Contacts of the strand formed by residues 126 - 135 (chain B) in PDB entry 3P3B
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 LEU 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR* 3.4 60.9 + - + -
125B SER* 1.3 74.7 + - - +
127B VAL* 1.3 68.7 - - - +
128B VAL* 4.0 9.9 - - + -
323B GLY 3.7 17.9 - - - +
324B HIS* 4.2 1.8 - - - +
326B SER* 3.8 16.6 - - - +
327B ALA* 4.8 11.0 - - + +
358B HIS* 3.8 1.2 - - - +
359B VAL* 3.1 43.4 + - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER* 3.7 14.1 + - - +
126B LEU* 1.3 83.5 - - - +
128B VAL* 1.3 65.6 + - - +
129B PRO* 4.2 4.5 - - - +
356B GLU* 3.0 42.6 - - + +
357B ILE 3.7 3.1 - - - +
358B HIS* 3.1 35.2 - - + +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.0 14.8 - - + -
127B VAL* 1.3 80.1 - - - +
129B PRO* 1.3 79.3 - - + +
323B GLY* 3.7 15.5 - - - +
326B SER* 3.1 22.9 - - - +
332B PHE* 3.4 35.0 - - + -
335B VAL* 3.9 6.3 - - + -
356B GLU* 3.2 5.5 - - - -
357B ILE* 2.7 51.5 + - + +
359B VAL* 4.5 2.0 - - + -
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL 4.2 4.3 - - - +
128B VAL* 1.3 98.3 - - + +
130B CYS* 1.3 59.2 + - - +
166B HIS* 5.7 0.4 - - + -
332B PHE* 5.3 2.5 - - + +
333B GLU 3.5 21.1 - - - +
334B PHE* 3.3 19.3 - - + -
335B VAL* 2.8 21.8 + - - +
355B GLY 3.5 10.5 - - - +
356B GLU* 4.1 9.6 - - + +
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Residues in contact with CYS 130 (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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128B VAL 4.4 0.2 - - - +
129B PRO* 1.3 75.5 - - - +
131B TYR* 1.3 61.6 + - - +
164B GLN* 3.7 28.6 - - - +
166B HIS* 3.4 16.5 - - - +
334B PHE* 3.8 4.7 - - - -
335B VAL* 3.3 24.2 - - + +
337B TYR* 4.4 7.4 - - + -
352B ILE* 4.2 11.0 - - - -
355B GLY* 3.1 17.6 + - - +
356B GLU 3.8 29.4 - - - -
357B ILE* 3.9 8.1 - - + +
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Residues in contact with TYR 131 (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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130B CYS* 1.3 75.3 - - - +
132B ASP* 1.3 63.0 + - - +
133B THR* 3.6 18.8 - - - -
164B GLN* 3.4 7.0 - - - -
166B HIS* 3.4 24.7 - - + +
167B PHE 4.3 1.3 - - - +
168B LYS* 3.0 57.3 + - + +
205B MET* 4.3 10.3 - - - -
231B TRP* 3.9 18.4 - + - -
283B GLN* 5.1 1.4 + - - -
309B ALA* 5.9 0.9 - - + -
334B PHE* 3.4 38.1 - + + -
335B VAL 3.1 6.8 + - - -
336B GLU* 3.0 32.3 + - + +
337B TYR* 3.0 30.1 + - - +
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Residues in contact with ASP 132 (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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28B ARG* 5.7 0.2 + - - -
131B TYR* 1.3 70.5 - - - +
133B THR* 1.3 62.1 + - - +
134B SER* 2.8 30.0 + - - -
135B LEU* 4.5 6.5 - - - +
155B GLU 4.5 5.5 - - - +
159B GLY* 3.7 15.0 + - - -
164B GLN* 3.3 20.0 + - + +
166B HIS 2.7 18.0 + - - +
167B PHE* 3.5 29.1 - - + +
168B LYS 2.9 27.5 + - - +
337B TYR* 3.8 7.6 - - - +
338B ASP* 5.5 0.7 - - - -
339B ASP 5.8 0.5 + - - -
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Residues in contact with THR 133 (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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131B TYR* 3.5 13.6 + - - -
132B ASP* 1.3 71.1 - - - +
134B SER* 1.3 57.7 + - - +
135B LEU 3.3 8.8 + - - -
136B TYR* 3.5 15.4 - - - -
168B LYS* 3.3 24.9 - - - +
170B LYS* 4.3 5.5 + - - +
312B CYS 4.9 0.2 - - - +
313B TYR* 3.8 24.1 - - + -
336B GLU* 2.8 36.3 + - + +
337B TYR 2.9 25.1 + - - +
338B ASP* 4.0 5.2 - - + -
395B TAR 4.3 0.5 + - - -
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Residues in contact with SER 134 (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 ARG* 5.8 2.0 - - - -
28B ARG* 2.7 41.9 + - - -
30B ALA* 5.2 6.2 - - - +
132B ASP* 2.8 26.8 + - - -
133B THR* 1.3 77.7 - - - +
135B LEU* 1.3 57.5 + - - +
136B TYR* 3.2 18.6 + - - +
138B ASP* 4.0 2.9 - - - +
313B TYR* 5.5 0.4 - - - -
337B TYR 5.2 0.9 - - - -
338B ASP* 3.7 22.7 - - - -
339B ASP 5.6 1.3 - - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.8 8.7 - - - +
132B ASP* 4.5 6.3 - - - +
133B THR 3.3 4.8 - - - -
134B SER* 1.3 77.9 - - - +
136B TYR* 1.3 65.2 - - - +
138B ASP* 4.4 0.2 - - - -
152B MET* 3.9 15.1 - - + +
155B GLU* 3.7 33.0 - - + +
156B ALA* 3.9 13.2 - - + +
167B PHE* 3.9 33.9 - - + -
168B LYS 3.8 11.1 + - - +
169B ILE* 3.9 11.6 - - + +
170B LYS* 2.9 28.0 + - - +
194B ILE* 3.6 23.1 - - + -
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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