Contacts of the helix formed by residues 311 - 317 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ASP* 6.3 1.3 - - + -
50C ILE* 4.3 28.0 - - + +
277C ILE* 4.0 41.7 - - + +
278C LEU 5.5 4.5 - - - -
279C ASP* 4.8 2.0 - - - -
307C HIS* 6.4 0.4 - - + -
309C GLY* 3.3 6.7 + - - -
310C GLY* 1.3 76.7 - - - +
312C SER* 1.3 65.6 + - - +
313C GLY 3.0 0.5 + - - -
314C THR* 3.3 15.8 + - - +
315C PHE* 3.5 23.8 + - + -
49D GLY 4.8 3.6 - - - +
50D ILE* 4.2 17.0 - - + -
311D ILE* 5.3 11.0 - - + -
315D PHE* 5.9 2.2 - - + -
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 3.4 20.2 - - - +
82C ASN* 3.9 5.6 - - - +
110C GLY* 4.3 2.3 - - - -
111C ASN* 3.0 45.1 + - - -
114C LEU* 3.6 1.7 - - - +
310C GLY 2.8 0.8 + - - -
311C ILE* 1.3 81.1 - - - +
313C GLY* 1.3 63.3 + - - +
315C PHE* 3.0 15.6 + - - +
316C HIS* 3.1 13.6 + - - +
315D PHE* 3.4 22.5 - - - -
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Residues in contact with GLY 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 4.8 1.8 - - - +
279C ASP* 4.1 7.2 - - - -
280C PRO* 4.0 10.1 - - - +
281C VAL* 5.0 9.6 - - - -
310C GLY 2.7 19.9 + - - -
311C ILE 2.9 0.2 - - - -
312C SER* 1.3 67.7 - - - +
314C THR* 1.3 52.9 + - - -
315C PHE 2.6 17.1 + - - -
316C HIS* 2.8 18.6 + - - -
317C TYR* 3.1 16.4 + - - +
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Residues in contact with THR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ILE* 4.2 4.9 - - + +
277C ILE* 4.3 13.2 - - + -
278C LEU 2.4 32.2 + - - -
279C ASP* 3.7 3.6 - - - +
280C PRO* 3.9 11.0 - - - +
311C ILE* 3.3 11.4 + - - -
313C GLY* 1.3 72.6 - - - +
315C PHE* 1.3 58.6 + - - +
318C GLY* 3.8 5.4 - - - -
321C LEU* 4.4 4.9 - - + -
113D LEU* 4.1 1.4 - - - +
114D LEU* 3.8 26.1 - - + +
117D ILE* 3.3 39.0 - - + +
118D MET* 5.0 3.6 - - + -
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Residues in contact with PHE 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 5.2 2.8 - - - +
110C GLY* 5.2 2.0 - - - +
311C ILE* 3.5 37.9 - - + -
312C SER 3.0 8.0 + - - +
313C GLY 2.6 5.5 + - - -
314C THR* 1.3 77.1 - - - +
316C HIS* 1.3 67.5 + - - +
317C TYR 3.5 0.2 - - - -
318C GLY 3.3 8.7 + - - -
50D ILE* 4.7 1.8 - - + -
110D GLY* 3.6 33.4 - - - -
113D LEU* 3.4 18.9 - - + +
114D LEU* 3.7 21.1 - - + -
311D ILE* 5.4 1.6 - - + -
312D SER* 3.5 38.1 - - - -
315D PHE* 3.9 47.8 - + + -
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Residues in contact with HIS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 5.4 6.5 - - - +
80C HIS* 3.5 33.5 + - + +
107C GLU* 3.1 31.5 + - + -
109C LYS* 2.9 68.1 + - + +
110C GLY* 3.8 26.9 - - - +
111C ASN 4.7 0.4 - - - -
112C TYR* 5.8 0.6 - - - +
312C SER 3.1 4.6 + - - +
313C GLY* 2.8 12.7 + - - +
315C PHE* 1.3 82.3 - - - +
317C TYR* 1.3 81.9 + + + +
318C GLY 3.4 1.7 + - - -
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Residues in contact with TYR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C HIS* 2.6 42.8 + + + +
107C GLU* 4.7 4.5 - - - -
109C LYS* 4.9 4.0 - - - +
257C GLY 5.2 4.9 - - - -
259C ILE* 3.3 35.0 - - + -
280C PRO* 4.4 13.5 - - + -
281C VAL* 4.9 13.7 - - + -
313C GLY* 3.1 9.8 + - - +
316C HIS* 1.3 112.5 + + + +
318C GLY* 1.3 57.0 + - - +
319C ASP 3.5 2.9 - - - +
320C LYS* 4.0 9.6 - - + -
321C LEU* 2.8 32.8 + - - +
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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