Contacts of the helix formed by residues 309 - 316 (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 TRP 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 3.3 47.0 - + + -
166B PHE* 4.2 11.2 - + - -
262B LEU* 4.1 2.2 - - - -
263B TYR 5.4 3.1 - - - -
306B ASP* 3.1 29.5 + - + +
308B GLY* 1.3 91.6 - - - +
310B VAL* 1.3 67.6 + - - +
311B THR* 4.1 1.8 - - - +
312B GLY* 2.9 11.5 + - - +
313B HIS* 3.0 17.3 + - - -
525B HIS* 3.6 37.7 + + + -
526B ARG 6.1 2.7 - - - -
590B LEU* 4.2 4.3 - - + -
800B EDO 4.0 20.2 - - - -
991B COA 3.8 42.0 + - - -
998B PRX 5.8 3.6 - - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PHE* 5.2 2.9 - - + -
262B LEU* 3.4 26.6 - - + +
276B HIS* 5.0 3.4 - - - +
309B TRP* 1.3 74.1 - - + +
311B THR* 1.3 59.9 + - - +
313B HIS* 3.2 3.3 + - + -
314B SER* 2.9 37.0 + - - +
414B TRP* 3.5 29.4 - - + -
416B THR* 3.7 41.2 + - + +
419B GLY* 4.7 3.4 - - - +
998B PRX 3.8 21.8 - - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B CYS* 3.8 2.9 - - - -
305B ALA* 3.3 27.6 - - + -
309B TRP* 3.1 1.2 - - - +
310B VAL* 1.3 78.4 - - - +
312B GLY* 1.3 56.0 + - - +
315B TYR* 2.7 32.3 + - + -
316B LEU 3.5 1.2 + - - -
355B TYR* 3.6 31.2 - - + -
386B VAL* 4.1 9.3 - - + +
414B TRP* 3.7 15.3 - - + -
991B COA 3.4 10.5 - - - +
998B PRX 3.3 27.5 - - - +
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Residues in contact with GLY 312 (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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305B ALA* 3.9 4.0 - - - +
306B ASP 3.3 24.4 + - - -
307B VAL* 4.1 9.6 - - - -
309B TRP 2.9 4.8 + - - -
311B THR* 1.3 76.5 - - - +
313B HIS* 1.3 66.2 + - - +
316B LEU* 3.0 34.1 + - - +
317B LEU* 3.3 8.3 + - - +
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Residues in contact with HIS 313 (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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149B MET* 3.8 13.2 - - + +
159B HIS* 3.4 33.7 - + - -
161B VAL* 3.4 18.7 + - + +
260B PHE* 3.8 26.8 - + + -
261B ILE 5.1 0.2 + - - -
262B LEU* 3.4 32.3 - - + +
281B TYR* 3.5 11.4 - - - +
307B VAL 3.1 21.7 + - - -
308B GLY 4.4 0.4 - - - -
309B TRP 3.0 23.9 + - - -
310B VAL* 3.2 10.3 + - - +
312B GLY* 1.3 79.2 - - - +
314B SER* 1.3 57.9 + - - +
317B LEU* 4.0 1.0 - - - +
318B TYR* 3.2 32.9 + + + -
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Residues in contact with SER 314 (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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281B TYR* 2.6 26.7 + - - -
285B ALA* 4.2 5.4 - - - +
310B VAL* 2.9 22.3 + - - +
313B HIS* 1.3 73.3 - - - +
315B TYR* 1.3 80.9 + - - -
316B LEU 3.7 0.2 - - - -
319B GLY* 2.9 31.4 + - - +
414B TRP* 4.1 0.7 - - - -
419B GLY 2.8 26.7 + - - -
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Residues in contact with TYR 315 (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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285B ALA* 3.7 12.5 - - - -
288B THR* 2.6 30.0 + - - -
289B PHE* 3.8 12.6 - + + -
293B PHE* 4.1 8.1 - + - -
301B TYR* 2.7 42.6 + - - +
303B CYS* 3.1 4.6 - - - +
311B THR* 2.7 18.0 + - + +
314B SER* 1.3 88.5 - - - +
316B LEU* 1.3 58.0 + - - +
320B PRO* 3.8 7.2 - - - -
355B TYR* 4.1 10.8 - + + -
414B TRP* 3.4 34.5 - + - -
420B GLY* 3.0 8.9 - - - -
421B PHE* 2.9 59.6 + + - -
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Residues in contact with LEU 316 (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 MET* 3.4 26.5 - - + -
303B CYS* 4.0 19.5 - - + +
305B ALA 3.2 25.1 - - - +
307B VAL* 4.4 7.2 - - + +
311B THR 3.5 0.2 + - - -
312B GLY* 3.0 25.6 + - - +
315B TYR* 1.3 79.9 - - - +
317B LEU* 1.3 76.4 + - + +
320B PRO* 3.1 7.5 - - - +
327B THR* 2.7 39.9 + - + +
328B LEU 4.3 10.8 - - - +
329B MET* 4.4 13.5 - - + -
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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