Contacts of the helix formed by residues 308 - 317 (chain A) in PDB entry 5I4A
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 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A GLN* 3.3 17.5 - - + +
305A PHE* 3.1 8.9 + - - +
307A GLU* 1.3 79.5 - - + +
309A GLN* 1.3 59.7 + - - +
310A LYS 3.3 2.9 - - - -
311A SER* 3.2 12.1 + - - +
312A LEU* 2.8 42.3 + - + +
375A LEU* 3.7 26.7 - - + -
401A LYS* 4.0 22.7 - - + +
404A LEU* 5.1 4.7 - - + -
405A GLU* 3.7 27.4 - - + +
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Residues in contact with GLN 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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305A PHE* 2.9 42.7 + - + +
306A PHE* 3.5 32.4 + - - +
307A GLU 3.6 0.2 - - - -
308A VAL* 1.3 77.6 - - - +
310A LYS* 1.3 58.0 + - - +
312A LEU* 3.2 9.0 + - + +
313A LYS* 2.8 60.8 + - + +
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Residues in contact with LYS 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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306A PHE 5.1 0.6 + - - -
307A GLU 5.4 0.8 + - - +
308A VAL 3.3 0.6 - - - -
309A GLN* 1.3 78.3 - - - +
311A SER* 1.3 58.6 + - - +
313A LYS* 3.3 10.6 + - - +
314A GLU* 2.4 68.5 + - + +
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Residues in contact with SER 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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308A VAL* 3.2 11.8 + - - +
310A LYS* 1.3 74.9 - - - +
312A LEU* 1.3 61.4 + - - +
314A GLU* 3.2 6.2 + - - +
315A LEU* 2.8 37.4 + - - +
404A LEU* 3.1 24.6 + - - -
405A GLU* 3.1 27.6 + - - +
407A ILE* 3.6 15.1 - - - +
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Residues in contact with LEU 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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297A PHE* 4.5 7.9 - - + -
299A PHE* 3.5 39.9 - - + -
305A PHE* 3.6 21.8 - - + -
308A VAL* 2.8 32.6 + - + +
309A GLN* 3.2 9.4 + - + +
311A SER* 1.3 73.8 - - - +
313A LYS* 1.3 57.3 + - + +
315A LEU* 5.8 0.4 - - + -
316A PHE* 2.8 61.7 + - + +
317A HIS* 3.8 2.2 + - - -
375A LEU* 5.0 0.2 - - + -
404A LEU* 4.4 19.3 - - + -
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Residues in contact with LYS 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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309A GLN* 2.8 45.4 + - + +
310A LYS* 3.5 10.5 - - - +
311A SER 3.2 0.2 - - - -
312A LEU* 1.3 74.8 - - + +
314A GLU* 1.3 64.5 + - + +
317A HIS* 2.9 65.6 + - + +
318A ASN* 3.3 4.9 + - - +
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Residues in contact with GLU 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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310A LYS* 2.4 55.7 + - + +
311A SER* 3.2 6.9 + - - +
313A LYS* 1.3 76.8 - - + +
315A LEU* 1.3 59.2 + - - +
318A ASN* 3.7 13.5 + - - +
321A SER* 3.1 19.8 - - - -
407A ILE* 3.4 24.7 - - + +
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Residues in contact with LEU 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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311A SER* 2.8 19.3 + - - +
312A LEU* 5.3 0.2 - - - -
314A GLU* 1.3 80.6 - - - +
316A PHE* 1.3 87.1 + - + +
318A ASN 4.4 0.2 - - - -
321A SER* 2.4 26.5 + - - -
322A VAL* 3.8 28.7 - - + -
323A PHE* 3.9 14.1 - - + +
324A TYR* 3.3 8.0 - - - -
404A LEU* 3.6 32.5 - - + +
407A ILE* 3.9 29.4 - - + -
412A ILE* 4.1 13.0 - - + -
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Residues in contact with PHE 316 (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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297A PHE* 3.6 33.2 - + + -
312A LEU* 2.8 43.6 + - + +
315A LEU* 1.3 100.1 - - + +
317A HIS* 1.3 71.0 + - + +
318A ASN 3.5 1.3 - - - -
319A LYS* 4.2 6.2 - - - -
323A PHE* 3.7 41.5 - + - -
324A TYR* 2.8 26.8 + - - +
337A PHE* 3.3 30.9 - + + -
373A ILE* 4.6 6.3 - - + -
404A LEU* 5.2 8.3 - - + -
415A TYR* 5.9 2.9 - + - -
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Residues in contact with HIS 317 (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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312A LEU 3.8 2.9 + - - -
313A LYS* 2.9 54.2 + - + +
316A PHE* 1.3 84.0 - - + +
318A ASN* 1.3 61.5 + - - +
319A LYS* 3.5 13.4 + - - +
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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