Contacts of the strand formed by residues 421 - 429 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323C GLN* 3.1 4.5 - - - -
324C LEU* 2.9 36.4 + - + +
386C TYR* 3.1 31.6 - - + +
419C THR* 4.0 1.3 - - - +
420C ARG* 1.3 80.8 - - + +
422C THR* 1.3 61.7 + - - +
423C PHE* 4.0 3.8 + - + -
442C LEU* 4.4 14.8 - - + -
443C VAL 3.3 8.3 - - - +
444C GLU* 4.7 4.9 - - + -
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Residues in contact with THR 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C PHE* 4.4 20.5 - - + -
321C ILE* 5.4 1.6 - - + -
322C ARG 3.8 10.1 - - - +
323C GLN* 4.0 7.6 - - + +
415C LEU* 5.4 5.8 - - + -
416C ASP* 3.3 22.0 + - - +
419C THR* 3.9 6.1 - - - +
420C ARG 4.3 0.4 + - - -
421C ALA* 1.3 73.2 - - - +
423C PHE* 1.3 75.0 + - - +
424C ILE* 4.0 15.0 + - + -
441C LEU 3.8 2.6 - - - +
443C VAL* 2.9 38.3 + - - +
445C PHE* 5.9 3.3 - - - -
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Residues in contact with PHE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ARG 4.7 0.7 - - - +
321C ILE* 3.3 1.0 - - - -
322C ARG* 2.3 100.4 + - + +
323C GLN 3.9 1.7 - - - +
379C HIS* 3.2 40.6 - + + -
386C TYR* 3.8 19.7 - - - -
421C ALA* 4.0 2.2 + - + -
422C THR* 1.3 74.8 - - - +
424C ILE* 1.3 60.3 + - - +
425C ASP* 4.0 17.3 - - - +
440C ARG* 5.5 0.9 - - + -
441C LEU 3.0 18.6 - - - -
442C LEU* 3.4 29.4 - - + -
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Residues in contact with ILE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C PHE* 6.0 4.3 - - + -
282C PHE* 5.3 12.8 - - + -
283C THR* 5.7 9.4 - - + -
287C LEU* 4.9 15.9 - - + -
319C PRO* 4.4 15.5 - - + -
320C ARG 4.2 3.1 - - - -
321C ILE* 3.6 39.3 - - + -
395C LEU* 5.7 2.5 - - + -
422C THR* 4.0 16.5 + - + -
423C PHE* 1.3 78.2 - - - +
425C ASP* 1.3 70.8 + - - +
426C PHE* 4.9 2.7 - - + -
441C LEU* 3.2 25.7 + - + +
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Residues in contact with ASP 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C PRO* 3.6 0.5 - - - +
320C ARG* 3.1 33.3 + - - +
423C PHE* 4.0 17.6 - - + +
424C ILE* 1.3 87.6 - - - +
426C PHE* 1.3 69.4 + - - +
439C VAL 3.2 7.6 - - - +
440C ARG* 3.1 25.9 + - + +
441C LEU 2.2 43.1 + - - +
545C PHE* 4.9 1.0 - - - -
549C GLU* 6.5 0.9 - - + -
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Residues in contact with PHE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C PHE* 6.0 2.7 - + - -
287C LEU* 4.2 26.2 - - + -
291C LEU* 3.8 31.6 - - + -
315C LEU* 5.2 1.3 - - + -
316C LEU 5.9 0.2 - - - -
319C PRO* 3.3 39.0 - - + -
424C ILE* 4.9 2.2 - - + -
425C ASP* 1.3 81.8 - - - +
427C SER* 1.3 71.4 + - - +
428C VAL* 4.0 19.7 - - + -
438C VAL* 3.9 1.2 - - - +
439C VAL* 2.5 79.8 + - + +
545C PHE* 3.9 18.4 - + + -
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Residues in contact with SER 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LEU* 3.2 25.6 - - - +
426C PHE* 1.3 82.4 - - - +
428C VAL* 1.3 68.7 + - - +
436C PHE* 2.9 21.4 - - - -
437C CYS 2.1 33.9 + - - -
438C VAL* 3.1 18.3 - - - +
439C VAL 3.8 1.6 - - - +
545C PHE* 4.0 7.7 - - - -
548C PHE* 5.1 9.0 - - - -
549C GLU* 6.3 0.4 - - - -
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C TYR* 5.2 0.4 - - - -
253C MET* 3.8 25.8 - - + -
291C LEU* 5.1 4.9 - - + -
309C ILE* 4.9 5.2 - - + -
314C LEU 3.6 5.8 - - - +
315C LEU* 3.6 38.6 - - + -
316C LEU* 3.6 8.7 - - - +
426C PHE* 4.0 20.0 - - + -
427C SER* 1.3 83.7 - - - +
429C TYR* 1.3 59.7 + - - +
436C PHE* 3.3 2.8 - - - -
437C CYS* 2.4 53.7 + - + +
439C VAL* 4.6 8.3 - - + +
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Residues in contact with TYR 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C TYR* 3.8 5.6 + - - -
313C ASN* 3.2 4.0 - - - +
314C LEU* 2.4 83.2 + - + +
316C LEU* 4.0 5.2 - - + -
428C VAL* 1.3 82.9 - - - +
430C ASN* 1.3 72.2 + - - +
431C ALA* 3.5 12.7 + - + -
434C ASN* 2.7 45.1 - - + +
435C LEU 3.3 11.7 - - - -
436C PHE* 3.6 12.6 - + + +
462C LEU* 3.5 27.8 - - + -
334D PRO* 3.9 22.6 - - + +
337D LEU* 4.6 9.2 - - + -
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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