Contacts of the strand formed by residues 140 - 145 (chain F) in PDB entry 3STJ
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 PHE 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E PRO* 3.1 41.5 + - + -
14E SER* 3.8 11.0 - - - -
15E LEU* 3.9 24.5 - - + -
156E SER* 5.2 3.8 - - - -
138F GLY 4.5 0.4 - - - -
139F ASP* 1.3 77.3 - - - +
141F ALA* 1.3 60.2 + - - +
156F SER* 5.6 4.7 - - - +
157F GLY 3.6 7.4 - - - +
158F ILE* 3.7 24.9 - - + -
193F ASN* 3.9 19.6 - - - +
194F LEU* 3.9 33.7 + - + +
199F ILE* 4.9 2.9 - - - +
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Residues in contact with ALA 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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139F ASP 3.8 0.4 + - - -
140F PHE* 1.3 75.5 - - - +
142F VAL* 1.3 66.0 + - - +
143F ALA 4.2 0.2 - - - -
155F THR 4.2 0.2 - - - +
156F SER* 3.6 3.8 + - - -
157F GLY 2.9 33.9 + - - +
158F ILE 4.5 0.9 - - - -
159F VAL* 4.5 9.6 - - + -
178F THR* 4.2 12.1 - - - +
180F ALA* 4.5 1.0 - - - +
191F LEU* 3.8 23.3 - - + -
192F LEU 3.2 9.9 - - - +
199F ILE* 4.1 12.1 - - + -
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Residues in contact with VAL 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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158D ILE* 4.7 2.9 - - + -
15F LEU* 3.8 25.1 - - + -
18F MET* 3.9 22.2 - - + -
19F LEU* 4.1 23.6 - - + -
140F PHE* 6.3 0.2 - - + -
141F ALA* 1.3 76.6 - - - +
143F ALA* 1.3 65.3 + - - +
144F VAL* 4.3 5.8 - - + -
154F ALA* 4.3 9.0 - - + -
155F THR 3.3 16.2 - - - +
156F SER* 4.4 4.0 - - - +
190F ALA 3.6 1.7 - - - +
191F LEU* 3.5 4.1 - - - -
192F LEU* 2.8 45.2 + - + +
193F ASN 4.9 0.4 - - - +
194F LEU* 4.9 9.0 - - + -
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Residues in contact with ALA 143 (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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141F ALA 4.2 0.6 - - - -
142F VAL* 1.3 71.0 - - - +
144F VAL* 1.3 60.4 + - - +
145F GLY 4.2 0.2 - - - -
153F THR 3.6 1.2 - - - +
154F ALA* 3.2 4.9 - - - -
155F THR* 2.8 53.4 + - - +
180F ALA* 4.0 10.5 - - + +
181F SER 4.4 0.7 - - - +
182F ILE* 4.0 25.1 - - + -
186F ASN* 4.8 4.9 - - - +
190F ALA 3.3 5.2 - - - -
191F LEU* 4.2 6.9 - - + +
202F ASN* 4.0 8.7 - - - +
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Residues in contact with VAL 144 (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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19F LEU* 4.5 0.7 - - + -
23F LEU* 3.6 32.5 - - + -
26F VAL* 3.7 32.8 - - + +
142F VAL* 4.3 10.8 - - + -
143F ALA* 1.3 79.7 - - - +
145F GLY* 1.3 60.6 + - - +
152F GLN* 3.8 15.3 - - + -
153F THR 3.3 5.2 - - - +
154F ALA* 4.4 2.9 - - + -
186F ASN* 4.1 2.2 - - - -
189F GLY* 3.5 4.3 - - - -
190F ALA* 2.8 36.8 + - + +
192F LEU* 3.8 27.4 - - + -
202F ASN* 4.1 1.8 - - - +
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Residues in contact with GLY 145 (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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26F VAL* 4.7 3.4 - - - -
66F SER* 3.2 15.9 - - - -
144F VAL* 1.3 77.9 - - - +
146F ASN* 1.3 58.4 + - - -
147F PRO* 3.3 9.4 - - - +
151F GLY 3.5 0.7 - - - +
152F GLN* 3.6 4.2 - - - -
153F THR 2.9 32.5 + - - +
186F ASN* 3.5 14.3 + - - -
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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