Contacts of the helix formed by residues 312 - 317 (chain A) 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 SER 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 2.8 18.5 - - - +
82A ASN* 4.0 0.7 - - - -
110A GLY* 3.9 4.7 - - - -
111A ASN* 2.5 52.0 + - - -
114A LEU* 3.4 11.4 - - - +
310A GLY 2.7 5.5 + - - -
311A ILE* 1.3 76.6 - - - +
313A GLY* 1.3 62.3 + - - -
315A PHE* 2.9 17.9 + - - +
316A HIS* 3.0 12.4 + - - +
315B PHE* 3.7 10.4 - - - -
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Residues in contact with GLY 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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80A HIS* 5.8 2.9 + - - -
82A ASN* 4.7 2.2 - - - +
111A ASN* 5.0 0.4 - - - +
279A ASP* 4.5 1.6 - - - -
280A PRO* 3.6 11.7 - - - +
281A VAL* 4.9 6.3 - - - -
310A GLY 2.9 10.7 + - - -
312A SER* 1.3 78.5 - - - +
314A THR* 1.3 56.1 + - - +
315A PHE 3.2 0.2 - - - -
316A HIS* 3.6 12.6 - - - -
317A TYR* 2.9 44.3 + - - +
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Residues in contact with THR 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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267A ILE* 4.9 7.2 - - + -
277A ILE* 4.3 13.2 - - + +
278A LEU 3.0 27.1 + - - +
279A ASP* 3.2 12.3 - - - +
280A PRO* 3.9 5.6 - - - +
310A GLY 4.1 0.2 + - - -
311A ILE* 3.4 15.0 + - - -
312A SER 2.9 1.4 + - - -
313A GLY* 1.3 77.6 - - - +
315A PHE* 1.3 61.1 + - - +
318A GLY* 3.4 17.2 + - - -
321A LEU* 4.3 8.7 - - + -
113B LEU* 3.6 10.2 - - - +
114B LEU* 4.2 13.7 - - + -
117B ILE* 4.0 17.7 - - + -
118B MET* 5.6 0.2 - - + -
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Residues in contact with PHE 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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109A LYS* 4.8 6.5 - - - +
110A GLY* 5.1 1.1 - - - +
311A ILE* 3.3 48.7 - - + -
312A SER 2.9 6.9 + - - +
314A THR* 1.3 75.0 - - - +
316A HIS* 1.3 66.6 + - - +
317A TYR 3.2 2.3 + - - -
318A GLY* 3.5 8.0 + - - -
319A ASP* 5.6 1.2 - - - +
50B ILE* 4.7 2.9 - - + -
110B GLY* 4.1 20.9 - - - +
113B LEU* 4.1 9.9 - - + +
114B LEU* 4.1 28.0 - - + -
311B ILE* 4.9 2.2 - - + -
312B SER* 3.4 39.9 - - - -
315B PHE* 4.0 47.1 - + + -
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Residues in contact with HIS 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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79A VAL* 4.7 9.3 + - + +
80A HIS* 3.6 29.1 + - + +
107A GLU* 3.7 25.0 - - + +
109A LYS* 3.1 45.4 + - + +
110A GLY* 3.1 37.1 - - - +
111A ASN* 3.9 3.6 - - - -
112A TYR* 5.0 0.4 - - - +
312A SER* 3.0 11.0 + - - +
313A GLY* 3.5 4.7 - - - +
315A PHE* 1.3 77.1 - - - +
317A TYR* 1.3 94.8 + + + +
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Residues in contact with TYR 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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80A HIS* 2.5 39.6 + + + +
107A GLU* 5.2 4.9 + - - -
109A LYS* 5.1 2.7 - - - +
257A GLY 6.0 1.3 - - - -
259A ILE* 3.5 30.1 - - + -
280A PRO* 4.2 10.5 - - + -
281A VAL* 4.6 8.5 - - + -
313A GLY* 2.9 32.6 + - - +
314A THR 4.3 0.2 - - - -
316A HIS* 1.3 116.6 - + + +
318A GLY* 1.3 51.4 + - - +
319A ASP* 2.7 18.6 + - - +
320A LYS* 3.1 16.5 + - + +
321A LEU* 3.1 14.5 + - - +
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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