Contacts of the strand formed by residues 137 - 142 (chain F) in PDB entry 1XSK
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 ASN 137 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F HIS* 3.0 19.6 + - - +
19F PRO* 3.5 30.5 - - - +
55F LEU* 5.1 1.0 - - - +
69F ILE* 3.5 18.8 - - + +
118F TRP* 4.8 9.7 + - - +
120F LEU* 4.5 7.3 - - - +
132F SER* 3.5 13.9 + - - -
133F GLN 4.4 2.3 - - - +
135F LYS 3.4 3.0 + - - -
136F ASN* 1.3 78.1 + - - +
138F GLY* 1.3 59.6 + - - +
151F PHE* 3.1 22.0 - - - +
152F GLU* 3.0 34.3 + - + +
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Residues in contact with GLY 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ILE 3.5 9.2 - - - -
19F PRO* 4.0 10.8 - - - -
53F PHE* 4.1 5.6 - - - -
69F ILE* 5.5 2.1 - - - +
137F ASN* 1.3 76.8 - - - +
139F TYR* 1.3 59.8 + - - -
150F MET* 3.3 19.0 - - - +
151F PHE* 3.0 38.4 + - - -
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Residues in contact with TYR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASN 3.7 1.0 - - - +
16F LEU* 3.4 6.8 - - - +
17F ILE* 3.0 61.1 + - + +
53F PHE* 3.8 9.8 - - + -
71F HIS* 3.2 30.6 + + - -
72F PHE* 4.6 4.2 - + - -
138F GLY* 1.3 72.3 - - - -
140F VAL* 1.3 62.8 + - - +
141F GLN* 3.5 33.7 + - + -
148F ASN* 3.2 32.4 + - + -
149F TYR 3.4 12.6 - - - -
150F MET* 3.6 13.9 - - - -
151F PHE* 4.5 0.8 - - - -
234F SER 4.5 5.4 - - - -
235F GLU* 2.5 33.7 + - - -
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.6 4.7 - - + -
3F ILE* 3.9 13.2 - - + -
14F LEU* 4.2 26.2 - - + -
15F ASN 3.7 2.0 - - - -
16F LEU* 3.5 25.8 - - + -
139F TYR* 1.3 76.2 - - - +
141F GLN* 1.3 68.2 + - - +
142F ASP 3.9 0.2 + - - -
148F ASN* 3.2 8.1 - - - +
149F TYR* 2.6 62.0 + - + +
151F PHE* 3.6 27.1 - - + -
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Residues in contact with GLN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLY 3.5 0.5 - - - +
14F LEU* 3.5 1.6 - - - -
15F ASN* 2.8 59.7 + - + +
17F ILE* 5.3 7.3 - - - +
71F HIS* 5.8 0.8 - - - -
139F TYR* 3.5 30.1 + - + -
140F VAL* 1.3 73.9 - - - +
142F ASP* 1.3 62.2 + - - +
143F THR* 3.2 7.5 + - - +
148F ASN* 3.5 19.9 + - - +
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Residues in contact with ASP 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 5.6 2.1 - - - +
14F LEU* 3.5 20.5 - - + +
140F VAL* 3.9 2.0 - - - +
141F GLN* 1.3 70.3 - - - +
143F THR* 1.3 55.4 + - - +
144F ASN* 2.9 34.9 + - - +
145F ASN* 3.0 30.0 + - - +
146F GLN* 3.0 28.4 + - - -
147F ARG 2.8 21.1 + - - +
148F ASN* 4.2 0.4 + - - +
149F TYR* 4.0 18.2 + - + -
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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