Contacts of the helix formed by residues 381 - 391 (chain C) in PDB entry 3DLX
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 SER 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C ARG* 3.5 19.7 - - - +
229C ASN* 3.7 12.6 - - - +
232C LEU* 4.1 19.6 - - - +
346C GLY* 4.7 1.1 - - - -
380C PHE* 1.3 79.7 - - - +
382C SER* 1.3 60.1 + - - +
383C ASP* 2.7 30.1 + - - -
384C GLU* 3.3 10.7 + - - +
385C SER* 2.9 27.2 + - - -
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Residues in contact with SER 382 (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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138C GLN* 4.9 0.5 + - - -
142C ALA* 3.7 6.0 - - - +
229C ASN* 3.0 40.5 + - - +
230C PHE* 3.5 31.0 + - - -
233C PRO* 5.1 0.7 - - - -
344C GLU 4.4 8.3 + - - -
345C ASN* 4.3 5.8 + - - -
381C SER* 1.3 69.8 - - - +
383C ASP* 1.3 66.3 + - - +
385C SER* 4.1 6.5 - - - -
386C PHE* 3.2 31.3 + - - +
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Residues in contact with ASP 383 (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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142C ALA* 3.6 30.4 - - - +
143C GLU* 4.3 9.2 - - - +
146C ARG* 3.6 26.5 + - + +
232C LEU* 4.2 6.2 - - - +
233C PRO* 3.3 23.7 - - + +
236C LYS* 5.6 2.1 + - - -
381C SER* 2.7 30.0 + - - -
382C SER* 1.3 74.9 - - - +
384C GLU* 1.3 56.6 + - - +
386C PHE* 4.0 1.8 - - - +
387C ALA* 3.1 24.8 + - - +
390C ARG* 5.1 0.9 + - - +
146D ARG* 4.1 8.1 + - - +
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Residues in contact with GLU 384 (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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380C PHE* 3.9 24.9 - - + -
381C SER* 3.3 18.3 + - - +
382C SER 3.2 0.4 - - - -
383C ASP* 1.3 79.6 - - - +
385C SER* 1.3 67.2 + - - +
387C ALA* 3.4 8.7 + - - +
388C MET* 3.1 23.6 + - + +
146D ARG* 5.3 6.1 + - - +
236D LYS* 2.8 31.9 + - - +
262D PRO* 6.0 3.1 - - + -
265D TYR* 2.7 35.7 + - + -
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Residues in contact with SER 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLN* 3.2 16.8 + - - +
343C SER 3.8 0.5 + - - -
344C GLU* 2.7 36.8 + - - +
346C GLY* 4.3 1.3 - - - -
380C PHE* 3.8 20.5 - - - -
381C SER 2.9 17.0 + - - -
382C SER* 3.6 4.9 - - - -
384C GLU* 1.3 77.5 - - - +
386C PHE* 1.3 57.3 + - - -
388C MET* 3.1 22.1 - - - +
389C ILE* 3.1 13.4 + - - +
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Residues in contact with PHE 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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138C GLN* 3.3 45.8 - - + -
139C GLY* 3.4 23.3 - - - +
142C ALA* 4.7 0.7 - - + -
344C GLU* 3.5 31.4 - - + -
382C SER* 3.2 26.4 + - - +
383C ASP* 4.3 2.7 - - - +
385C SER* 1.3 74.8 - - - +
387C ALA* 1.3 56.1 - - - +
389C ILE* 3.7 19.5 - - + +
390C ARG* 2.7 49.5 + - - +
425C GLY* 3.9 12.6 - - - -
428C ASP* 3.6 36.6 - - + -
429C LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 387 (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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383C ASP 3.1 15.8 + - - +
384C GLU* 3.5 21.5 - - - +
386C PHE* 1.3 74.5 - - - +
388C MET* 1.3 59.0 + - - +
390C ARG* 3.8 11.3 - - - +
391C GLY* 2.8 23.9 + - - -
146D ARG* 4.3 9.9 - - + +
149D GLY 3.3 14.8 - - - +
150D ALA* 3.6 24.1 - - + +
236D LYS* 6.0 1.8 - - + -
265D TYR* 4.4 2.7 - - - +
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Residues in contact with MET 388 (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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342C GLN* 3.5 29.6 - - - +
348C LEU* 5.1 2.2 - - + -
380C PHE* 3.6 38.4 - - + -
384C GLU* 3.1 13.8 + - - +
385C SER 3.1 12.5 + - - +
387C ALA* 1.3 78.2 - - - +
389C ILE* 1.3 55.8 + - - +
392C GLY 3.6 0.2 + - - -
393C HIS* 3.1 41.0 + - + +
394C VAL* 4.0 4.6 + - + -
262D PRO* 4.3 6.1 - - + -
264D ILE* 4.0 42.0 - - + -
265D TYR* 3.7 27.3 + - + +
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Residues in contact with ILE 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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342C GLN* 3.8 25.8 - - - +
344C GLU* 4.2 6.7 - - + -
385C SER* 3.1 22.5 + - - +
386C PHE* 3.7 27.1 - - + +
387C ALA 3.3 0.2 - - - -
388C MET* 1.3 74.3 - - - +
390C ARG* 1.3 66.1 + - - +
392C GLY* 3.2 13.9 + - - -
393C HIS 4.5 0.2 + - - -
394C VAL* 4.4 14.9 + - + +
428C ASP* 3.4 34.8 - - + +
429C LEU* 3.7 30.1 - - + +
432C SER* 4.2 7.4 - - - -
435C THR* 4.8 3.1 + - - -
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Residues in contact with ARG 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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139C GLY* 3.0 34.4 + - - -
140C THR* 4.8 0.8 - - - +
143C GLU* 3.6 28.1 + - - +
155C PHE* 5.4 0.8 - - - -
157C THR* 3.5 23.1 + - - +
158C PRO* 3.8 22.5 - - + +
159C THR* 4.2 4.0 - - - +
383C ASP 5.1 0.8 + - - -
386C PHE* 2.7 39.7 + - - +
387C ALA* 3.8 9.7 - - - +
389C ILE* 1.3 74.2 - - + +
391C GLY* 1.3 56.0 + - - +
392C GLY 3.2 0.9 + - - -
428C ASP* 3.9 8.5 + - - +
431C SER* 4.0 15.1 + - - +
432C SER* 4.1 10.7 + - - -
150D ALA* 3.1 31.4 + - - +
151D GLY* 3.6 24.1 - - - +
152D VAL* 4.2 9.4 - - - +
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Residues in contact with GLY 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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387C ALA 2.8 20.8 + - - -
390C ARG* 1.3 76.0 - - - +
392C GLY* 1.3 60.9 + - - +
393C HIS* 3.4 13.3 + - - -
432C SER* 4.5 1.3 - - - -
434C LYS* 4.6 10.4 + - - +
148D GLY 5.2 0.9 - - - -
149D GLY* 3.4 15.4 - - - -
150D ALA 3.8 0.4 + - - -
151D GLY* 3.7 12.3 - - - -
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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