Contacts of the strand formed by residues 308 - 315 (chain A) in PDB entry 4EFO
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 ARG 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A SER* 3.5 21.8 + - - +
302A THR* 3.4 32.5 + - - +
304A ASP 3.4 17.9 - - - +
305A ILE* 3.1 24.6 + - + +
306A LEU 4.9 1.7 - - - +
307A HIS* 1.3 82.6 - - - +
309A MET* 1.3 64.1 + - - +
325A TYR* 3.5 26.2 + - + +
326A ILE* 3.4 12.1 - - - +
327A HIS* 3.8 18.2 - - + +
328A SER* 4.4 1.7 + - - -
330A ASN* 5.1 1.4 + - - -
376B GLU* 3.1 41.6 + - - +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ARG* 1.3 76.0 - - - +
310A VAL* 1.3 67.8 + - - +
311A ILE* 3.9 21.8 - - + -
325A TYR* 3.3 10.5 - - - +
326A ILE* 2.8 46.4 + - + +
328A SER* 3.8 17.9 - - - +
367A ALA* 3.3 42.2 - - - +
368A GLN* 3.6 12.3 - - - +
370A PHE* 5.4 1.3 - - + -
372A LYS* 6.3 3.4 - - + -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 1.3 85.1 - - - +
311A ILE* 1.3 72.8 + - - +
312A HIS* 3.9 22.6 + - + +
323A LYS* 3.8 27.4 - - + -
324A ILE 3.5 8.3 - - - +
325A TYR* 3.7 29.8 - - + +
373A THR* 4.2 5.4 + - - +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 3.9 14.4 - - + -
310A VAL* 1.3 78.5 - - - +
312A HIS* 1.3 67.8 + - - +
313A VAL* 4.4 0.7 - - + -
323A LYS 3.8 0.3 - - - -
324A ILE* 2.8 38.7 + - + +
326A ILE* 3.9 20.2 - - + -
335A PHE* 3.7 35.2 - - + -
367A ALA* 4.3 10.1 - - + -
370A PHE* 3.7 30.3 - - + -
371A PRO 5.6 0.4 - - - +
373A THR* 3.6 11.0 - - + +
379A ILE* 4.0 22.0 - - + -
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A VAL* 3.9 26.0 - - + +
311A ILE* 1.3 74.5 - - - +
313A VAL* 1.3 63.4 + - - +
322A HIS 3.7 3.8 + - - +
323A LYS* 4.0 25.5 - - + +
373A THR* 2.9 24.9 + - - +
374A THR* 3.4 42.4 - - - +
375A GLU* 3.4 35.5 - - + +
378A PRO* 3.4 6.3 - - + +
379A ILE* 2.9 23.6 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ILE* 4.3 2.5 - - + +
312A HIS* 1.3 79.8 - - - +
314A PHE* 1.3 68.5 + - - +
315A SER* 4.4 2.5 - - - +
321A ALA* 3.5 4.9 - - - +
322A HIS* 2.9 45.5 + - + +
324A ILE* 3.7 19.5 - - + -
335A PHE* 3.7 32.1 - - + -
339A VAL* 4.4 8.7 - - + -
343A THR* 5.6 0.7 - - + -
378A PRO* 4.1 3.8 - - - +
379A ILE* 3.1 9.9 - - + +
381A VAL* 3.3 28.9 - - + -
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 1.3 75.1 - - - +
315A SER* 1.3 75.8 + - - +
316A LEU* 3.5 25.6 + - + -
319A MET* 3.7 37.2 - - + -
320A THR* 3.5 18.6 - - - -
321A ALA* 3.8 17.5 - - + -
378A PRO* 4.0 19.7 - - + -
379A ILE 2.9 10.7 + - - -
380A PHE* 3.3 19.1 - + + +
381A VAL 2.8 24.6 + - - -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 4.2 1.7 - - - +
314A PHE* 1.3 71.4 - - - +
316A LEU* 1.3 58.0 + - - +
317A GLN 3.7 2.6 + - - -
318A GLN* 2.5 33.6 + - - -
319A MET* 2.8 30.5 + - - -
320A THR* 2.8 24.1 + - - -
322A HIS* 4.0 10.2 + - - -
343A THR* 4.0 9.4 - - - -
345A ILE* 3.8 12.4 - - - +
381A VAL* 3.8 9.4 - - - -
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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