Contacts of the strand formed by residues 394 - 403 (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 LEU 394 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389G ARG* 3.8 1.7 - - - +
390G ILE* 3.0 59.2 + - + -
391G ASN* 2.8 32.2 + - - +
393G GLN* 1.3 79.8 - - - +
395G GLY* 1.3 58.7 + - - +
416G MET* 4.1 24.5 - - + -
417G GLU 3.6 15.9 - - - +
418G TYR* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387G PHE* 5.7 0.4 - - - -
388G TRP 3.6 6.7 - - - -
389G ARG* 4.8 2.7 - - - -
390G ILE* 4.6 2.5 - - - -
393G GLN 4.2 0.2 + - - -
394G LEU* 1.3 74.9 - - - +
396G LEU* 1.3 60.8 + - - -
416G MET* 3.4 7.7 - - - +
417G GLU 2.9 36.5 + - - -
556G PHE* 3.3 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G THR* 6.4 1.6 - - + -
387G PHE* 3.5 0.3 - - - -
388G TRP* 2.8 67.7 + - + +
390G ILE* 4.1 13.9 - - + -
395G GLY* 1.3 73.5 - - - +
397G LYS* 1.3 74.6 + - - +
414G ALA* 5.5 5.2 - - + -
415G ILE 3.6 16.2 - - - +
416G MET* 3.9 17.5 - - + -
556G PHE* 3.3 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G THR* 3.1 16.8 - - - +
387G PHE* 4.1 8.3 - - + -
396G LEU* 1.3 83.0 - - - +
398G GLY* 1.3 56.9 + - - +
414G ALA* 3.5 2.4 - - - +
415G ILE* 2.7 64.9 + - + +
555G ALA* 4.2 10.9 - - - +
556G PHE* 3.6 25.2 - - + +
79H GLN* 5.6 1.5 + - - -
103H PHE* 3.2 44.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ASP* 3.2 4.6 - - - +
386G THR* 2.8 42.1 + - - +
397G LYS* 1.3 77.0 - - - +
399G GLY* 1.3 58.5 + - - -
413G ASN* 3.2 19.7 - - - -
414G ALA* 3.9 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384G GLY 3.2 13.0 - - - -
385G ASP* 4.0 4.5 - - - -
398G GLY* 1.3 75.0 - - - -
400G ALA* 1.3 61.4 + - - +
401G GLN* 5.7 0.2 - - - -
412G GLY* 3.3 2.5 - - - -
413G ASN* 2.8 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383G ALA* 3.4 2.1 - - - -
384G GLY* 2.9 34.5 + - - +
399G GLY* 1.3 76.4 - - - +
401G GLN* 1.3 68.1 + - - +
402G TYR* 4.2 15.5 - - + +
409G LEU* 4.1 12.8 - - + -
411G LEU 3.4 10.8 - - - +
412G GLY* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G GLN* 3.8 11.9 - - - +
310G SER* 2.8 31.9 + - - +
311G ASP* 3.6 14.6 - - - +
382G TRP 3.6 7.6 - - - +
383G ALA* 4.5 7.6 - - + -
399G GLY 5.7 0.2 - - - -
400G ALA* 1.3 81.4 - - - +
402G TYR* 1.3 64.5 + - - +
409G LEU* 3.3 7.8 - - - +
410G THR* 2.9 36.9 + - - +
411G LEU* 2.9 45.6 + - + +
437G TYR* 4.2 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 402 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G LEU 4.5 0.4 - - - -
381G VAL* 3.6 5.0 - - - +
382G TRP* 2.9 57.4 + - + +
383G ALA* 5.2 1.1 - - - -
400G ALA* 4.2 17.0 - - + +
401G GLN* 1.3 78.4 - - - +
403G ASP* 1.3 64.1 + - - +
404G THR 4.3 0.4 - - - +
408G SER* 3.3 15.3 - - - +
409G LEU* 3.5 47.0 - - + +
410G THR* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G LEU 3.5 8.6 - - - +
381G VAL* 3.9 7.1 - - + +
402G TYR* 1.3 75.8 - - - +
404G THR* 1.3 59.7 + - - +
405G ARG* 2.9 51.8 + - - +
406G LEU* 2.9 37.0 + - + +
407G GLY 3.0 9.4 + - - -
408G SER* 2.8 16.9 + - - +
410G THR* 3.8 17.0 - - + +
----------------------------------------------------------
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