Contacts of the strand formed by residues 306 - 311 (chain A) in PDB entry 4JHN
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 HIS 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A HIS* 3.6 4.9 + - - -
273A GLN* 4.1 2.6 - - - +
302A CYS* 3.7 0.2 - - - -
303A GLY* 2.8 30.6 + - - +
304A GLU 3.8 0.2 - - - -
305A ASN* 1.3 79.6 + - - +
307A THR* 1.3 69.5 + - - +
318A THR* 5.2 0.2 - - - -
319A PHE 3.3 14.4 - - - +
321A ASP 4.0 7.9 - - - +
326A LYS* 3.6 40.1 + - + +
327A LEU* 3.7 25.4 - - + -
356A CYS* 3.4 37.5 - - + +
357A GLY 4.0 9.9 + - - -
360A HIS 3.7 16.8 - - - -
361A MET* 3.9 8.9 - - - +
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Residues in contact with THR 307 (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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254A HIS* 3.0 16.6 + - - -
256A VAL* 3.7 20.8 - - + +
273A GLN 3.0 21.0 + - - -
301A SER 3.4 14.6 - - - +
302A CYS* 4.6 0.2 - - - +
306A HIS* 1.3 75.9 - - - +
308A ALA* 1.3 68.1 + - - +
309A LEU* 4.3 6.7 - - + -
318A THR* 3.2 7.6 - - - +
319A PHE* 2.9 64.5 + - + +
356A CYS* 5.1 0.2 - - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR 4.1 0.2 - - - +
300A ILE* 3.6 2.9 - - - -
301A SER* 2.9 34.6 + - - +
307A THR* 1.3 74.4 - - - +
309A LEU* 1.3 67.3 + - - +
316A MET* 4.4 3.4 - - - -
317A TYR 3.4 4.7 - - - -
318A THR* 3.9 15.9 - - + -
354A VAL* 4.0 25.9 - - + +
356A CYS* 3.8 21.5 - - - -
361A MET* 4.2 0.4 - - - -
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Residues in contact with LEU 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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256A VAL* 4.6 0.4 - - + -
263A VAL* 4.4 13.5 - - + -
289A ILE* 5.0 1.8 - - + -
292A ILE* 4.3 17.9 - - + -
297A ILE* 4.1 29.6 - - + -
299A TYR 3.5 3.4 - - - -
300A ILE* 3.8 22.4 - - + -
307A THR* 4.3 8.5 - - + -
308A ALA* 1.3 81.1 - - - +
310A ILE* 1.3 62.5 + - - +
311A THR* 5.5 0.2 - - - -
316A MET* 3.2 8.2 - - - +
317A TYR* 2.8 49.9 + - + +
319A PHE* 3.8 31.0 - - + -
340A PRO* 4.4 6.1 - - + -
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Residues in contact with ILE 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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297A ILE* 3.4 4.9 - - - +
298A SER* 2.8 28.5 + - - +
299A TYR* 2.9 30.5 + - + -
309A LEU* 1.3 77.7 - - - +
311A THR* 1.3 73.6 - - - +
314A GLY* 4.3 1.8 - - - -
315A LEU 3.4 9.2 - - - +
316A MET* 4.7 2.5 - - + -
351A VAL* 3.5 43.1 - - + +
352A LYS 4.0 12.3 - - - +
353A LEU* 4.0 12.3 - - - -
354A VAL* 3.6 30.5 - - + +
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Residues in contact with THR 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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295A GLN* 3.4 26.9 + - + +
296A THR 3.3 10.8 - - - +
297A ILE* 3.8 21.3 - - + +
298A SER* 3.3 9.0 + - - -
309A LEU 5.3 0.2 - - - +
310A ILE* 1.3 79.8 - - - +
312A ASP* 1.3 64.2 + - - +
313A ILE* 3.5 12.3 - - - +
314A GLY* 2.9 16.6 + - - -
315A LEU* 2.9 38.9 + - + +
317A TYR* 4.0 15.5 - - + -
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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