Contacts of the strand formed by residues 422 - 430 (chain B) in PDB entry 5MKF
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 THR 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B PHE* 3.6 32.8 - - + -
321B ILE* 5.1 7.9 - - + -
322B ARG 3.5 5.4 - - - +
323B GLN* 4.3 6.3 - - + +
414B TRP* 6.3 0.2 - - - +
415B LEU* 4.8 6.9 - - + +
419B THR* 3.8 18.4 - - - +
421B ALA* 1.3 77.6 + - - +
423B PHE* 1.3 74.7 + - - +
424B ILE* 5.3 1.3 - - + -
441B LEU 3.5 1.0 - - - +
442B LEU* 3.3 0.7 - - - -
443B VAL* 2.9 50.7 + - - +
445B PHE* 4.0 8.4 - - - -
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ILE* 3.2 8.8 - - - +
322B ARG* 2.4 100.3 + - + +
379B HIS* 4.2 12.1 - + + -
386B TYR* 4.2 31.9 - + + -
421B ALA* 4.5 8.1 - - + -
422B THR* 1.3 81.4 - - - +
424B ILE* 1.3 66.0 + - - +
425B ASP* 4.6 14.4 - - - +
440B ARG* 3.1 25.4 - - + -
441B LEU 3.4 2.7 - - - +
442B LEU* 3.4 28.0 - - + -
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B PHE* 4.3 18.4 - - + -
282B PHE* 4.7 13.9 - - + -
283B THR* 4.3 24.2 - - + -
287B LEU* 4.4 21.1 - - + -
319B PRO* 4.9 7.4 - - + -
320B ARG 3.6 4.7 - - - +
321B ILE* 4.2 20.2 - - + -
395B LEU* 5.8 2.0 - - + -
422B THR* 5.3 0.7 - - + -
423B PHE* 1.3 79.0 - - - +
425B ASP* 1.3 73.1 + - - +
426B PHE* 4.6 11.4 - - + -
439B VAL* 3.7 1.9 - - - +
440B ARG* 3.6 1.2 - - - -
441B LEU* 2.9 40.5 + - + +
443B VAL* 5.9 2.0 - - + -
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B VAL 4.1 1.2 - - - +
319B PRO* 3.0 1.8 - - - +
320B ARG* 2.4 53.8 + - + +
322B ARG* 5.2 6.5 + - - +
423B PHE* 4.6 13.3 - - - +
424B ILE* 1.3 93.8 + - - +
426B PHE* 1.3 60.5 + - - +
439B VAL 3.4 3.8 - - - +
440B ARG* 3.1 42.8 + - - +
441B LEU 4.0 0.3 + - - -
545B PHE* 4.5 11.7 - - + -
549B GLU* 5.2 6.5 - - + +
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Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B MET* 4.0 17.3 - - + -
257B PHE* 4.5 11.0 - + - -
287B LEU* 3.9 22.2 - - + -
291B LEU* 3.7 36.3 - - + -
315B LEU* 4.8 3.8 - - + -
318B VAL 4.5 3.8 - - - +
319B PRO* 3.5 31.0 - - + -
424B ILE* 4.6 7.4 - - + -
425B ASP* 1.3 74.6 - - - +
427B SER* 1.3 75.0 + - - +
428B VAL* 4.3 6.5 - - + -
438B VAL* 4.8 0.3 - - - +
439B VAL* 3.1 66.4 + - + +
441B LEU* 4.8 2.7 - - + -
545B PHE* 4.9 6.1 - - - -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LEU* 3.2 9.2 - - - +
316B LEU* 3.2 36.2 + - - +
426B PHE* 1.3 83.1 - - - +
428B VAL* 1.3 65.6 + - - +
436B PHE* 4.5 7.7 - - - -
437B CYS 2.3 33.7 + - - -
438B VAL* 3.2 21.3 - - - +
439B VAL* 4.4 0.7 - - - +
545B PHE* 5.0 10.0 - - - -
548B PHE* 5.6 3.1 - - - -
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR* 3.7 21.5 - - - +
253B MET* 4.3 20.6 - - + -
291B LEU* 5.0 5.8 - - + -
309B ILE* 5.5 7.9 - - + -
313B ASN* 5.4 4.9 - - + +
314B LEU 3.2 13.0 - - - +
315B LEU* 3.6 20.0 - - + -
316B LEU* 4.0 7.6 - - - -
426B PHE* 4.3 14.1 - - + -
427B SER* 1.3 86.1 + - - +
429B TYR* 1.3 62.2 + - - +
436B PHE* 3.8 3.6 - - - -
437B CYS* 2.8 40.9 + - + +
439B VAL* 5.6 1.1 - - + -
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Residues in contact with TYR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR* 4.9 1.3 - - - -
313B ASN* 3.6 4.9 - - - +
314B LEU* 2.7 65.2 + - + +
316B LEU* 3.6 18.6 - - + +
428B VAL* 1.3 76.3 - - - +
430B ASN* 1.3 79.0 + - - +
431B ALA* 3.5 14.2 + - + -
434B ASN* 2.9 40.9 + - - +
435B LEU 3.8 2.7 - - - -
436B PHE* 3.2 26.7 - + + -
462B LEU* 6.4 0.4 - - + -
463B ILE* 6.1 2.4 - - + +
333C ILE* 5.2 3.5 - - + +
334C PRO* 4.2 12.5 - - - +
337C LEU* 3.8 29.8 - - + +
341C ILE* 5.9 1.3 - - + -
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Residues in contact with ASN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR* 4.2 14.4 + - + +
312B GLU 2.8 23.0 - - - +
313B ASN* 2.8 13.7 - - - +
429B TYR* 1.3 84.9 - - - +
431B ALA* 1.3 64.5 + - - +
432B ASN* 3.4 12.0 + - - +
433B ILE* 3.2 41.8 - - - +
434B ASN* 3.1 15.1 - - - -
435B LEU* 2.6 24.3 + - + +
448C THR* 4.1 15.1 - - - +
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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