Contacts of the strand formed by residues 334 - 343 (chain G) in PDB entry 2ABJ
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 VAL 334 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G LYS* 5.8 2.0 - - - +
99G PHE* 6.4 0.2 - - + -
288G THR* 3.4 12.8 - - + +
329G SER* 3.2 21.8 - - - -
330G GLY 2.8 17.2 + - - -
331G THR* 4.1 6.9 + - - +
332G ALA 3.7 0.8 - - - +
333G CYS* 1.3 79.3 - - - +
335G VAL* 1.3 65.9 + - + +
364G LEU* 3.9 29.6 - - + -
367G LEU* 3.6 39.7 - - + -
368G THR* 5.2 1.6 - - - +
371G GLN* 4.5 22.7 - - - +
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Residues in contact with VAL 335 (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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197G PHE* 3.6 26.3 - - + -
292G ILE* 4.1 5.4 - - + -
327G PHE* 3.6 29.8 - - + -
328G SER 3.3 3.6 - - - +
333G CYS* 2.8 17.7 + - - +
334G VAL* 1.3 83.9 - - + +
336G CYS* 1.3 64.2 + - - +
337G PRO* 4.0 1.3 - - + +
360G ALA* 3.7 37.2 - - + +
363G ILE* 3.8 28.5 - - + -
364G LEU* 4.8 3.1 - - + +
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Residues in contact with CYS 336 (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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198G ASN 4.7 4.7 - - - -
200G VAL* 3.7 38.1 - - - -
259G MET* 3.8 3.6 - - - -
327G PHE* 3.2 4.0 - - - -
328G SER* 2.8 46.9 + - - +
333G CYS* 3.7 15.5 - - + -
335G VAL* 1.3 76.8 - - - +
337G PRO* 1.3 70.4 - - - +
338G VAL* 3.6 1.9 + - - +
3401G CBC 3.9 19.1 - - + -
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Residues in contact with PRO 337 (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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197G PHE* 3.5 52.7 - - + -
198G ASN 4.9 3.1 - - - +
199G PRO* 3.3 8.7 - - + +
200G VAL* 3.0 26.3 + - - +
326G MET 3.6 7.0 - - - +
327G PHE* 4.0 4.4 - - + -
335G VAL* 4.6 0.7 - - + -
336G CYS* 1.3 88.5 - - + +
338G VAL* 1.3 60.0 + - - +
352G THR* 3.8 17.9 - - + -
353G MET* 3.9 13.9 - - - -
357G PRO* 4.2 7.4 - - + -
360G ALA* 4.7 3.6 - - + -
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Residues in contact with VAL 338 (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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199G PRO* 4.7 0.7 - - - -
200G VAL* 3.6 17.7 - - + +
202G LEU* 3.8 39.5 - - + -
256G VAL* 4.9 4.3 - - + -
326G MET* 2.8 37.9 + - + +
327G PHE* 4.4 5.4 - - - -
328G SER* 4.7 5.2 - - - +
336G CYS 4.0 7.9 - - - +
337G PRO* 1.3 75.8 - - - +
339G SER* 1.3 61.5 + - - +
340G ASP 3.8 13.2 - - - +
341G ILE* 4.4 0.9 - - + -
350G ILE* 3.6 11.4 - - + +
352G THR* 2.6 30.3 + - - -
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Residues in contact with SER 339 (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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199G PRO* 3.7 25.0 + - - +
200G VAL 3.0 15.1 + - - -
201G SER* 4.3 1.9 + - - -
337G PRO 4.2 0.8 + - - -
338G VAL* 1.3 74.1 - - - +
340G ASP* 1.3 81.4 + - - +
349G HIS* 3.2 10.0 + - - -
350G ILE* 2.6 41.4 + - - +
352G THR* 5.1 0.9 - - - -
353G MET* 4.8 7.2 - - - -
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Residues in contact with ASP 340 (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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200G VAL 3.7 1.2 + - - -
201G SER* 3.5 18.8 + - - +
202G LEU 2.9 24.7 + - - -
338G VAL* 3.8 5.3 - - - +
339G SER* 1.3 103.0 + - - +
341G ILE* 1.3 67.3 + - - +
342G LEU* 4.3 3.4 - - + -
347G THR* 4.0 22.7 - - + +
348G ILE 3.2 6.5 - - - +
349G HIS* 3.0 30.8 + - - +
350G ILE* 4.0 0.9 - - - +
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Residues in contact with ILE 341 (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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202G LEU* 3.3 16.4 - - + +
204G ALA* 3.9 25.4 - - + -
244G LEU* 3.8 23.6 - - + -
311G MET* 4.0 12.8 - - + -
314G LEU* 3.6 32.1 - - + -
326G MET* 4.0 13.0 - - + -
338G VAL* 4.4 0.9 - - + -
340G ASP* 1.3 78.5 - - - +
342G LEU* 1.3 66.3 + - - +
343G TYR* 3.7 2.0 + - + -
346G GLU 3.6 1.0 - - - +
348G ILE* 2.7 49.6 + - + +
350G ILE* 3.8 15.3 - - + -
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Residues in contact with LEU 342 (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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201G SER* 5.1 2.9 - - - +
202G LEU 2.8 9.9 + - - +
203G TRP* 3.4 27.2 + - + +
204G ALA* 2.8 31.7 + - - +
238G ASN* 3.7 24.7 - - + +
240G CYS* 3.4 17.3 - - - -
340G ASP* 4.7 7.4 - - + -
341G ILE* 1.3 73.2 - - - +
343G TYR* 1.3 60.5 + - - +
345G GLY 6.3 0.4 - - - -
346G GLU 3.3 6.5 - - - +
347G THR* 3.5 37.9 - - + +
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Residues in contact with TYR 343 (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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204G ALA* 3.5 26.7 - - + -
206G PRO* 4.3 11.6 - - + +
246G LEU* 3.5 21.1 - - + -
251G HIS* 3.2 34.1 + - - +
311G MET* 3.6 39.3 - - + +
312G ASP* 5.7 3.1 + - - -
315G THR* 5.7 2.5 - - - -
341G ILE* 3.7 1.9 + - + -
342G LEU* 1.3 74.1 - - - +
344G LYS* 1.3 106.8 + - + +
345G GLY 3.2 1.9 - - - +
346G GLU* 2.9 26.6 + - - +
348G ILE* 3.9 21.1 - - + +
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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