Contacts of the strand formed by residues 308 - 314 (chain G) in PDB entry 4P0S
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 308 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271G LEU* 4.8 6.5 - - + -
272G CYS 3.6 3.8 - - - +
273G VAL* 3.2 45.3 - - + -
277G GLU* 4.6 7.4 - - + -
287G LEU* 4.2 9.6 - - + -
303G LEU* 4.1 1.1 - - - +
306G GLY 3.9 0.6 - - - -
307G ASP* 1.4 87.0 - - + +
309G VAL* 1.3 69.7 + - - +
310G TRP* 5.8 0.4 - - + -
331G ILE* 3.1 1.6 - - - +
332G VAL* 2.7 69.1 + - + +
334G ARG* 3.4 39.0 - - + -
367G LEU* 5.1 2.9 - - + -
412G LEU* 3.7 34.5 - - + -
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Residues in contact with VAL 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G LEU* 4.0 2.4 - - - +
272G CYS* 2.5 54.9 + - + +
303G LEU* 3.7 29.8 - - + -
308G PHE* 1.3 79.6 - - - +
310G TRP* 1.3 63.1 + - - +
311G VAL* 4.9 1.1 - - + -
327G VAL* 4.1 15.7 - - + -
330G HIS 4.0 6.7 - - - +
331G ILE* 3.3 29.2 - - + +
361G LEU* 3.8 10.1 - - + -
456G PHE* 4.9 4.3 - - + -
459G PHE* 4.1 9.0 - - + -
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Residues in contact with TRP 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G VAL* 4.7 6.1 - - + -
270G LEU* 3.7 5.4 - - - -
271G LEU* 3.3 47.5 - - + +
308G PHE* 5.9 0.4 - - + -
309G VAL* 1.3 76.5 - - - +
311G VAL* 1.3 60.4 + - - +
327G VAL* 3.1 5.2 - - - +
328G LEU* 2.3 54.5 + - + -
330G HIS* 3.6 39.5 + + + -
331G ILE* 5.2 0.9 - - - -
332G VAL* 4.5 13.5 - - + -
365G VAL* 6.4 0.2 - - + -
412G LEU* 4.0 7.0 - - + -
415G LEU* 3.7 30.5 - - + -
416G THR* 3.1 45.5 + - + +
419G LEU* 3.5 23.6 - - + -
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Residues in contact with VAL 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G VAL* 3.7 1.4 - - - +
270G LEU* 3.1 54.4 + - + +
272G CYS* 4.3 17.0 - - + -
299G THR* 5.2 2.5 - - - +
301G ARG* 6.1 2.7 - - - +
309G VAL* 4.9 0.7 - - + -
310G TRP* 1.3 82.5 - - - +
312G ALA* 1.3 61.1 + - - +
313G GLN* 5.8 0.4 - - + -
325G GLU* 5.1 13.0 - - + -
326G LEU 3.0 13.9 - - - +
327G VAL* 3.9 11.4 - - + -
328G LEU* 4.0 5.2 - - - -
456G PHE* 3.7 34.3 - - + -
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Residues in contact with ALA 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G LEU* 3.4 24.6 - - + +
267G TYR* 4.5 7.2 - - + -
268G ARG 3.6 5.6 - - - -
269G VAL* 4.7 2.7 - - + +
311G VAL* 1.3 71.1 - - - +
313G GLN* 1.3 58.5 + - - +
324G GLY 3.3 6.2 - - - +
325G GLU* 4.5 1.1 - - - -
326G LEU* 2.5 38.3 + - + +
328G LEU* 3.8 11.5 - - + +
428G LEU* 4.0 18.4 - - + -
453G LEU* 5.6 0.9 - - + -
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Residues in contact with GLN 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267G TYR* 4.0 1.8 - - - -
268G ARG* 2.6 77.5 + - + +
270G LEU* 4.3 14.8 - - + +
301G ARG* 4.8 5.3 - - - +
311G VAL* 3.9 1.9 + - + -
312G ALA* 1.3 72.4 - - - +
314G GLU* 1.3 75.4 + - - +
315G THR 3.2 0.2 + - - -
323G PRO* 3.3 36.4 - - + +
324G GLY 3.3 6.3 - - - +
325G GLU* 4.0 19.6 + - + +
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Residues in contact with GLU 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G LEU* 3.8 23.0 - - - +
261G GLU 4.7 1.6 - - - +
262G LEU* 3.5 17.0 - - + +
266G GLU* 3.0 32.2 - - + +
267G TYR* 3.9 2.6 - - - +
312G ALA 4.0 1.2 + - - -
313G GLN* 1.3 87.3 - - - +
315G THR* 1.3 64.0 + - - +
316G ASN 3.3 6.6 - - - +
317G PRO* 3.8 36.6 - - + +
318G ARG* 4.4 3.7 + - - +
323G PRO* 4.0 2.1 - - - +
324G GLY 3.2 28.3 + - - +
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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