Contacts of the strand formed by residues 258 - 264 (chain B) in PDB entry 1PG3
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 PRO 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A SER* 4.8 17.0 - - - +
132B GLY* 5.4 7.4 - - - -
156B GLY* 4.6 10.5 - - - +
157B ALA 5.0 0.7 - - - +
158B VAL* 3.6 30.9 - - + +
256B GLU 3.6 4.2 - - - +
257B ASP* 1.3 92.2 - - + +
259B LEU* 1.3 62.0 + - - +
275B LEU* 4.1 27.1 - - + -
276B HIS 3.9 5.6 - - - +
277B THR* 4.2 4.7 - - + -
278B THR* 4.5 0.9 + - - -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.3 32.8 - - + -
153B ALA* 3.6 33.7 - - + +
157B ALA 3.8 4.9 - - - +
158B VAL* 3.4 9.1 - - - -
159B HIS* 3.3 23.6 + - + +
257B ASP 3.4 0.8 + - - -
258B PRO* 1.3 72.9 - - - +
260B PHE* 1.3 76.8 + - + +
276B HIS 2.9 7.7 + - - +
277B THR 3.4 18.6 - - - +
278B THR* 4.0 15.3 - - + +
281B TYR* 3.5 27.4 - - + -
318B TYR* 4.8 1.8 - - + +
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.9 4.0 - - - +
159B HIS* 3.2 39.7 - + + +
258B PRO 4.0 0.2 - - - -
259B LEU* 1.3 97.0 - - + +
261B ILE* 1.3 79.9 + - - +
262B LEU* 3.9 16.2 - - + -
274B VAL 5.1 0.4 - - - -
275B LEU* 3.7 1.9 - - - +
276B HIS* 3.3 62.1 + + + +
281B TYR* 3.5 43.5 - + - -
310B VAL* 5.2 2.0 - - + -
313B HIS* 3.8 25.1 - + + -
314B SER* 5.2 0.7 - - - -
318B TYR* 4.3 3.1 - + - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 4.4 10.3 - - + -
158B VAL* 3.9 20.2 - - + -
159B HIS 3.0 6.4 + - - +
160B SER* 3.5 25.8 + - - +
161B VAL 3.9 5.5 + - - +
178B SER* 4.8 4.9 - - - -
260B PHE* 1.3 83.6 - - - +
262B LEU* 1.3 68.3 + - - +
263B TYR* 3.6 20.2 - - + +
273B GLY* 3.6 28.9 - - - +
274B VAL 3.4 4.3 - - - +
275B LEU* 4.1 13.0 - - + -
313B HIS* 5.1 0.3 + - - -
478B PHE* 3.5 40.4 - - + -
800B EDO 4.7 0.2 + - - -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL 3.8 18.2 - - - +
260B PHE* 3.9 15.2 - - + -
261B ILE* 1.3 75.1 - - - +
263B TYR* 1.3 66.3 + - - +
264B THR* 3.1 7.8 + - - +
274B VAL* 2.9 31.6 + - - +
308B GLY 3.9 13.9 - - - +
309B TRP* 4.8 0.4 - - + -
310B VAL* 3.4 43.1 - - + +
313B HIS* 3.4 40.8 - - + +
416B THR* 4.0 13.5 - - + -
800B EDO 4.0 5.4 - - - +
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Residues in contact with TYR 263 (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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160B SER* 3.5 24.7 - - - -
162B ILE* 5.6 0.4 - - + -
166B PHE* 4.9 5.0 - - + -
173B GLY 5.3 0.2 - - - -
174B CYS* 3.7 42.0 - - + -
177B ASP* 2.8 36.5 + - + -
178B SER* 3.4 24.1 + - - -
261B ILE* 3.6 12.6 - - + +
262B LEU* 1.3 70.7 - - - +
264B THR* 1.3 59.6 + - - +
271B PRO* 3.6 24.5 - - + +
272B LYS* 3.1 9.0 - - - -
273B GLY* 3.3 22.9 - - - -
309B TRP* 5.4 3.5 - - - -
478B PHE* 4.4 2.3 - - - -
800B EDO 3.0 37.7 + - - +
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Residues in contact with THR 264 (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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262B LEU 3.1 5.9 + - - -
263B TYR* 1.3 75.2 + - - +
265B SER* 1.3 64.4 + - - +
266B GLY* 3.5 1.2 + - - -
271B PRO* 3.2 4.3 - - - +
272B LYS* 2.8 30.8 + - - +
274B VAL* 3.1 28.9 - - - +
416B THR* 3.5 22.5 - - - +
417B GLU* 4.7 0.9 - - - +
488B TYR* 5.9 0.2 - - - -
526B ARG* 3.4 47.1 - - + +
998B PRX 4.2 2.2 - - - +
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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