Contacts of the helix formed by residues 385 - 396 (chain A) in PDB entry 3ITX
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 VAL 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.3 5.4 - - - -
348A ARG* 3.6 42.3 - - + +
351A ALA* 3.9 14.6 - - + -
352A GLN* 3.9 10.3 - - + +
355A LEU* 3.7 30.5 - - + -
383A THR* 3.2 12.2 + - + +
384A ASP* 1.3 72.2 + - - +
386A GLU* 1.3 64.9 + - - +
387A PRO* 3.2 3.8 - - - -
388A ILE* 3.0 25.0 + - + +
389A LEU* 3.1 22.3 + - + +
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Residues in contact with GLU 386 (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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344A ASN* 5.7 0.5 - - - +
348A ARG* 2.9 36.7 + - - +
384A ASP* 3.0 19.0 + - - +
385A VAL* 1.3 77.5 - - - +
387A PRO* 1.3 62.0 - - + +
389A LEU* 3.1 8.9 + - - +
390A ALA* 2.9 31.9 + - + +
393A ARG* 3.0 27.4 + - - -
400A VAL 4.3 2.8 - - - +
382D ARG* 4.7 14.8 - - - +
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Residues in contact with PRO 387 (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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22A LEU* 3.6 14.7 - - + +
25A ASP* 3.8 27.1 - - + +
26A TYR* 3.5 33.3 - - + +
29A LEU* 4.1 10.8 - - + -
384A ASP* 3.4 17.9 - - - +
385A VAL* 3.3 5.2 - - - -
386A GLU* 1.3 94.8 - - + +
388A ILE* 1.3 56.3 + - - +
390A ALA* 3.5 0.6 + - + -
391A GLU* 2.9 31.2 + - - +
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Residues in contact with ILE 388 (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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26A TYR* 4.1 6.3 - - - -
29A LEU* 3.8 25.8 - - + -
33A LEU* 4.3 9.2 - - + -
40A ILE* 3.8 25.8 - - + -
43A VAL* 3.9 19.1 - - + -
44A THR* 3.6 28.6 - - - +
47A VAL* 4.0 20.2 - - + -
351A ALA* 5.1 0.4 - - + -
355A LEU* 5.2 1.3 - - + -
385A VAL* 3.0 24.0 + - + +
387A PRO* 1.3 75.8 - - - +
389A LEU* 1.3 62.7 + - + +
391A GLU* 3.3 1.7 + - - +
392A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 389 (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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47A VAL* 4.3 9.6 - - + -
344A ASN* 3.4 27.6 - - + +
347A ARG* 4.2 18.9 + - + +
348A ARG* 3.8 31.4 - - + +
351A ALA* 4.1 15.9 - - + -
385A VAL* 3.1 25.9 + - + +
386A GLU* 3.6 12.3 - - - +
388A ILE* 1.3 78.9 - - + +
390A ALA* 1.3 63.1 + - - +
392A ALA* 3.3 6.7 + - - +
393A ARG* 3.1 44.5 + - - +
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Residues in contact with ALA 390 (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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22A LEU* 3.8 21.5 - - + -
386A GLU* 2.9 20.4 + - + +
387A PRO* 4.5 0.2 - - + -
389A LEU* 1.3 76.9 - - - +
391A GLU* 1.3 56.8 + - - +
393A ARG* 3.2 17.7 + - - +
394A ARG* 2.9 26.9 + - - +
400A VAL* 3.8 32.2 - - + +
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Residues in contact with GLU 391 (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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22A LEU* 4.1 11.1 - - + +
26A TYR* 3.6 31.8 - - + -
44A THR* 4.1 2.2 - - + -
387A PRO 2.9 18.4 + - - +
388A ILE 3.8 1.6 - - - +
390A ALA* 1.3 74.6 - - - +
392A ALA* 1.3 66.4 + - - +
394A ARG* 2.8 44.2 + - - +
395A ARG* 2.5 66.2 + - - +
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Residues in contact with ALA 392 (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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44A THR* 4.0 13.4 - - + +
47A VAL* 4.2 10.8 - - + -
48A GLU* 3.8 31.2 - - + +
347A ARG* 4.2 6.1 - - - +
388A ILE 2.9 17.5 + - - +
389A LEU 3.5 5.6 - - - +
391A GLU* 1.3 76.6 - - - +
393A ARG* 1.3 60.5 + - - +
395A ARG* 3.5 4.1 + - - +
396A THR* 2.8 30.8 + - - +
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Residues in contact with ARG 393 (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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91A LEU 3.4 14.4 - - - +
92A THR* 3.5 24.7 - - - +
344A ASN* 3.2 26.8 + - - +
347A ARG* 4.9 7.1 - - - +
386A GLU* 3.0 23.8 + - - -
389A LEU* 3.1 34.5 + - - +
390A ALA* 3.5 14.7 - - - +
392A ALA* 1.3 74.9 - - - +
394A ARG* 1.3 62.4 + - - +
396A THR* 3.1 12.0 + - - -
398A GLY* 2.7 30.3 + - - -
399A ALA 2.8 33.5 + - - +
400A VAL 2.9 21.2 + - - -
402A PRO* 3.3 18.5 - - - +
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Residues in contact with ARG 394 (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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15A ASN* 4.7 15.4 + - + +
19A ALA* 6.5 0.9 - - - -
22A LEU* 4.6 10.5 - - + -
390A ALA 2.9 14.2 + - - +
391A GLU* 2.8 45.7 + - - +
393A ARG* 1.3 77.9 - - - +
395A ARG* 1.3 75.6 + - - +
396A THR 3.3 0.2 + - - -
397A GLY* 3.5 9.2 + - - -
398A GLY 4.2 9.0 - - - +
399A ALA 5.2 0.4 - - - -
400A VAL* 4.5 11.0 - - + -
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Residues in contact with ARG 395 (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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26A TYR* 3.6 17.2 + - - -
41A GLU* 2.5 45.0 + - - -
44A THR* 3.7 16.6 - - - +
45A ALA* 4.6 1.0 - - - +
48A GLU* 3.4 28.5 + - - +
391A GLU* 2.5 46.6 + - - +
392A ALA* 3.7 4.5 - - - +
394A ARG* 1.3 88.8 - - - +
396A THR* 1.3 64.7 + - + +
397A GLY 3.5 0.6 + - - -
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Residues in contact with THR 396 (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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48A GLU* 3.6 37.0 - - + +
93A ARG* 3.2 47.1 + - + +
347A ARG* 5.4 1.4 + - - -
392A ALA 2.8 22.0 + - - +
393A ARG* 3.1 7.6 + - - -
395A ARG* 1.3 78.5 - - - +
397A GLY* 1.3 57.7 - - - +
398A GLY 3.4 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