Contacts of the helix formed by residues 310 - 318 (chain A) in PDB entry 3S3J
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 ASN 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A HIS 5.2 5.3 + - - +
311A LEU* 1.3 69.5 + - - +
312A LEU* 3.3 11.4 + - - +
313A ILE* 3.7 30.7 - - + +
314A GLU* 3.3 20.1 + - - +
417A ASN* 3.9 9.3 - - - +
419A SER* 3.2 32.3 + - - +
564A ARG* 3.8 12.1 - - - +
577A LEU* 3.3 24.8 - - - +
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Residues in contact with LEU 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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310A ASN* 1.3 77.7 + - - +
312A LEU* 1.3 64.5 + - - +
314A GLU* 3.2 16.9 + - + +
315A TYR* 2.9 22.7 + - - +
508A LEU* 3.6 23.6 - - + -
510A CYS* 3.9 13.0 - - - -
564A ARG* 3.4 72.1 - - + +
565A ALA 3.7 15.0 - - - +
566A LEU* 3.9 14.4 - - + +
577A LEU* 5.1 4.9 - - + -
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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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310A ASN* 3.9 15.9 + - - +
311A LEU* 1.3 77.0 - - - +
313A ILE* 1.3 74.0 + - + +
315A TYR* 3.3 4.2 + - - +
316A PHE* 3.2 33.1 + - + -
401A VAL* 4.0 14.1 - - + -
419A SER* 4.7 6.7 - - - +
420A LEU* 4.4 24.9 - - + -
566A LEU* 3.6 22.1 - - + +
575A TYR* 3.6 39.0 - - + -
577A LEU* 3.8 24.2 - - + -
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Residues in contact with ILE 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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304A ALA* 4.4 16.8 - - + -
305A HIS 4.7 12.8 - - - +
310A ASN* 3.7 32.1 - - + +
312A LEU* 1.3 81.3 - - + +
314A GLU* 1.3 67.3 + - + +
316A PHE* 3.0 6.5 + - - +
317A ARG* 3.0 22.9 + - + +
419A SER* 4.8 4.3 - - - +
420A LEU* 6.4 0.7 - - + -
281B LEU* 4.4 28.5 - - - +
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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 ASN 3.3 16.4 + - - +
311A LEU* 3.5 16.2 - - + +
313A ILE* 1.3 75.6 - - + +
315A TYR* 1.3 66.8 + - - +
316A PHE 3.0 1.2 + - - -
317A ARG* 3.0 16.9 + - - +
318A ASN 3.2 19.4 + - - +
512A ARG* 4.7 10.2 + - - -
520A LEU* 5.3 1.7 - - - +
564A ARG* 3.0 39.0 + - - -
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Residues in contact with TYR 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 LEU* 2.9 7.4 + - - +
312A LEU* 3.4 7.6 - - - +
314A GLU* 1.3 78.5 - - - +
316A PHE* 1.3 94.9 + + - +
318A ASN* 4.2 9.6 + - - +
506A ARG* 3.9 22.8 + - + +
508A LEU* 4.9 17.2 - - + +
528A TYR* 4.4 26.8 + + - -
566A LEU* 3.5 30.5 - - + -
568A VAL* 4.1 24.6 - - + +
570A PRO* 6.0 0.2 - - - +
575A TYR* 4.9 3.4 - + - -
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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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312A LEU* 3.2 26.7 + - + -
313A ILE 3.0 4.6 + - - +
315A TYR* 1.3 97.4 - + - +
317A ARG* 1.3 70.3 + - - +
318A ASN* 4.4 0.3 - - - -
329A GLU 5.2 1.1 - - - -
330A MET* 3.3 45.8 - - + +
331A ILE* 3.5 52.3 - - + -
420A LEU* 5.1 9.9 - - + -
575A TYR* 3.7 17.7 - + - -
280B PRO* 4.1 5.4 - - + +
281B LEU* 3.4 29.4 - - - +
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Residues in contact with ARG 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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313A ILE* 3.0 14.0 + - + +
314A GLU* 3.6 11.4 - - - +
316A PHE* 1.3 80.4 - - - +
318A ASN* 1.3 75.2 + - - +
280B PRO* 4.7 13.4 - - - +
281B LEU 5.0 0.4 + - - -
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Residues in contact with ASN 318 (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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314A GLU* 3.2 16.2 + - - +
315A TYR* 4.5 7.2 - - - +
316A PHE 3.4 2.4 - - - -
317A ARG* 1.3 91.5 - - - +
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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