Contacts of the strand formed by residues 378 - 389 (chain G) in PDB entry 5IXM
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 GLY 378 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G ILE 3.5 0.2 - - - +
358G TYR* 3.9 16.8 - - - -
359G TYR* 2.9 42.2 + - - +
377G THR* 1.3 75.6 + - - +
379G SER* 1.3 60.6 + - - -
380G LEU* 2.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G GLN* 2.9 26.8 + - - +
357G ILE 3.4 7.8 + - - -
358G TYR* 3.4 17.9 - - - -
378G GLY* 1.3 67.6 - - - -
380G LEU* 1.3 63.1 + - - +
382G TRP* 3.2 28.9 + - - -
404G THR* 4.0 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G ILE 3.0 3.0 + - - -
359G TYR* 3.9 22.2 - - + -
376G ALA* 3.6 37.2 - - + +
377G THR* 3.6 26.5 - - + +
378G GLY 2.9 14.6 + - - +
379G SER* 1.3 79.3 - - - +
381G VAL* 1.3 61.6 + - - +
382G TRP* 4.6 3.0 - - - -
402G TYR 4.0 0.3 - - - +
403G ASP* 3.5 5.5 - - - +
404G THR* 3.0 45.2 + - + -
405G ARG* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 381 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G SER* 4.7 12.1 - - - +
315G LEU* 3.6 24.2 - - + -
356G GLN* 3.1 7.8 - - - +
357G ILE* 2.9 43.1 + - + +
359G TYR* 3.9 14.6 - - + +
380G LEU* 1.3 80.2 + - - +
382G TRP* 1.3 70.5 + - - +
383G ALA* 5.3 0.9 - - + -
402G TYR 3.6 5.2 - - - +
403G ASP* 3.9 10.8 - - + +
405G ARG* 3.4 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 382 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU* 4.7 0.2 - - - -
354G VAL* 4.0 24.0 - - + -
355G GLY 3.4 17.5 - - - -
356G GLN* 3.7 24.0 - - + -
379G SER* 3.2 31.0 + - - -
380G LEU 4.6 4.9 - - - -
381G VAL* 1.3 86.2 - - - +
383G ALA* 1.3 63.9 + - - +
401G GLN* 3.6 2.3 - - - +
402G TYR* 2.9 57.0 + - + +
404G THR* 5.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G SER 5.0 1.3 - - - +
311G ASP 3.8 23.8 - - - +
312G TYR* 3.8 4.2 - - - +
315G LEU* 3.8 22.4 - - + -
354G VAL* 3.7 3.4 - - - +
355G GLY* 2.9 32.6 + - - -
381G VAL* 5.3 0.7 - - + -
382G TRP* 1.3 78.7 - - - +
384G GLY* 1.3 58.5 + - - +
400G ALA 3.4 10.3 - - - +
401G GLN* 4.5 7.6 - - + -
402G TYR* 5.2 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 384 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G TYR* 4.4 7.4 + - - +
353G SER 3.1 13.0 - - - -
354G VAL* 4.5 4.3 - - - -
383G ALA* 1.3 76.3 - - - +
385G ASP* 1.3 62.2 + - - +
399G GLY* 3.2 3.3 - - - -
400G ALA* 2.9 34.3 + - - +
402G TYR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 385 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G ASP* 6.0 0.9 - - - +
312G TYR* 3.6 20.3 - - + +
351G ASN* 4.5 9.0 - - - +
352G VAL* 3.6 2.4 - - - +
353G SER* 3.0 51.1 + - - +
384G GLY* 1.3 75.5 - - - +
386G THR* 1.3 65.1 + - - +
398G GLY 3.2 12.6 - - - +
399G GLY* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 386 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G PHE* 4.2 13.2 - - - -
351G ASN* 3.2 15.9 + - - -
352G VAL* 4.6 8.2 - - - +
385G ASP* 1.3 80.1 - - - +
387G PHE* 1.3 66.6 + - - +
388G TRP* 5.4 0.7 - - - +
396G LEU* 6.4 1.8 - - + -
397G LYS* 3.1 8.8 - - - +
398G GLY* 2.8 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 387 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348G GLU* 3.6 30.1 - - + -
349G ARG 4.2 2.9 - - - -
350G PHE* 3.4 4.1 - - - -
351G ASN* 2.8 57.5 + - + +
386G THR* 1.3 77.8 + - - +
388G TRP* 1.3 72.4 + - - +
389G ARG* 3.9 29.4 - - + -
395G GLY* 5.7 1.1 - - - -
396G LEU 3.5 4.0 - - - -
397G LYS* 4.1 6.1 - - + -
556G PHE* 3.6 38.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 388 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G ARG 3.4 11.9 - - - -
350G PHE* 3.9 14.1 - + + -
386G THR* 5.4 0.7 - - - +
387G PHE* 1.3 82.0 - - - +
389G ARG* 1.3 70.0 + - - +
390G ILE* 3.4 42.7 + - + +
395G GLY* 3.6 1.0 - - - -
396G LEU* 2.8 69.2 + - + +
601G C8E 3.3 52.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347G VAL* 3.6 33.5 - - - +
348G GLU 4.7 2.2 - - - -
349G ARG* 2.6 49.6 + - - +
387G PHE* 3.9 19.8 - - + -
388G TRP* 1.3 75.3 + - - +
390G ILE* 1.3 62.1 + - - +
391G ASN 3.5 21.6 + - - +
392G ASP* 3.4 32.4 + - - +
394G LEU 4.1 3.4 - - - +
395G GLY* 4.8 1.6 - - - -
601G C8E 4.8 0.5 - - - +
----------------------------------------------------------
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