Contacts of the helix formed by residues 376 - 385 (chain A) in PDB entry 5MLE
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 ASP 376 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 4.9 2.5 - - - -
374A LYS 4.2 1.2 + - - -
375A MET* 1.3 78.6 - - - +
377A GLU* 1.3 63.4 + - - +
378A ASN* 3.9 18.8 - - - +
379A GLN* 3.2 22.9 + - - +
380A PHE* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 2.7 34.3 + - - -
25A VAL* 3.7 23.8 - - + +
30A SER* 4.7 4.5 + - - +
64A MET* 3.7 28.3 - - - +
366A TRP* 4.2 16.7 - - + -
370A VAL* 5.2 3.6 - - + -
376A ASP* 1.3 75.2 - - - +
378A ASN* 1.3 64.4 + - - +
380A PHE* 3.4 9.6 + - - +
381A VAL* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.8 1.8 - - - +
26A ASN 2.8 26.1 + - - -
27A ASP* 3.4 28.3 - - - +
28A ASP 5.0 0.4 - - - -
29A GLN* 3.3 34.2 + - - +
30A SER* 3.6 15.9 + - - -
376A ASP* 3.3 16.1 + - - +
377A GLU* 1.3 76.9 - - - +
379A GLN* 1.3 56.9 + - - +
381A VAL* 3.6 1.6 + - - +
382A ALA* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 3.0 21.1 - - - +
322A SER 3.3 20.5 - - - +
323A CYS 5.6 0.2 - - - -
324A GLY* 3.7 13.9 + - - -
326A LEU 4.8 0.7 - - - +
375A MET* 3.7 16.4 - - + -
376A ASP* 3.2 21.0 + - - +
378A ASN* 1.3 73.8 - - - +
380A PHE* 1.3 60.5 + - - +
381A VAL 3.2 0.7 - - - -
382A ALA* 3.8 15.9 - - - +
383A VAL* 2.8 41.7 + - + +
387A ASN* 5.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 4.2 9.4 - - + -
66A ILE* 3.8 24.7 - - + -
362A MET* 3.4 49.6 - - + -
365A ILE* 3.7 20.9 - - + -
366A TRP* 3.5 44.4 - + + -
370A VAL* 3.9 11.7 - - + -
375A MET* 3.3 10.9 - - - -
376A ASP 3.1 12.6 + - - +
377A GLU* 3.4 11.9 - - - +
379A GLN* 1.3 74.8 - - - +
381A VAL* 1.3 57.6 + - - +
383A VAL* 4.4 0.7 - - - -
384A THR* 2.7 42.8 + - + +
412A TRP* 4.3 8.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.5 31.2 - - + +
26A ASN 3.9 3.4 - - - +
27A ASP 3.8 14.8 - - - +
66A ILE* 3.5 28.0 - - + -
67A PRO* 3.6 22.9 - - + +
377A GLU 3.2 4.6 + - - +
378A ASN 3.7 7.4 - - - +
379A GLN 3.2 0.2 - - - -
380A PHE* 1.3 81.1 - - + +
382A ALA* 1.3 59.1 + - - +
384A THR* 3.4 5.4 + - - -
385A SER* 2.9 29.8 + - - +
386A THR* 3.3 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 4.0 13.9 - - + +
378A ASN 3.1 16.6 + - - +
379A GLN* 3.2 23.5 + - - +
381A VAL* 1.3 77.4 - - - +
383A VAL* 1.3 60.5 + - - +
384A THR 3.5 0.3 + - - -
385A SER 3.8 0.5 + - - -
386A THR* 3.5 12.3 + - - -
387A ASN* 2.8 46.9 + - - +
388A ALA 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.6 39.7 - - + +
326A LEU 4.6 1.3 - - - +
327A GLN 3.6 18.4 - - - +
328A VAL* 3.9 1.9 - - - -
329A THR* 2.6 36.7 + - + -
361A ARG* 4.4 0.2 + - - -
365A ILE* 4.3 4.0 - - + -
375A MET* 4.0 21.5 - - + -
379A GLN* 2.8 48.8 + - + +
380A PHE 4.0 4.3 - - - +
382A ALA* 1.3 71.0 - - - +
384A THR* 1.3 62.7 + - + +
387A ASN* 4.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 5.3 0.7 - - - +
67A PRO 5.6 1.0 + - - -
69A GLY* 3.4 2.8 - - - -
70A ILE 3.0 23.3 + - - +
329A THR* 4.1 0.7 - - - +
361A ARG* 3.4 15.9 + - - +
362A MET* 3.6 35.0 - - + +
365A ILE* 3.9 25.1 - - + -
380A PHE* 2.7 39.7 + - + +
381A VAL* 3.4 7.1 + - - -
383A VAL* 1.3 85.4 - - + +
385A SER* 1.3 59.5 + - - +
388A ALA* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.9 13.6 + - - +
68A GLY 3.5 24.2 - - - -
69A GLY* 4.1 1.3 - - - -
70A ILE* 3.8 17.7 - - - +
381A VAL* 2.9 11.7 + - - +
382A ALA 4.0 0.2 - - - -
383A VAL 3.7 1.2 - - - -
384A THR* 1.3 82.0 - - - +
386A THR* 1.3 77.2 + - - +
387A ASN 3.4 2.0 - - - -
388A ALA* 3.3 9.3 + - - +
389A ALA* 3.0 22.3 + - - +
399A GLY* 3.5 16.6 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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