Contacts of the helix formed by residues 381 - 391 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ARG* 3.7 12.0 - - - +
229A ASN* 3.7 13.5 - - - +
232A LEU* 3.9 28.3 - - - +
346A GLY* 4.8 1.1 - - - -
380A PHE* 1.3 79.7 - - - +
382A SER* 1.3 60.2 + - - +
383A ASP* 2.5 32.3 + - - -
384A GLU* 3.2 9.9 + - - +
385A SER* 2.9 27.0 + - - -
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Residues in contact with SER 382 (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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64A PHE* 5.2 0.2 - - - -
138A GLN* 5.1 0.5 + - - -
142A ALA* 3.8 4.0 - - - +
229A ASN* 3.1 39.5 + - - +
230A PHE* 3.6 33.1 - - - -
233A PRO* 5.3 0.7 - - - -
344A GLU 4.2 10.7 + - - -
345A ASN* 4.3 4.0 + - - -
381A SER* 1.3 72.0 - - - +
383A ASP* 1.3 65.7 + - - +
385A SER* 3.4 7.1 - - - -
386A PHE* 3.1 31.8 + - - -
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Residues in contact with ASP 383 (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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142A ALA* 3.7 30.2 - - + +
143A GLU* 4.4 9.7 - - - +
146A ARG* 3.9 25.7 + - + +
232A LEU* 4.3 5.3 - - - +
233A PRO* 3.3 24.2 - - + +
236A LYS* 5.7 1.0 + - - -
381A SER* 2.5 32.7 + - - -
382A SER* 1.3 75.5 - - - +
384A GLU* 1.3 58.3 + - - +
386A PHE* 3.6 1.8 + - - +
387A ALA* 3.1 26.9 + - - +
390A ARG* 5.1 0.9 + - - -
146B ARG* 4.2 7.3 + - - +
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Residues in contact with GLU 384 (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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380A PHE* 3.8 23.6 - - + -
381A SER* 3.2 21.1 + - - +
383A ASP* 1.3 79.5 - - - +
385A SER* 1.3 66.6 + - - +
387A ALA* 3.4 8.8 + - - +
388A MET* 3.1 24.3 + - + +
146B ARG* 5.4 4.7 + - - +
236B LYS* 2.9 25.7 + - - +
262B PRO* 5.3 3.8 - - + +
265B TYR* 2.4 41.8 + - - -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 3.2 14.3 + - - +
343A SER 3.5 1.4 + - - -
344A GLU* 2.8 43.7 + - - -
346A GLY* 4.3 1.6 - - - -
380A PHE* 3.6 19.4 - - - -
381A SER 2.9 14.1 + - - -
382A SER* 3.4 9.0 - - - -
384A GLU* 1.3 76.3 - - - +
386A PHE* 1.3 58.7 + - - +
388A MET* 3.1 22.9 - - - +
389A ILE* 3.3 8.8 + - - +
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Residues in contact with PHE 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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138A GLN* 3.4 42.0 - - + -
139A GLY* 3.3 24.7 - - - +
142A ALA* 4.6 2.2 - - + -
344A GLU* 3.5 32.8 - - + -
382A SER* 3.1 26.5 + - - +
383A ASP 4.3 2.2 - - - +
385A SER* 1.3 77.8 - - - +
387A ALA* 1.3 56.9 + - - +
389A ILE* 3.7 19.5 - - + +
390A ARG* 2.6 49.3 + - - +
425A GLY* 3.9 12.1 - - - -
428A ASP* 3.6 36.8 - - + -
429A LEU* 5.4 0.4 - - + -
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Residues in contact with ALA 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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383A ASP 3.1 17.7 + - - +
384A GLU* 3.6 17.9 - - - +
386A PHE* 1.3 74.5 - - - +
388A MET* 1.3 56.5 + - - +
390A ARG* 3.9 5.1 - - - +
391A GLY* 2.8 30.5 + - - -
146B ARG* 4.3 9.4 - - - +
149B GLY 3.5 9.5 - - - +
150B ALA* 3.4 29.7 - - + -
236B LYS* 6.2 1.3 - - + -
265B TYR* 4.5 3.8 - - - +
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Residues in contact with MET 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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342A GLN* 3.6 28.3 - - - +
348A LEU* 5.0 2.0 - - + -
380A PHE* 3.8 36.3 - - + -
384A GLU* 3.1 26.7 + - - +
385A SER 3.1 9.4 - - - +
387A ALA* 1.3 78.0 - - - +
389A ILE* 1.3 58.8 + - + +
392A GLY 3.5 0.2 + - - -
393A HIS* 3.0 39.9 + - + +
394A VAL* 3.8 4.0 + - + -
262B PRO* 4.1 10.8 - - + -
264B ILE* 3.7 44.0 - - + -
265B TYR* 3.7 19.2 + - + +
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Residues in contact with ILE 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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320A ASN* 4.5 0.2 - - - +
342A GLN* 3.9 27.4 - - - +
344A GLU* 4.2 8.7 - - + -
385A SER* 3.3 17.9 + - - +
386A PHE* 3.7 30.1 - - + +
388A MET* 1.3 75.6 - - - +
390A ARG* 1.3 65.9 + - - +
391A GLY 3.1 1.1 - - - -
392A GLY* 3.1 14.2 + - - -
394A VAL* 4.4 14.8 - - + -
397A THR* 5.7 0.2 - - - +
428A ASP* 3.4 29.2 - - + +
429A LEU* 3.8 35.9 - - + +
431A SER* 4.7 0.3 + - - -
432A SER* 3.9 9.0 - - - -
435A THR* 4.7 2.4 + - - -
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Residues in contact with ARG 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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139A GLY* 2.9 34.6 + - - -
140A THR* 4.8 1.2 - - - +
143A GLU* 3.7 25.8 + - - +
155A PHE* 5.6 0.6 - - - -
157A THR* 3.7 23.8 + - - +
158A PRO* 3.9 20.4 - - + +
159A THR* 4.4 2.9 - - - +
383A ASP 5.1 0.8 + - - -
386A PHE* 2.6 38.5 + - - +
387A ALA* 3.9 9.5 - - - +
389A ILE* 1.3 75.3 - - - +
391A GLY* 1.3 57.6 + - - +
392A GLY 3.3 1.2 + - - -
428A ASP* 4.3 9.2 + - + +
431A SER* 4.0 14.2 + - - +
432A SER* 3.9 10.9 + - - -
150B ALA* 3.1 33.6 + - - +
151B GLY* 3.6 20.9 - - - +
152B VAL* 4.1 10.6 - - - +
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Residues in contact with GLY 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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387A ALA 2.8 21.0 + - - -
389A ILE 3.1 0.6 - - - -
390A ARG* 1.3 76.8 - - - +
392A GLY* 1.3 59.1 + - - +
393A HIS* 3.4 14.2 + - - -
432A SER* 4.2 1.8 - - - -
434A LYS* 4.7 8.5 - - - +
148B GLY 5.3 0.7 - - - -
149B GLY 3.5 15.5 - - - +
150B ALA 3.6 0.6 + - - -
151B GLY* 3.8 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