Contacts of the strand formed by residues 147 - 155 (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 ARG 147 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142F ASP* 2.8 31.0 + - - +
145F ASN* 2.9 35.6 + - - +
146F GLN* 1.3 79.0 - - - +
148F ASN* 1.3 63.0 + - - +
149F TYR* 3.3 29.6 - - + +
233F GLU* 3.0 37.9 + - - +
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Residues in contact with ASN 148 (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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139F TYR* 3.2 31.5 + - + +
140F VAL 3.2 6.5 - - - +
141F GLN* 3.5 26.8 + - - +
142F ASP 4.2 0.2 + - - -
146F GLN 4.4 9.7 + - - +
147F ARG* 1.3 82.6 - - - +
149F TYR* 1.3 63.6 + - - +
233F GLU* 3.3 21.9 + - - +
234F SER* 3.5 11.0 + - - +
235F GLU* 4.0 7.6 + - - +
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Residues in contact with TYR 149 (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* 3.6 42.4 - - + -
139F TYR* 3.4 7.6 - - - -
140F VAL* 2.6 58.8 + - + -
142F ASP* 4.0 24.7 + - + -
145F ASN* 4.3 6.2 + - - -
147F ARG* 3.3 33.9 - - + -
148F ASN* 1.3 74.3 - - - +
150F MET* 1.3 66.4 + - - +
231F SER* 4.9 2.5 - - - -
232F VAL* 3.4 10.1 - - - +
233F GLU* 3.4 40.0 + - + -
234F SER 4.0 2.7 - - - -
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Residues in contact with MET 150 (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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53F PHE* 4.2 7.2 - - + -
69F ILE* 3.2 47.3 - - + +
70F GLU* 4.5 0.9 - - - +
71F HIS* 4.4 4.3 - - - -
138F GLY* 3.3 25.8 - - - +
139F TYR* 3.6 26.5 - - - -
149F TYR* 1.3 73.2 - - - +
151F PHE* 1.3 63.7 + - - +
231F SER* 3.3 4.2 - - - -
232F VAL* 3.1 34.0 + - + +
234F SER 3.4 18.8 - - - +
235F GLU 3.7 6.5 - - - +
236F TYR* 3.6 19.3 - - - +
237F LEU* 3.7 20.2 - - + +
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Residues in contact with PHE 151 (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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3F ILE* 3.6 23.8 - - + -
16F LEU* 5.1 1.8 - - + -
18F HIS* 4.0 21.1 - + - -
69F ILE* 5.1 1.2 - - - +
135F LYS 4.3 2.0 - - - -
136F ASN 3.4 19.7 - - - -
137F ASN* 3.1 17.6 - - - +
138F GLY* 3.0 54.9 + - - +
139F TYR 4.5 1.6 - - - -
140F VAL* 3.6 25.1 - - + -
150F MET* 1.3 77.2 - - - +
152F GLU* 1.3 66.6 + - - +
153F ARG* 3.8 27.4 - - - -
229F GLN* 4.4 4.5 - - + -
230F PHE 3.3 13.2 - - - +
231F SER* 3.7 12.8 - - - -
237F LEU* 3.5 8.1 - - - +
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Residues in contact with GLU 152 (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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69F ILE* 3.8 3.3 - - + +
120F LEU* 4.1 1.0 - - - +
132F SER* 2.7 33.4 + - - -
136F ASN 3.4 4.6 - - - +
137F ASN* 3.0 28.2 + - + +
151F PHE* 1.3 77.9 - - - +
153F ARG* 1.3 76.9 + - - +
154F LEU* 3.7 18.6 - - + -
228F VAL 3.7 1.0 - - - +
229F GLN* 3.3 2.9 - - - +
230F PHE* 2.9 47.1 + - + -
237F LEU* 3.6 16.6 - - + -
239F TYR* 2.9 26.8 + - + +
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Residues in contact with ARG 153 (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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3F ILE* 4.0 17.4 - - - +
4F SER* 4.0 5.9 - - - -
131F GLY 3.4 9.9 - - - +
132F SER* 3.7 5.7 - - - -
135F LYS 4.1 7.9 + - - -
136F ASN* 2.9 47.5 + - + +
151F PHE* 3.8 15.3 - - + -
152F GLU* 1.3 84.2 + - - +
154F LEU* 1.3 61.2 + - - +
155F ASP* 3.7 1.2 + - - +
223F GLU* 2.7 28.1 + - - -
224F LYS* 3.7 33.5 - - + +
227F LYS* 3.7 20.9 - - + +
228F VAL 3.4 5.2 - - - -
229F GLN* 2.7 38.7 + - + +
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Residues in contact with LEU 154 (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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122F PHE* 4.0 15.0 - - + -
130F THR* 3.8 14.8 - - + +
131F GLY* 3.2 12.6 - - - +
132F SER* 4.4 0.2 - - - -
152F GLU* 3.7 12.8 - - + -
153F ARG* 1.3 72.3 - - - +
155F ASP* 1.3 67.2 + - - +
156F LEU* 4.9 0.2 - - - +
200F TYR* 3.6 24.5 - - - +
206F TYR* 5.5 0.4 - - - +
208F VAL* 4.1 15.9 - - + -
227F LYS* 4.3 0.9 - - - -
228F VAL* 3.0 31.3 + - - +
230F PHE* 3.9 19.5 - - + -
239F TYR* 3.7 37.9 - - + +
241F VAL* 4.9 4.7 - - + -
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Residues in contact with ASP 155 (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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488E GLU* 6.5 0.2 - - + -
128F ARG* 2.7 40.6 + - - +
129F ILE 4.9 0.2 - - - +
130F THR* 2.7 25.7 + - - +
131F GLY 2.8 16.0 + - - +
133F GLN* 3.6 17.9 + - - +
153F ARG 4.4 0.7 - - - +
154F LEU* 1.3 75.4 - - - +
156F LEU* 1.3 64.0 + - - +
160F GLU* 4.1 1.0 - - - +
206F TYR* 3.5 10.4 + - - -
226F SER 3.8 6.9 - - - +
227F LYS* 3.0 33.7 + - - +
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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