Contacts of the helix formed by residues 338 - 343 (chain A) in PDB entry 2ID5
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 LEU 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A THR 4.3 0.9 - - - +
310A THR* 3.9 16.2 - - + -
311A LEU* 3.5 35.4 - - + +
327A LEU* 4.5 7.4 - - + -
332A LEU* 3.8 34.1 - - + -
333A ALA 3.7 19.7 - - - +
334A CYS* 4.8 1.6 - - - -
335A ASP* 3.2 11.1 + - - +
336A CYS 3.1 0.6 - - - -
337A ARG* 1.3 76.0 - - - +
339A LEU* 1.3 64.1 + - - +
340A TRP* 3.1 4.3 - - - -
341A VAL* 3.0 24.1 + - + +
342A PHE* 3.0 21.3 + - - +
368A PHE* 4.5 8.9 - - + -
380A PHE* 4.2 11.1 - - + -
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Residues in contact with LEU 339 (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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335A ASP 3.8 1.2 + - - -
336A CYS* 3.1 27.4 + - + +
338A LEU* 1.3 77.7 - - - +
340A TRP* 1.3 57.8 + - - +
342A PHE* 3.3 10.2 + - + +
343A ARG* 2.9 55.5 + - + +
375A LEU* 3.7 30.1 - - + -
380A PHE* 3.9 21.3 - - + +
73D PRO* 5.2 7.2 - - + -
97D LEU* 5.2 5.8 - - + +
98D GLY* 4.1 27.4 - - - +
101D THR* 5.4 2.5 - - + +
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Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 2.9 32.2 + - + -
312A GLU 4.2 0.4 - - - -
313A GLU* 3.3 45.9 - - + +
316A PHE* 3.6 31.4 - + - -
319A VAL* 3.6 28.5 - - + -
322A LEU* 4.1 9.2 - - + -
325A LEU* 3.9 11.4 - - + -
336A CYS 4.6 1.0 + - - -
337A ARG 3.0 21.7 + - - -
338A LEU* 4.2 0.9 - - - -
339A LEU* 1.3 81.1 - - - +
341A VAL* 1.3 86.8 + - + +
343A ARG* 3.7 3.1 + - - +
344A ARG* 2.9 53.2 + - - +
348A LEU* 5.1 2.5 - - + -
101D THR* 4.8 8.3 - - + -
126D ASP* 5.6 0.2 - - - +
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Residues in contact with VAL 341 (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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311A LEU* 5.4 0.2 - - + -
325A LEU* 4.0 7.6 - - + -
327A LEU* 4.0 16.6 - - + -
338A LEU* 3.0 24.3 + - + +
340A TRP* 1.3 114.7 - - + +
342A PHE* 1.3 67.7 + - - +
344A ARG* 2.8 15.8 + - - +
345A ARG* 3.1 9.5 + - - -
348A LEU* 4.1 10.0 - - + +
350A PHE* 3.6 26.5 - - + -
368A PHE* 4.0 10.8 - - + -
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Residues in contact with PHE 342 (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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338A LEU 3.0 12.4 + - - +
339A LEU* 3.3 14.1 + - + +
341A VAL* 1.3 75.6 - - - +
343A ARG* 1.3 86.6 + - - +
345A ARG* 2.9 76.4 + - + +
368A PHE* 3.9 16.0 - + + -
371A PHE* 3.4 23.6 - + + -
372A PRO 3.6 16.4 - - - -
373A ASP 4.4 0.2 - - - -
375A LEU* 3.5 21.8 - - + -
380A PHE* 3.6 31.6 - + + -
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Residues in contact with ARG 343 (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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339A LEU* 2.9 37.1 + - + +
340A TRP* 3.9 7.0 - - - +
341A VAL 3.2 0.4 - - - -
342A PHE* 1.3 102.4 - - - +
344A ARG* 1.3 62.3 + - + +
345A ARG 3.4 1.3 + - - -
347A ARG* 3.9 13.3 + - - +
373A ASP* 3.5 20.6 + - - -
374A VAL* 5.8 0.6 - - - +
375A LEU* 3.6 27.4 - - - +
74D GLY* 5.8 5.3 - - - -
77D ASN* 5.1 15.3 + - - +
101D THR* 4.9 19.0 + - + +
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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