Contacts of the strand formed by residues 140 - 145 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.3 30.1 + - + -
14A SER* 3.7 23.1 - - - -
15A LEU* 3.9 24.5 - - + -
156A SER* 5.2 2.7 - - - -
138B GLY 4.4 0.2 - - - -
139B ASP* 1.3 77.0 - - - +
141B ALA* 1.3 59.3 + - - +
156B SER* 5.7 3.8 - - - +
157B GLY 3.6 7.6 - - - +
158B ILE* 3.7 24.2 - - + -
159B VAL* 5.2 0.2 - - - +
193B ASN* 3.9 19.6 - - - +
194B LEU* 3.8 35.3 + - + +
199B ILE* 4.9 2.6 - - - +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP 3.8 0.2 + - - -
140B PHE* 1.3 75.9 - - - +
142B VAL* 1.3 65.0 + - - +
143B ALA 4.2 0.4 + - - -
155B THR 4.2 0.2 - - - +
156B SER* 3.6 3.3 + - - -
157B GLY 2.9 35.2 + - - +
158B ILE 4.5 1.8 - - - -
159B VAL* 4.5 9.0 - - + -
178B THR* 4.2 12.1 - - - +
180B ALA* 4.5 1.3 - - - +
191B LEU* 3.9 22.9 - - + -
192B LEU 3.2 9.4 - - - +
199B ILE* 4.1 13.0 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.7 27.4 - - + -
18B MET* 4.0 21.8 - - + -
19B LEU* 4.1 23.3 - - + -
141B ALA* 1.3 77.1 - - - +
143B ALA* 1.3 65.8 + - - +
144B VAL* 4.3 3.6 - - + -
154B ALA* 4.2 12.3 - - + -
155B THR 3.3 14.8 - - - +
156B SER* 4.4 3.4 - - - +
190B ALA 3.6 1.2 - - - +
191B LEU* 3.5 4.0 - - - -
192B LEU* 2.8 46.1 + - + +
193B ASN 4.9 0.7 - - - +
194B LEU* 4.9 6.3 - - + -
158C ILE* 4.7 3.4 - - + -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 4.2 0.6 - - - -
142B VAL* 1.3 71.4 - - - +
144B VAL* 1.3 60.6 + - - +
145B GLY 4.2 0.4 - - - -
153B THR 3.6 1.3 - - - +
154B ALA* 3.2 5.7 - - - -
155B THR* 2.7 51.3 + - - +
180B ALA* 4.0 9.3 - - + +
181B SER 4.4 0.2 - - - +
182B ILE* 4.0 19.7 - - + -
186B ASN* 4.5 4.5 - - - +
190B ALA 3.3 4.9 - - - -
191B LEU* 4.2 6.4 - - + +
202B ASN* 3.7 14.8 - - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.6 1.3 - - + -
23B LEU* 3.7 31.6 - - + -
26B VAL* 3.6 33.1 - - + +
142B VAL* 4.3 10.5 - - + -
143B ALA* 1.3 78.5 - - - +
145B GLY* 1.3 61.2 + - - +
152B GLN* 3.8 14.6 - - + -
153B THR 3.4 6.3 - - - +
154B ALA* 4.3 3.4 - - + -
186B ASN* 4.3 2.6 - - - +
189B GLY* 3.4 4.5 - - - -
190B ALA* 2.8 33.7 + - + +
192B LEU* 3.8 27.8 - - + -
202B ASN* 4.3 1.0 - - - +
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.8 2.7 - - - -
66B SER* 3.3 17.0 - - - -
144B VAL* 1.3 76.5 - - - +
146B ASN* 1.4 57.8 + - - -
147B PRO* 3.4 7.6 - - - +
152B GLN* 3.7 5.8 - - - -
153B THR 2.9 33.5 + - - +
186B ASN* 3.8 15.8 + - - -
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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