Contacts of the strand formed by residues 394 - 403 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389E ARG* 3.9 2.3 - - - +
390E ILE* 3.1 43.7 + - + -
391E ASN* 2.9 30.0 + - - +
393E GLN* 1.3 79.8 - - - +
395E GLY* 1.3 58.9 + - - +
416E MET* 4.0 20.0 - - + -
417E GLU 3.6 17.0 - - - +
418E TYR* 3.7 23.3 - - + -
261G PHE* 3.6 32.3 - - + -
289G TYR* 3.8 17.7 - - + +
603G C8E 4.6 5.4 - - - +
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Residues in contact with GLY 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E PHE* 5.5 1.3 - - - -
388E TRP 3.6 6.5 - - - -
389E ARG* 4.8 2.9 - - - -
390E ILE* 4.8 2.2 - - - -
393E GLN 4.2 0.4 + - - -
394E LEU* 1.3 76.0 - - - +
396E LEU* 1.3 59.6 + - - -
416E MET* 3.3 7.1 - - - +
417E GLU 2.8 37.2 + - - -
556E PHE* 3.3 20.6 - - - -
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Residues in contact with LEU 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E THR* 6.3 0.7 - - + -
387E PHE* 3.5 0.3 - - - -
388E TRP* 2.8 58.3 + - + +
390E ILE* 4.1 11.4 - - + -
395E GLY* 1.3 75.0 - - - +
397E LYS* 1.3 70.3 + - - +
414E ALA* 5.4 3.4 - - + -
415E ILE 3.6 20.4 - - - +
416E MET* 3.9 17.5 - - + -
556E PHE* 3.3 7.0 - - - -
603E C8E 3.4 40.8 - - - +
224G THR* 4.5 9.2 - - + -
261G PHE* 4.3 15.7 - - + -
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Residues in contact with LYS 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E THR* 3.1 16.4 - - - +
387E PHE* 4.2 8.5 - - + +
396E LEU* 1.3 81.4 - - - +
398E GLY* 1.3 61.3 + - - +
413E ASN* 5.7 5.6 - - - +
414E ALA* 3.5 2.8 - - - +
415E ILE* 2.9 57.7 + - + +
555E ALA* 5.0 6.0 - - - +
556E PHE* 3.6 25.0 - - + +
603E C8E 4.7 4.3 - - - -
79F GLN* 5.5 1.8 + - - -
103F PHE* 3.6 40.8 - - - +
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Residues in contact with GLY 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E ASP* 3.2 5.2 - - - +
386E THR* 2.9 34.6 + - - +
397E LYS* 1.3 78.9 - - - +
399E GLY* 1.3 58.9 + - - -
413E ASN* 3.2 17.9 - - - -
414E ALA* 4.0 1.1 - - - -
603E C8E 3.8 16.2 - - - -
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Residues in contact with GLY 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E GLY 3.2 12.8 - - - -
385E ASP* 4.0 4.0 - - - -
398E GLY* 1.3 74.4 - - - -
400E ALA* 1.3 62.7 + - - +
401E GLN* 5.8 0.2 - - - -
412E GLY* 3.4 0.9 - - - -
413E ASN* 2.9 42.8 + - - +
603E C8E 3.5 8.5 - - - +
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Residues in contact with ALA 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E ALA* 3.4 2.3 - - - -
384E GLY* 2.9 35.2 + - - +
399E GLY* 1.3 75.1 - - - +
401E GLN* 1.3 67.3 + - - +
402E TYR* 4.2 19.9 - - + -
409E LEU* 4.2 5.6 - - + -
411E LEU 3.4 11.4 - - - +
412E GLY* 4.6 2.0 - - - -
603E C8E 4.6 4.3 - - - -
180G PRO* 4.5 18.6 - - + -
181G PHE* 6.4 0.2 - - + -
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Residues in contact with GLN 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E GLN* 3.6 24.5 - - - +
310E SER* 2.8 29.6 + - - +
311E ASP* 3.7 14.2 - - - +
382E TRP 3.6 7.2 - - - +
383E ALA* 4.5 7.9 - - + -
399E GLY 5.8 0.2 - - - -
400E ALA* 1.3 81.1 - - - +
402E TYR* 1.3 63.4 + - - +
409E LEU* 3.3 8.1 - - - +
410E THR* 2.9 36.2 + - - +
411E LEU* 2.9 37.7 + - + +
437E TYR* 4.7 4.9 + - - -
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Residues in contact with TYR 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E LEU 4.3 0.9 - - - -
381E VAL* 3.4 7.3 - - - +
382E TRP* 2.9 55.7 + - + +
383E ALA* 5.4 0.7 - - - -
400E ALA* 4.2 13.2 - - + -
401E GLN* 1.3 78.2 - - - +
403E ASP* 1.3 62.5 + - - +
408E SER* 3.3 13.2 - - - -
409E LEU* 3.3 53.9 - - + +
410E THR* 4.4 2.2 - - - -
179G GLY* 3.0 41.7 + - - -
180G PRO* 3.0 10.2 - - + +
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Residues in contact with ASP 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E LEU 3.4 5.7 - - - +
381E VAL* 3.7 12.7 - - + +
402E TYR* 1.3 76.4 - - - +
404E THR* 1.3 60.1 + - - +
405E ARG* 2.9 56.1 + - - +
406E LEU* 2.9 38.5 + - + +
407E GLY 3.1 9.5 + - - -
408E SER* 2.9 16.2 + - - +
410E THR* 3.9 16.5 - - + +
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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