Contacts of the strand formed by residues 140 - 145 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D GLY 4.4 0.2 - - - -
139D ASP* 1.3 76.7 - - - +
141D ALA* 1.3 59.6 + - - +
156D SER* 5.6 4.9 - - - +
157D GLY 3.6 8.1 - - - +
158D ILE* 3.7 24.5 - - + -
193D ASN* 3.9 19.6 - - - +
194D LEU* 3.8 33.4 + - + +
199D ILE* 4.9 2.9 - - - +
13F PRO* 3.3 28.9 + - + -
14F SER* 3.7 22.9 - - - -
15F LEU* 3.8 25.1 - - + -
156F SER* 5.1 3.6 - - - -
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ASP 3.8 0.2 + - - -
140D PHE* 1.3 74.7 - - - +
142D VAL* 1.3 64.7 + - - +
143D ALA 4.4 0.2 + - - -
155D THR 4.2 0.2 - - - +
156D SER* 3.6 3.5 + - - -
157D GLY 2.9 34.7 + - - +
158D ILE 4.6 1.6 - - - -
159D VAL* 4.5 10.3 - - + -
178D THR* 4.2 12.6 - - - +
180D ALA* 4.5 1.1 - - - +
191D LEU* 3.9 21.8 - - + -
192D LEU 3.2 10.5 - - - +
199D ILE* 4.0 13.0 - - + -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.8 26.2 - - + -
18D MET* 3.9 22.2 - - + -
19D LEU* 3.9 25.6 - - + -
141D ALA* 1.3 75.9 - - - +
143D ALA* 1.3 65.0 + - - +
144D VAL* 4.2 5.4 - - + -
154D ALA* 4.3 9.6 - - + -
155D THR 3.3 14.4 - - - +
156D SER* 4.4 3.6 - - - +
190D ALA 3.6 1.2 - - - +
191D LEU* 3.5 3.9 - - - -
192D LEU* 2.8 45.7 + - + +
193D ASN 4.9 0.7 - - - +
194D LEU* 4.8 8.7 - - + -
158E ILE* 4.8 3.1 - - + -
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA 4.2 1.0 - - - -
142D VAL* 1.3 71.8 - - - +
144D VAL* 1.3 60.0 + - - +
145D GLY 4.2 0.2 - - - -
153D THR 3.6 1.3 - - - +
154D ALA* 3.2 4.9 - - - -
155D THR* 2.7 53.8 + - - +
180D ALA* 4.0 9.4 - - + +
181D SER 4.5 0.2 - - - +
182D ILE* 4.0 19.1 - - + -
186D ASN* 4.8 4.7 - - - +
190D ALA 3.3 5.4 - - - -
191D LEU* 4.1 6.9 - - + +
202D ASN* 3.6 15.5 - - - +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.5 0.4 - - + -
23D LEU* 3.7 32.3 - - + -
26D VAL* 3.6 28.8 - - + +
142D VAL* 4.2 11.0 - - + -
143D ALA* 1.3 77.7 - - - +
145D GLY* 1.3 61.6 + - - +
152D GLN* 3.7 18.8 - - + -
153D THR 3.4 5.4 - - - +
154D ALA* 4.4 3.4 - - + -
186D ASN* 4.2 2.9 - - - +
189D GLY* 3.5 4.3 - - - -
190D ALA 2.8 35.6 + - - +
192D LEU* 3.9 27.4 - - + -
202D ASN* 4.1 1.7 - - - +
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Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 4.6 3.1 - - - -
66D SER* 3.1 16.2 - - - -
144D VAL* 1.3 77.6 - - - +
146D ASN* 1.3 58.3 + - - -
147D PRO* 3.3 7.2 - - - +
152D GLN* 3.5 5.7 - - - -
153D THR 2.8 34.4 + - - +
186D ASN* 3.6 13.9 + - - -
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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