Contacts of the strand formed by residues 140 - 145 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J ASP* 1.3 76.9 - - - +
141J ALA* 1.3 59.8 + - - +
156J SER* 5.6 4.7 - - - +
157J GLY 3.6 8.1 - - - +
158J ILE* 3.7 24.2 - - + -
193J ASN* 3.9 19.1 - - - +
194J LEU* 3.9 35.9 + - + +
199J ILE* 4.9 2.6 - - - +
13L PRO* 3.2 37.0 + - + -
14L SER* 3.7 16.8 - - - -
15L LEU* 3.9 25.8 - - + -
156L SER* 5.1 3.6 - - - -
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ASP 3.8 0.4 + - - -
140J PHE* 1.3 76.2 - - - +
142J VAL* 1.3 64.2 + - - +
143J ALA 4.3 0.2 - - - -
156J SER* 3.6 4.0 + - - -
157J GLY 2.9 34.2 + - - +
158J ILE 4.6 1.6 - - - -
159J VAL* 4.5 8.7 - - + -
178J THR* 4.2 11.7 - - - +
180J ALA* 4.5 0.9 - - - +
191J LEU* 3.6 28.3 - - + -
192J LEU 3.2 8.7 - - - +
199J ILE* 4.1 9.0 - - + -
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Residues in contact with VAL 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 3.6 27.1 - - + -
18J MET* 4.1 20.6 - - + -
19J LEU* 4.0 25.4 - - + -
141J ALA* 1.3 78.1 - - - +
143J ALA* 1.4 64.8 + - - +
144J VAL* 4.3 2.7 - - + -
154J ALA* 4.2 11.0 - - + -
155J THR 3.3 15.5 - - - +
156J SER* 4.4 2.9 - - - +
190J ALA 3.6 1.2 - - - +
191J LEU* 3.5 3.3 - - - -
192J LEU* 2.8 46.3 + - + +
193J ASN 4.9 1.3 - - - +
194J LEU* 5.0 7.9 - - + -
158K ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J ALA 4.3 0.2 - - - -
142J VAL* 1.4 70.7 - - - +
144J VAL* 1.3 59.2 + - - +
145J GLY 4.3 0.2 - - - -
153J THR 3.6 1.0 - - - +
154J ALA* 3.2 5.0 - - - -
155J THR* 2.8 50.3 + - - +
180J ALA* 4.0 14.3 - - + +
181J SER 4.4 0.4 - - - +
182J ILE* 4.0 13.2 - - + -
186J ASN* 4.8 5.2 - - - +
190J ALA 3.3 5.6 - - - -
191J LEU* 4.2 7.0 - - + +
202J ASN* 3.6 17.0 - - - +
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J LEU* 4.4 0.2 - - + -
23J LEU* 3.8 17.9 - - + -
26J VAL* 3.7 30.9 - - + +
142J VAL* 4.3 10.3 - - + -
143J ALA* 1.3 78.8 - - - +
145J GLY* 1.3 62.1 + - - +
152J GLN* 3.6 29.6 - - - +
153J THR 3.3 7.0 - - - +
154J ALA* 4.4 3.4 - - + -
186J ASN* 4.3 2.8 - - - +
189J GLY* 3.5 5.2 - - - -
190J ALA 2.8 35.1 + - - +
192J LEU* 3.8 28.3 - - + -
202J ASN* 4.4 1.9 - - - +
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Residues in contact with GLY 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J VAL* 4.7 3.1 - - - -
27J VAL 5.6 0.4 - - - -
66J SER* 3.2 17.3 - - - -
144J VAL* 1.3 79.0 - - - +
146J ASN* 1.4 59.4 + - - -
147J PRO* 3.4 7.9 - - - +
152J GLN* 3.6 6.1 - - - +
153J THR 2.8 33.6 + - - +
186J ASN* 3.8 12.8 + - - -
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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