Contacts of the helix formed by residues 385 - 396 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LEU* 4.2 5.8 - - - -
348D ARG* 3.6 44.8 - - + +
351D ALA* 4.0 20.0 - - + -
352D GLN* 3.8 10.3 - - + +
355D LEU* 3.8 28.9 - - + -
383D THR* 3.1 12.4 + - + +
384D ASP* 1.3 72.0 + - - +
386D GLU* 1.3 64.3 + - - +
387D PRO* 3.2 3.6 - - - -
388D ILE* 3.0 25.8 + - + +
389D LEU* 3.1 12.4 + - + +
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Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ARG* 4.8 14.1 - - - +
344D ASN* 5.8 0.2 - - - +
348D ARG* 2.9 36.8 + - - +
384D ASP* 3.1 19.5 + - - +
385D VAL* 1.3 77.5 - - - +
387D PRO* 1.3 64.0 - - + +
389D LEU* 3.1 8.7 + - - +
390D ALA* 2.8 32.8 + - + +
393D ARG* 2.9 29.9 + - - -
400D VAL 4.4 1.7 - - - +
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Residues in contact with PRO 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.6 14.6 - - + +
25D ASP* 3.7 29.6 - - + +
26D TYR* 3.6 29.8 - - + +
29D LEU* 4.2 10.5 - - + -
384D ASP* 3.4 20.0 - - - +
385D VAL 3.3 3.8 - - - -
386D GLU* 1.3 94.8 - - + +
388D ILE* 1.3 55.5 + - - +
390D ALA* 4.5 0.4 - - + -
391D GLU* 2.9 31.5 + - - +
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Residues in contact with ILE 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 4.1 5.8 - - - -
29D LEU* 3.8 25.8 - - + -
33D LEU* 4.2 9.0 - - + -
40D ILE* 3.8 28.0 - - + -
43D VAL* 3.9 20.2 - - + -
44D THR* 3.6 28.4 - - - +
47D VAL* 4.0 20.2 - - + -
351D ALA* 5.1 0.9 - - + -
355D LEU* 5.2 1.3 - - + -
385D VAL* 3.0 22.9 + - + +
387D PRO* 1.3 75.8 - - - +
389D LEU* 1.3 62.9 + - + +
391D GLU* 3.5 1.2 + - - +
392D ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 4.1 15.5 - - + -
344D ASN* 3.5 23.6 - - - +
347D ARG* 3.9 30.3 + - + +
348D ARG* 3.6 35.7 - - + +
351D ALA* 4.1 6.3 - - + -
385D VAL* 3.1 23.1 + - + +
386D GLU* 3.5 11.9 - - - +
388D ILE* 1.3 78.6 - - + +
390D ALA* 1.3 61.7 + - - +
392D ALA* 3.4 6.5 + - - +
393D ARG* 3.1 44.1 + - - +
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Residues in contact with ALA 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.8 21.6 - - + +
386D GLU* 2.8 25.0 + - + +
389D LEU* 1.3 73.9 - - - +
391D GLU* 1.3 57.4 + - - +
393D ARG* 3.3 17.9 + - - +
394D ARG* 2.9 28.1 + - - +
400D VAL* 3.6 29.6 - - + +
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Residues in contact with GLU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.5 16.2 - - + +
26D TYR* 3.7 32.8 - - + +
44D THR* 4.6 2.5 - - + -
387D PRO 2.9 19.0 + - - +
388D ILE 3.9 1.3 - - - +
390D ALA* 1.3 74.8 - - - +
392D ALA* 1.3 60.9 + - - +
394D ARG* 2.6 45.4 + - - -
395D ARG* 2.6 71.1 + - - +
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Residues in contact with ALA 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 4.1 6.0 - - + +
47D VAL* 4.1 18.8 - - + -
48D GLU* 3.6 31.4 - - + -
347D ARG* 4.3 8.7 - - - +
388D ILE 3.0 18.6 + - - +
389D LEU 3.6 4.9 - - - +
390D ALA 3.3 0.2 - - - -
391D GLU* 1.3 77.5 - - - +
393D ARG* 1.3 54.5 + - - +
395D ARG* 3.6 0.5 + - - -
396D THR* 2.6 38.4 + - - +
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Residues in contact with ARG 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU 3.5 8.7 - - - +
92D THR* 3.5 25.1 - - - +
93D ARG* 5.0 0.4 - - - -
344D ASN* 3.3 27.5 + - - +
347D ARG* 4.9 6.3 - - - +
386D GLU* 2.9 26.9 + - - -
389D LEU* 3.1 35.1 + - - +
390D ALA* 3.5 10.9 - - - +
392D ALA* 1.3 76.8 - - - +
394D ARG* 1.3 60.5 + - - +
396D THR* 3.1 12.1 + - - -
397D GLY 3.2 0.2 + - - -
398D GLY* 2.7 30.0 + - - -
399D ALA 2.8 33.3 + - - +
400D VAL 2.9 18.2 + - - -
402D PRO* 3.3 24.9 - - - +
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Residues in contact with ARG 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASN* 4.2 14.2 - - + +
19D ALA* 5.4 11.0 - - - -
22D LEU* 4.2 12.1 - - - +
390D ALA 2.9 17.0 + - - +
391D GLU* 2.6 43.6 + - - +
393D ARG* 1.3 77.1 - - - +
395D ARG* 1.3 73.0 + - - +
396D THR 3.4 0.5 + - - -
397D GLY* 3.6 8.1 + - - -
398D GLY 4.1 9.8 - - - +
399D ALA 4.9 0.4 - - - -
400D VAL* 4.2 18.8 - - + -
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Residues in contact with ARG 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D TYR* 3.9 10.1 + - - -
41D GLU* 2.8 41.0 + - - -
44D THR* 4.1 13.9 - - - +
48D GLU* 3.6 21.5 + - - +
391D GLU* 2.6 51.7 + - - +
392D ALA 4.1 0.4 - - - +
394D ARG* 1.3 85.8 - - - +
396D THR* 1.3 61.2 + - + +
397D GLY 3.5 1.0 + - - -
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Residues in contact with THR 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLU* 4.1 32.8 - - + +
93D ARG* 3.2 43.2 + - - +
347D ARG* 5.5 1.2 + - - -
392D ALA 2.6 23.3 + - - +
393D ARG* 3.1 6.1 + - - -
395D ARG* 1.3 81.8 - - - +
397D GLY* 1.3 57.0 + - - +
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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