Contacts of the strand formed by residues 394 - 403 (chain C) 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 LEU 394 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.8 7.4 - - + -
289A TYR* 3.8 29.8 - - + +
291A TYR* 5.0 0.2 - - + -
605A C8E 4.4 5.8 - - - -
389C ARG* 3.8 2.3 - - - +
390C ILE* 3.0 56.8 + - + -
391C ASN* 3.0 28.6 + - - +
393C GLN* 1.3 79.2 - - - +
395C GLY* 1.3 63.8 + - - +
416C MET* 4.0 21.3 - - + -
417C GLU 3.7 12.6 - - - +
418C TYR* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C PHE* 5.6 0.9 - - - -
388C TRP 3.6 7.6 - - - -
389C ARG* 4.7 2.2 - - - -
390C ILE* 4.7 2.0 - - - -
393C GLN 4.2 0.2 + - - -
394C LEU* 1.3 76.2 - - - +
396C LEU* 1.3 60.5 + - - -
416C MET* 3.4 8.2 - - - +
417C GLU 2.9 36.7 + - - -
556C PHE* 3.4 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 4.5 11.7 - - + -
261A PHE* 4.1 15.7 - - + -
601A C8E 4.1 36.8 - - + -
386C THR* 6.4 1.1 - - + -
388C TRP* 2.8 62.8 + - + +
390C ILE* 4.1 11.4 - - + -
395C GLY* 1.3 74.6 - - - +
397C LYS* 1.3 72.7 + - - +
414C ALA* 5.4 2.2 - - + -
415C ILE 3.6 16.8 - - - +
416C MET* 3.9 16.6 - - + -
556C PHE* 3.4 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A C8E 4.9 1.8 - - - -
386C THR* 3.1 17.3 - - - +
387C PHE* 4.1 8.5 - - + -
396C LEU* 1.3 83.4 - - - +
398C GLY* 1.3 60.7 + - - +
413C ASN* 6.1 1.1 - - - -
414C ALA* 3.5 3.2 - - - +
415C ILE* 2.9 56.2 + - + +
555C ALA* 4.9 5.6 - - - +
556C PHE* 3.6 23.8 - - + +
79D GLN* 5.7 0.6 + - - -
103D PHE* 3.5 41.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A C8E 3.6 17.7 - - - -
385C ASP* 3.2 5.6 - - - +
386C THR* 2.9 33.7 + - - +
397C LYS* 1.3 77.7 - - - +
399C GLY* 1.3 58.0 + - - -
413C ASN* 3.2 17.0 - - - -
414C ALA* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A C8E 3.5 8.2 - - - -
384C GLY 3.2 12.6 - - - -
385C ASP* 4.0 3.6 - - - -
398C GLY* 1.3 74.6 - - - -
400C ALA* 1.3 62.8 + - - +
401C GLN* 5.8 0.2 - - - -
412C GLY* 3.3 1.8 - - - -
413C ASN* 2.9 41.1 + - - +
609C C8E 3.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO* 4.5 7.0 - - + -
601A C8E 4.0 15.4 - - - +
383C ALA* 3.3 3.2 - - - +
384C GLY 2.9 33.1 + - - +
399C GLY* 1.3 75.9 - - - +
401C GLN* 1.3 68.6 + - - +
402C TYR* 4.1 19.5 - - + -
409C LEU* 4.2 6.5 - - + -
411C LEU 3.4 10.3 - - - +
412C GLY* 4.1 1.3 - - - -
609C C8E 4.3 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLN* 3.6 26.3 - - - +
310C SER* 2.9 34.5 + - - +
311C ASP* 3.9 10.9 - - - +
382C TRP 3.6 6.7 - - - +
383C ALA* 4.5 7.2 - - + -
400C ALA* 1.3 81.7 - - - +
402C TYR* 1.3 64.5 + - - +
409C LEU* 3.3 8.0 - - - +
410C THR* 2.9 37.2 + - - +
411C LEU* 2.9 34.5 + - + +
437C TYR* 4.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY* 3.0 10.7 + - - -
180A PRO* 3.0 33.6 - - - +
601A C8E 3.5 52.7 - - - +
380C LEU 4.4 0.7 - - - -
381C VAL* 3.4 7.4 - - - +
382C TRP* 2.9 47.6 + - + +
400C ALA* 4.1 6.5 - - + -
401C GLN* 1.3 78.6 - - - +
403C ASP* 1.3 62.6 + - - +
404C THR 4.3 0.4 - - - +
408C SER* 3.4 12.8 - - - +
409C LEU* 3.5 50.9 - - + +
410C THR* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU 3.5 5.3 - - - +
381C VAL* 3.8 11.1 - - + +
402C TYR* 1.3 74.7 - - - +
404C THR* 1.3 64.7 + - - +
405C ARG* 3.0 50.4 + - - +
406C LEU* 2.9 34.3 + - + +
407C GLY 3.2 8.8 + - - -
408C SER* 2.9 17.4 + - - +
410C THR* 4.0 15.6 - - + +
----------------------------------------------------------
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