Contacts of the strand formed by residues 378 - 389 (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 GLY 378 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357E ILE 3.5 0.2 - - - +
358E TYR* 3.8 19.1 - - - -
359E TYR* 2.9 33.5 + - - +
377E THR* 1.3 80.8 + - - +
379E SER* 1.3 61.4 + - - -
380E LEU* 2.9 17.5 + - - +
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Residues in contact with SER 379 (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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356E GLN* 2.7 23.8 + - - +
357E ILE 3.3 7.9 + - - -
358E TYR* 3.3 18.9 - - - -
378E GLY* 1.3 66.7 - - - -
380E LEU* 1.3 63.9 + - - +
382E TRP* 3.1 32.9 + - - -
404E THR* 4.1 6.2 + - - -
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Residues in contact with LEU 380 (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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357E ILE 3.0 3.4 + - - -
359E TYR* 4.0 24.5 - - + -
375E ASN* 5.2 9.9 - - - +
376E ALA 4.3 17.5 - - - +
377E THR* 3.8 21.5 - - - +
378E GLY 2.9 15.4 + - - +
379E SER* 1.3 79.6 - - - +
381E VAL* 1.3 62.5 + - + +
382E TRP* 4.2 3.9 + - - -
402E TYR 3.9 0.9 - - - +
403E ASP* 3.4 6.3 - - - +
404E THR* 3.0 49.6 + - + +
405E ARG* 3.8 38.8 - - + +
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Residues in contact with VAL 381 (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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310E SER* 5.1 7.6 - - - +
315E LEU* 3.9 23.3 - - + -
356E GLN* 3.1 6.6 - - - +
357E ILE* 2.8 45.3 + - + +
359E TYR* 4.1 12.6 - - + +
380E LEU* 1.3 81.9 - - - +
382E TRP* 1.3 69.4 + - - +
383E ALA* 5.3 0.4 - - + -
402E TYR 3.4 8.1 - - - +
403E ASP* 3.7 13.7 - - + +
405E ARG* 3.6 26.9 - - - +
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Residues in contact with TRP 382 (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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315E LEU* 4.8 0.4 - - - -
354E VAL* 3.9 24.9 - - + -
355E GLY* 3.4 18.2 - - - -
356E GLN* 3.5 22.2 - - + -
379E SER* 3.1 32.2 + - - -
380E LEU 4.7 2.5 - - - -
381E VAL* 1.3 86.2 - - - +
383E ALA* 1.3 65.3 + - - +
401E GLN* 3.6 1.7 - - - +
402E TYR* 2.9 52.9 + - + +
404E THR* 5.8 1.3 - - - -
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Residues in contact with ALA 383 (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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310E SER* 5.2 1.3 - - - +
311E ASP 3.9 17.0 - - - +
312E TYR* 3.8 11.1 - - - +
315E LEU* 3.8 23.1 - - + -
354E VAL* 3.7 3.3 - - - +
355E GLY* 2.9 32.3 + - - +
381E VAL* 5.3 0.7 - - + -
382E TRP* 1.3 77.9 - - - +
384E GLY* 1.3 59.9 + - - +
400E ALA 3.4 11.2 - - - +
401E GLN* 4.5 7.0 - - + -
402E TYR* 5.6 1.3 - - - -
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Residues in contact with GLY 384 (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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312E TYR* 4.5 6.7 + - - +
353E SER 3.1 12.6 - - - -
354E VAL* 4.4 5.4 - - - -
383E ALA* 1.3 75.5 - - - +
385E ASP* 1.3 64.5 + - - +
399E GLY* 3.2 2.9 - - - -
400E ALA* 2.9 34.8 + - - +
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Residues in contact with ASP 385 (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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312E TYR* 3.2 39.0 - - + +
351E ASN* 3.7 15.4 - - - +
352E VAL* 3.6 2.1 - - - +
353E SER* 2.8 40.5 + - - +
384E GLY* 1.3 75.0 - - - +
386E THR* 1.3 66.5 + - - +
398E GLY 3.2 13.0 - - - +
399E GLY* 4.0 3.4 - - - -
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Residues in contact with THR 386 (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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350E PHE* 4.1 14.9 - - - -
351E ASN* 3.0 14.9 + - - -
352E VAL* 4.4 8.9 - - - +
385E ASP* 1.3 81.4 + - - +
387E PHE* 1.3 67.0 + - - +
388E TRP* 5.4 0.3 - - - +
396E LEU* 6.3 0.4 - - + -
397E LYS* 3.1 8.0 - - - +
398E GLY 2.9 41.5 + - - +
603E C8E 3.8 43.0 + - - +
181G PHE* 5.2 4.7 - - + -
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Residues in contact with PHE 387 (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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348E GLU* 3.8 29.8 - - + -
349E ARG 4.1 3.6 - - - -
350E PHE* 3.4 5.6 - - - -
351E ASN* 2.7 63.9 + - + +
386E THR* 1.3 76.5 + - - +
388E TRP* 1.3 69.4 + - - +
389E ARG* 4.0 28.7 - - + -
395E GLY* 5.5 1.3 - - - -
396E LEU 3.5 4.3 - - - -
397E LYS* 4.2 5.4 - - + -
556E PHE* 3.6 39.3 - + + -
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Residues in contact with TRP 388 (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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349E ARG 3.4 11.0 - - - -
350E PHE* 3.7 16.8 - + + -
386E THR* 5.4 0.9 - - - +
387E PHE* 1.3 81.7 - - - +
389E ARG* 1.3 70.6 + - - +
390E ILE* 3.3 37.2 + - + +
395E GLY* 3.6 1.4 - - - -
396E LEU* 2.8 57.8 + - + +
603E C8E 4.6 7.6 - - - -
604E C8E 3.7 40.1 + - - -
226G ALA* 3.6 27.1 - - + -
227G LYS 5.2 0.9 - - - -
259G PRO* 4.4 15.9 - - + -
260G GLN 3.9 14.4 - - - -
261G PHE* 3.8 32.8 - + + -
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Residues in contact with ARG 389 (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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347E VAL* 3.4 28.1 - - - +
348E GLU 4.4 9.2 + - - -
349E ARG* 2.5 50.3 + - - +
387E PHE* 4.0 18.0 - - + -
388E TRP* 1.3 76.9 + - - +
390E ILE* 1.3 64.5 + - - +
391E ASN 3.4 20.4 + - - +
392E ASP* 3.3 34.6 + - - +
394E LEU 4.0 4.0 - - - +
395E GLY* 4.8 1.3 - - - -
604E C8E 5.6 0.3 - - - +
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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