Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 1XSB
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 HIS 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.1 48.1 + - + +
35A GLN 3.0 17.7 - - - +
36A ALA* 3.9 7.0 - - - +
37A SER* 4.2 0.2 - - - -
44A THR* 4.0 16.9 + - - -
45A PRO 4.8 0.6 + - - -
47A LYS* 4.8 8.8 - - + -
67A GLU* 3.5 28.5 + - - +
112A LEU* 3.4 25.9 - - + +
113A SER* 2.5 37.8 + - - +
114A HIS* 3.8 4.5 - - - +
115A GLU* 1.3 92.8 + - - +
117A GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 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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35A GLN* 2.7 29.7 + - + +
36A ALA 3.1 24.2 - - - +
37A SER* 3.6 22.7 + - - +
41A HIS* 3.8 11.0 + - - -
112A LEU* 3.4 12.4 - - - +
116A HIS* 1.3 72.6 - - - +
118A ALA* 1.3 67.6 + - + +
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Residues in contact with ALA 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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34A LEU* 3.3 0.5 - - - -
35A GLN* 2.4 60.2 + - - +
43A TRP* 4.2 3.1 - - + -
112A LEU* 3.3 7.8 - - - +
117A GLN* 1.3 88.0 - - + +
119A TYR* 1.3 59.3 + - - +
120A ARG* 5.9 1.3 - - + +
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Residues in contact with TYR 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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32A LEU* 3.8 13.2 - - + -
33A LEU 2.9 18.2 - - - +
34A LEU* 3.5 18.8 - - + -
43A TRP* 3.9 1.1 - - - -
110A ILE* 3.0 48.7 - - + +
112A LEU* 3.8 9.6 - - + -
118A ALA* 1.3 76.8 - - - +
120A ARG* 1.3 71.6 + - - +
121A TRP* 3.6 23.3 - + - -
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Residues in contact with ARG 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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31A PHE 3.6 2.9 - - - +
33A LEU 3.1 25.9 + - - -
35A GLN* 4.7 4.2 + - - +
43A TRP* 2.9 42.5 - - + -
118A ALA* 5.9 1.7 - - + +
119A TYR* 1.3 82.9 - - - +
121A TRP* 1.3 65.3 + - - +
122A LEU* 3.6 34.4 - - + +
130A LEU* 4.9 7.7 - - - +
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Residues in contact with TRP 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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15A ILE* 3.9 12.3 - - + -
17A ARG* 2.8 75.8 - - + +
30A GLU* 3.9 8.5 - - + +
31A PHE* 3.1 27.6 - - - -
32A LEU* 3.2 46.9 - - + +
103A VAL* 4.2 7.6 - - + -
106A TYR* 4.7 3.4 + - - +
108A VAL* 4.6 4.4 + - + +
110A ILE* 4.4 12.6 - - + +
119A TYR* 3.6 29.6 - + - -
120A ARG* 1.3 71.5 - - - +
122A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 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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30A GLU* 2.5 16.1 - - - +
31A PHE* 3.0 25.4 + - - +
33A LEU* 3.4 24.2 - - + -
120A ARG* 3.6 35.2 + - + +
121A TRP* 1.3 78.6 - - - +
123A GLY* 1.3 62.1 + - - +
126A GLU* 3.3 28.5 - - + -
127A ALA* 4.3 1.6 - - - +
130A LEU* 3.0 38.1 - - + -
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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