Contacts of the strand formed by residues 421 - 429 (chain D) in PDB entry 5MKE
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 ALA 421 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D GLN 3.1 4.3 - - - -
324D LEU* 2.9 36.9 + - + +
384D ALA 5.7 0.4 - - - +
386D TYR* 3.1 31.9 - - + +
419D THR* 4.3 0.9 - - - -
420D ARG* 1.3 81.0 - - + +
422D THR* 1.3 62.7 + - - +
423D PHE* 4.0 3.5 + - + -
442D LEU* 4.4 14.1 - - + -
443D VAL 3.3 7.4 - - - +
444D GLU* 4.7 5.6 - - + -
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Residues in contact with THR 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D PHE* 4.4 20.5 - - + -
321D ILE* 5.4 1.8 - - + -
322D ARG 3.8 10.1 - - - +
323D GLN* 4.0 6.8 - - + +
415D LEU* 5.4 5.4 - - + -
416D ASP* 3.3 22.6 + - - +
419D THR* 3.9 6.1 - - - +
420D ARG 5.4 0.2 + - - -
421D ALA* 1.3 74.1 - - - +
423D PHE* 1.3 74.9 + - - +
424D ILE* 4.0 15.7 + - + -
441D LEU 3.8 2.4 - - - +
443D VAL* 2.9 37.8 + - + +
445D PHE* 5.9 3.1 - - - -
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Residues in contact with PHE 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ARG 4.7 0.4 - - - +
321D ILE* 3.5 0.7 - - - -
322D ARG* 2.3 101.8 + - + +
323D GLN 3.9 1.3 - - - +
379D HIS* 3.2 40.4 - + + -
386D TYR* 3.8 20.6 - - - -
421D ALA* 4.0 2.8 + - + -
422D THR* 1.3 75.9 - - - +
424D ILE* 1.3 58.6 + - - +
425D ASP* 4.0 17.0 - - + +
440D ARG* 5.5 1.1 - - + -
441D LEU 3.0 17.9 - - - -
442D LEU* 3.4 28.9 - - + -
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Residues in contact with ILE 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D PHE* 6.0 4.7 - - + -
282D PHE* 5.3 14.4 - - + -
283D THR* 5.7 9.4 - - + -
287D LEU* 4.9 15.7 - - + -
319D PRO* 4.4 15.0 - - + -
320D ARG 4.2 3.4 - - - -
321D ILE* 3.6 39.7 - - + -
395D LEU* 5.7 3.1 - - + -
422D THR* 4.0 15.6 + - + -
423D PHE* 1.3 78.9 - - - +
425D ASP* 1.3 70.5 + - - +
426D PHE* 4.9 2.2 - - + -
441D LEU* 3.2 25.2 + - + +
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Residues in contact with ASP 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D PRO* 3.6 0.5 - - - +
320D ARG* 3.1 33.0 + - - +
423D PHE* 4.0 18.0 - - + +
424D ILE* 1.3 90.5 - - - +
426D PHE* 1.3 70.1 + - - +
439D VAL 3.2 8.1 - - - +
440D ARG* 3.1 25.9 + - + +
441D LEU 2.2 42.1 + - - +
545D PHE* 4.9 1.3 - - - -
549D GLU* 6.5 1.3 - - + -
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Residues in contact with PHE 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PHE* 6.0 2.9 - + - -
287D LEU* 4.2 26.9 - - + -
291D LEU* 3.8 30.3 - - + -
315D LEU* 5.2 1.6 - - + -
316D LEU 5.9 0.2 - - - -
319D PRO* 3.3 40.2 - - + -
424D ILE* 4.9 3.1 - - + -
425D ASP* 1.3 81.5 - - - +
427D SER* 1.3 70.9 + - - +
428D VAL* 4.0 19.7 - - + -
438D VAL* 3.6 1.4 - - - +
439D VAL* 2.5 80.7 + - + +
545D PHE* 3.9 18.2 - + + -
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Residues in contact with SER 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LEU* 3.2 23.9 - - - +
426D PHE* 1.3 81.6 - - - +
428D VAL* 1.3 70.7 + - - +
436D PHE* 2.9 22.2 - - - -
437D CYS 2.1 33.7 + - - -
438D VAL* 3.1 18.0 - - - +
439D VAL* 3.8 2.0 - - - +
545D PHE* 4.0 7.2 - - - -
548D PHE* 5.1 9.0 - - - -
549D GLU* 6.3 0.9 - - - -
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Residues in contact with VAL 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D TYR* 5.2 0.2 - - - -
253D MET* 3.8 25.6 - - + -
291D LEU* 5.1 6.3 - - + -
309D ILE* 5.7 3.8 - - + -
314D LEU 3.6 6.1 - - - +
315D LEU* 3.6 38.6 - - + -
316D LEU* 3.6 10.1 - - - +
426D PHE* 4.0 20.9 - - + -
427D SER* 1.3 83.6 - - - +
429D TYR* 1.3 58.0 + - - +
436D PHE* 3.3 2.6 - - - -
437D CYS* 2.4 52.5 + - + +
439D VAL* 4.6 8.1 - - + -
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Residues in contact with TYR 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A PRO* 3.8 22.2 - - + +
337A LEU* 4.6 8.1 - - + -
249D TYR* 3.8 5.2 - - - -
253D MET* 5.3 0.2 - - - -
313D ASN* 3.2 3.9 - - - +
314D LEU* 2.4 83.4 + - + +
316D LEU* 4.0 5.2 - - + -
428D VAL* 1.3 83.5 - - - +
430D ASN* 1.3 73.6 + - - +
431D ALA* 3.5 14.0 + - + -
434D ASN* 2.7 45.6 - - + +
435D LEU 3.3 11.9 - - - -
436D PHE* 3.6 14.4 - + + +
462D LEU* 3.5 27.1 - - + -
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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