Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 3A8X
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 LEU 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LYS* 4.3 2.5 - - + +
297A PHE* 3.7 40.7 + - + +
298A GLU* 4.6 1.8 - - - +
301A SER 4.7 2.0 + - - -
308A GLY* 1.3 71.5 - - - -
310A HIS* 1.3 60.9 + - - +
311A SER 3.4 28.3 - - - +
312A CYS* 3.9 13.0 - - - -
321A PHE* 4.0 15.5 - - + -
322A VAL 3.4 9.6 - - - +
323A ILE* 4.0 12.6 - - + -
575A TYR* 3.6 29.9 + - + -
577A ASN* 3.5 16.5 - - - +
237B MET* 4.0 11.7 - - + -
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Residues in contact with HIS 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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240A LEU* 3.6 17.0 - - + -
264A LEU* 3.6 21.8 - - + -
271A TYR* 3.5 36.9 + + + -
308A GLY 4.0 1.6 + - - -
309A LEU* 1.3 75.1 - - - +
311A SER* 1.3 79.3 + - - +
322A VAL* 2.7 29.5 + - + +
323A ILE* 4.3 0.9 - - - +
324A GLU 5.3 0.4 - - - +
575A TYR* 4.9 0.2 - - - -
576A ILE* 3.8 1.7 - - + -
577A ASN* 2.9 52.7 + - - +
578B PRO* 2.6 29.4 + - + -
579B LEU* 3.4 9.8 + - - -
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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
----------------------------------------------------------
240A LEU* 3.9 17.2 - - - +
245A PHE* 4.4 1.2 - - - -
309A LEU* 3.4 9.8 - - - +
310A HIS* 1.3 103.0 + - - +
312A CYS* 1.3 65.3 + - - +
313A PHE* 5.0 2.6 - - - -
322A VAL* 2.8 44.8 + - - +
575A TYR* 3.2 19.3 - - - -
576A ILE* 4.2 4.0 - - - +
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Residues in contact with CYS 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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240A LEU* 5.1 1.7 - - - +
294A LYS* 4.2 14.8 - - - -
309A LEU* 3.9 22.7 - - - -
311A SER* 1.3 78.7 - - - +
313A PHE* 1.3 66.4 + - - +
320A PHE 3.2 5.6 - - - -
321A PHE* 4.0 20.6 - - - -
573A PHE* 3.5 37.0 - - + +
574A GLU* 3.4 3.7 - - - +
575A TYR* 2.8 31.6 + - - +
576A ILE* 5.5 0.2 - - - +
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Residues in contact with PHE 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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240A LEU* 3.6 20.4 - - + +
241A GLY* 3.9 8.1 - - - -
242A LEU* 3.2 42.4 - - + -
245A PHE* 3.5 26.9 - + - -
273A MET* 4.0 11.9 - - - -
311A SER* 5.0 3.1 - - - -
312A CYS* 1.3 77.9 - - - +
314A GLN* 1.3 71.1 + - - +
320A PHE* 3.0 66.9 + + + +
322A VAL* 3.9 15.7 - - + -
573A PHE* 3.2 12.3 - - - -
574A GLU* 4.2 11.9 - - + -
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Residues in contact with GLN 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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241A GLY* 6.0 0.2 - - - -
278A LYS* 2.7 32.9 + - - +
313A PHE* 1.3 85.2 - - - +
315A THR* 1.3 68.1 + - - +
318A ARG 3.2 13.7 - - - +
319A LEU* 4.1 6.7 - - + -
320A PHE* 4.0 3.8 - - - -
567A GLN* 4.3 1.9 - - - +
570A PHE* 3.1 35.5 + - - +
571A GLU* 4.8 2.8 - - - +
573A PHE* 3.9 5.5 - - + +
574A GLU* 3.0 32.3 + - - +
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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