Contacts of the helix formed by residues 311 - 316 (chain H) in PDB entry 1J0B
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 ILE 311 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G GLY 5.7 0.2 - - - +
50G ILE* 4.4 14.4 - - + -
114G LEU* 6.5 0.2 - - + -
311G ILE* 5.6 8.1 - - + -
315G PHE* 4.5 14.8 - - + -
50H ILE* 5.0 16.2 + - + +
277H ILE* 4.1 50.5 - - + +
278H LEU 5.3 0.2 - - - -
279H ASP* 4.8 3.1 - - - -
307H HIS* 6.4 0.9 - - + -
309H GLY 3.3 4.6 - - - -
310H GLY* 1.3 77.0 - - - +
312H SER* 1.3 73.0 + - - +
314H THR* 3.0 18.9 + - + -
315H PHE* 4.1 21.1 + - + -
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Residues in contact with SER 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G PHE* 3.5 33.1 - - - -
50H ILE* 3.8 12.1 - - - +
82H ASN* 4.3 3.4 - - - -
110H GLY* 4.4 0.9 - - - -
111H ASN* 2.8 43.0 + - - -
114H LEU* 4.3 1.9 - - - +
310H GLY 3.0 0.6 - - - -
311H ILE* 1.3 78.5 - - - +
313H GLY* 1.3 51.8 - - - -
314H THR 2.2 18.9 + - - -
315H PHE* 2.6 18.8 + - - +
316H HIS* 3.2 8.7 + - - -
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Residues in contact with GLY 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H HIS* 6.0 2.0 - - - -
82H ASN* 5.0 3.4 - - - +
111H ASN* 5.2 0.8 - - - +
279H ASP* 4.6 3.1 - - - -
280H PRO* 3.0 23.8 - - - +
281H VAL* 5.4 7.0 - - - -
310H GLY 3.7 6.9 + - - -
311H ILE 3.2 2.2 + - - -
312H SER* 1.3 73.7 - - - +
314H THR* 1.3 55.7 + - - -
316H HIS* 3.8 7.1 - - - +
317H TYR* 2.9 39.8 - - - +
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Residues in contact with THR 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LEU* 4.4 0.5 - - - +
114G LEU* 3.7 28.7 - - + -
117G ILE* 4.0 10.8 - - + -
267H ILE* 4.7 4.3 - - + +
277H ILE* 4.5 12.1 - - + -
278H LEU 2.7 27.1 + - - -
279H ASP* 3.6 8.0 - - - -
280H PRO* 3.6 6.3 - - - +
311H ILE* 3.0 14.0 + - + -
312H SER 2.2 17.0 + - - -
313H GLY* 1.3 67.6 - - - +
315H PHE* 1.3 55.5 + - + +
316H HIS 3.2 1.1 - - - -
317H TYR 3.4 0.2 - - - -
318H GLY* 2.6 35.3 + - - -
321H LEU* 3.9 8.2 - - + +
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Residues in contact with PHE 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 4.4 6.1 - - + -
110G GLY* 4.0 17.3 - - - -
113G LEU* 4.0 22.8 - - + +
114G LEU* 3.3 41.7 - - + -
311G ILE* 5.3 2.7 - - + -
312G SER* 3.1 27.1 - - - -
315G PHE* 3.1 60.3 - + + +
109H LYS* 4.7 10.5 + - - +
110H GLY 5.6 0.9 - - - +
311H ILE* 4.3 23.3 - - + -
312H SER 2.6 11.5 + - - +
314H THR* 1.3 72.3 - - + +
316H HIS* 1.3 57.7 + - - +
317H TYR 3.2 2.8 + - - -
318H GLY 3.8 4.5 + - - -
319H ASP 5.4 0.3 + - - -
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Residues in contact with HIS 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H VAL* 5.0 7.2 - - - +
80H HIS* 3.5 32.0 - - + +
105H LYS 5.7 0.2 + - - -
107H GLU* 3.4 31.9 + - - +
109H LYS* 3.2 39.8 + - + +
110H GLY* 4.0 16.4 - - - -
111H ASN* 4.9 1.3 - - - -
112H TYR* 5.9 0.4 - - + -
312H SER 3.2 3.6 + - - +
313H GLY* 3.8 11.7 - - - +
314H THR 3.2 0.2 - - - -
315H PHE* 1.3 78.1 - - - +
317H TYR* 1.3 98.4 + + + +
318H GLY 3.7 0.2 - - - -
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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