - - +
120A SER* 1.3 70.7 + - - +
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Residues in contact with SER 120 (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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27A ILE 3.6 0.5 - - - +
28A LEU* 3.8 6.8 - - - +
29A LEU* 2.9 32.0 + - - +
45A TRP* 3.5 22.7 - - - -
108A LEU* 3.4 13.4 - - - +
118A GLU* 4.6 5.8 + - - -
119A ALA* 1.3 79.5 - - - +
121A PHE* 1.3 67.9 + - - +
122A VAL* 3.8 7.7 + - - +
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Residues in contact with PHE 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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20A LEU* 3.6 32.8 - - + -
22A ASN* 3.9 33.7 - - + +
24A ARG* 5.8 1.8 - - - +
26A ASP* 4.0 13.9 - - + +
27A ILE 3.4 4.5 - - - -
28A LEU* 3.7 24.9 - - + -
72A LEU* 4.1 24.7 - - + -
102A PRO* 5.2 4.9 - - + -
108A LEU* 4.3 16.3 - - + +
120A SER* 1.3 79.2 - - - +
122A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 122 (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 ASP* 3.3 3.5 - - - -
27A ILE* 2.8 41.5 + - + +
29A LEU* 4.3 17.3 - - + -
45A TRP* 5.1 7.0 - - + -
120A SER* 4.1 16.2 - - - +
121A PHE* 1.3 80.1 - - - +
123A SER* 1.3 75.7 + - - +
126A ASP* 3.7 13.7 - - + -
127A PHE* 3.7 17.9 - - + +
130A LEU* 4.0 19.3 - - + -
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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