Contacts of the helix formed by residues 385 - 396 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.2 5.6 - - + -
348C ARG* 3.6 45.0 - - + +
351C ALA* 4.0 19.7 - - + -
352C GLN* 4.0 9.8 + - + +
355C LEU* 3.7 27.6 - - + -
383C THR* 3.1 13.6 + - + +
384C ASP* 1.3 71.8 + - - +
386C GLU* 1.3 64.5 + - - +
387C PRO* 3.2 4.3 - - - -
388C ILE* 2.9 26.2 + - + +
389C LEU* 3.1 12.3 + - + +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ARG* 4.8 14.6 - - - +
344C ASN* 5.8 0.3 - - - +
348C ARG* 2.9 37.3 + - - +
384C ASP* 3.1 20.6 + - - +
385C VAL* 1.3 76.8 - - - +
387C PRO* 1.3 64.1 - - + +
389C LEU* 3.0 8.7 + - - +
390C ALA* 2.8 34.6 + - + +
393C ARG* 3.0 27.8 + - - -
400C VAL 4.4 2.1 - - - +
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Residues in contact with PRO 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.7 13.3 - - + +
25C ASP* 3.7 29.4 - - + +
26C TYR* 3.6 30.6 - - + +
29C LEU* 4.1 10.8 - - + -
384C ASP* 3.5 17.0 - - - +
385C VAL 3.3 5.2 - - - -
386C GLU* 1.3 94.9 - - + +
388C ILE* 1.3 55.3 + - - +
390C ALA* 4.4 0.4 - - + -
391C GLU* 2.8 33.3 + - - +
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Residues in contact with ILE 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 4.1 6.7 - - - -
29C LEU* 3.7 26.0 - - + -
33C LEU* 4.2 9.0 - - + -
40C ILE* 3.8 26.7 - - + -
43C VAL* 3.9 20.4 - - + -
44C THR* 3.6 29.3 - - - +
47C VAL* 4.0 20.6 - - + -
351C ALA* 5.1 1.1 - - + -
355C LEU* 5.3 0.9 - - + -
385C VAL* 2.9 24.7 + - + +
387C PRO* 1.3 74.9 - - - +
389C LEU* 1.3 60.6 + - + +
391C GLU* 4.0 0.5 - - - +
392C ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.9 19.3 - - + -
344C ASN* 3.5 26.0 - - + +
347C ARG* 3.8 30.5 + - + +
348C ARG* 3.6 36.1 - - + +
351C ALA* 4.3 8.7 - - + -
385C VAL 3.1 14.1 + - - +
386C GLU* 3.0 12.0 + - - +
388C ILE* 1.3 75.9 - - + +
390C ALA* 1.3 57.8 + - - +
392C ALA* 3.4 6.1 + - - +
393C ARG* 3.1 49.6 + - - +
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.8 22.2 - - + +
386C GLU* 2.8 25.2 + - + +
389C LEU* 1.3 70.9 - - - +
391C GLU* 1.3 60.3 + - - +
393C ARG* 3.2 18.7 + - - +
394C ARG* 2.9 27.9 + - - +
400C VAL* 3.8 30.4 - - + +
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Residues in contact with GLU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.5 17.3 - - + +
26C TYR* 3.6 33.6 - - + +
44C THR* 4.7 1.8 - - + -
387C PRO 2.8 22.7 + - - +
388C ILE 4.0 1.1 - - - +
390C ALA* 1.3 71.0 - - - +
392C ALA* 1.3 67.0 + - - +
394C ARG* 2.7 39.9 + - - +
395C ARG* 2.6 70.8 + - - +
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Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR* 4.1 6.9 - - + +
47C VAL* 4.1 19.5 - - + -
48C GLU* 3.8 29.0 - - + +
347C ARG* 4.4 8.5 - - - +
388C ILE 2.8 19.3 + - - +
389C LEU 3.5 6.3 - - - +
390C ALA 3.2 0.2 - - - -
391C GLU* 1.3 77.9 - - - +
393C ARG* 1.3 53.0 + - - +
395C ARG 3.5 0.2 + - - -
396C THR* 2.7 37.9 + - - +
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Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU 3.4 15.0 - - - +
92C THR* 3.6 23.8 - - - +
344C ASN* 3.3 27.3 + - - +
347C ARG* 4.9 7.1 - - - +
386C GLU* 3.0 23.2 + - - -
389C LEU* 3.1 38.6 + - - +
390C ALA* 3.5 10.5 - - - +
391C GLU 3.2 0.2 - - - -
392C ALA* 1.3 74.2 - - - +
394C ARG* 1.3 63.4 + - - +
396C THR* 3.1 11.7 + - - -
398C GLY* 2.7 30.9 + - - -
399C ALA 2.7 33.9 + - - +
400C VAL 2.9 22.2 + - - -
402C PRO* 3.3 19.5 - - - +
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASN* 4.5 15.2 + - + +
19C ALA* 5.3 11.0 - - - -
22C LEU* 4.2 12.1 - - - +
390C ALA 2.9 16.3 + - - +
391C GLU* 2.7 44.1 + - - +
393C ARG* 1.3 76.9 - - - +
395C ARG* 1.3 72.4 + - - +
396C THR 3.4 0.3 + - - -
397C GLY* 3.7 7.8 + - - -
398C GLY 4.1 9.6 - - - +
399C ALA 5.0 0.4 - - - -
400C VAL* 4.2 18.6 - - + -
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Residues in contact with ARG 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.9 8.9 + - - -
41C GLU* 2.8 41.8 + - - -
44C THR* 4.1 13.9 - - - +
48C GLU* 3.6 22.2 + - - +
391C GLU* 2.6 52.0 + - - +
394C ARG* 1.3 86.3 - - - +
396C THR* 1.3 61.0 + - - +
397C GLY 3.5 0.2 - - - -
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Residues in contact with THR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLU* 4.0 31.6 - - + +
93C ARG* 3.1 43.6 + - - +
347C ARG* 5.4 1.2 + - - -
392C ALA 2.7 22.9 + - - +
393C ARG* 3.1 7.0 + - - -
395C ARG* 1.3 80.7 - - - +
397C GLY* 1.3 57.4 + - - +
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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