Contacts of the helix formed by residues 348 - 353 (chain A) in PDB entry 2JIP
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 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY* 2.6 30.5 + - - +
112A CYS 2.9 22.7 + - - +
113A LEU 3.5 0.2 - - - -
114A THR* 2.9 31.4 + - - +
347A PRO* 1.3 74.9 - - - +
349A ALA* 1.3 64.2 + - - +
350A CYS 3.2 1.6 - - - -
351A GLY* 3.4 2.1 + - - -
352A GLY* 3.0 28.3 + - - +
353A VAL 3.8 0.2 + - - -
470A VAL 3.5 4.4 + - - -
471A TYR* 3.5 16.5 - - + -
472A GLY 2.6 29.8 + - - -
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Residues in contact with ALA 349 (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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110A GLY* 3.4 10.4 + - - -
137A PRO* 4.0 26.0 - - + -
141A MET* 4.1 12.1 - - + -
344A THR* 3.7 21.1 - - + -
346A GLN* 3.8 15.7 + - + +
348A ASN* 1.3 75.7 - - - +
350A CYS* 1.3 58.4 + - - +
353A VAL* 3.3 3.9 + - - +
354A ARG* 2.9 34.4 + - - +
813A UNX 4.4 1.8 - - - -
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Residues in contact with CYS 350 (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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156A GLU* 3.3 31.6 - - - +
157A PRO* 5.8 0.2 - - - -
344A THR* 3.1 36.1 - - - -
348A ASN 3.2 0.6 - - - -
349A ALA* 1.3 77.3 - - - +
351A GLY* 1.3 57.1 + - - +
354A ARG* 3.4 8.3 - - - +
355A ASP* 2.7 40.9 + - - +
472A GLY 3.1 13.8 + - - +
473A CYS 3.5 16.4 - - - +
474A GLY* 4.0 4.7 - - - -
476A ARG* 5.9 2.0 - - - +
478A TYR* 6.0 0.7 - - + -
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Residues in contact with GLY 351 (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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114A THR* 3.4 20.8 + - - +
348A ASN* 3.4 7.1 + - - -
350A CYS* 1.3 78.7 - - - +
352A GLY* 1.3 62.0 + - - +
355A ASP* 3.5 12.0 + - - +
356A GLY* 3.5 16.5 + - - -
472A GLY* 3.2 11.9 + - - -
478A TYR* 4.1 16.5 - - - -
524A TRP* 4.5 2.4 + - - -
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Residues in contact with GLY 352 (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 SER 5.6 0.2 - - - -
112A CYS 5.0 0.9 - - - -
114A THR* 3.7 13.5 - - - +
117A SER* 3.5 22.3 - - - -
118A TYR 5.1 0.2 + - - -
348A ASN* 3.0 32.0 + - - -
351A GLY* 1.3 78.4 - - - +
353A VAL* 1.3 63.6 + - - +
356A GLY* 4.1 9.3 - - - -
358A ALA* 3.8 6.2 - - - +
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Residues in contact with VAL 353 (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 SER* 3.6 25.4 - - - +
110A GLY* 3.8 6.5 - - - +
117A SER* 4.4 5.6 - - - +
135A GLY* 5.5 1.1 - - - -
137A PRO* 3.4 37.0 - - + -
349A ALA 3.3 4.4 + - - +
352A GLY* 1.3 80.6 - - - +
354A ARG* 1.3 66.5 + - - +
355A ASP 3.8 0.2 - - - -
357A GLY* 3.3 2.6 + - - -
358A ALA* 2.7 40.3 + - + +
359A LEU* 3.4 36.8 + - + +
362A LEU* 4.7 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