Contacts of the strand formed by residues 436 - 444 (chain D) 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 PHE 436 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D LEU* 3.3 38.4 - - + -
427D SER* 4.5 8.5 - - - -
428D VAL 3.9 3.1 - - - -
429D TYR* 3.2 29.4 - + + -
434D ASN 4.4 2.9 - - - +
435D LEU* 1.3 74.2 - - - +
437D CYS* 1.3 55.5 + - - +
438D VAL* 4.5 1.0 + - + +
460D LEU* 2.5 54.1 + - + +
462D LEU* 4.4 28.9 - - + +
536D LEU* 5.7 1.6 - - + -
540D GLU* 5.0 10.5 - - + -
546D PRO* 6.3 1.3 - - + -
548D PHE* 3.4 53.4 - + + -
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Residues in contact with CYS 437 (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* 3.8 35.9 - - + +
250D THR* 5.9 2.0 - - - -
253D MET* 5.3 6.5 - - - -
427D SER* 2.3 25.2 + - - -
428D VAL* 2.8 31.0 + - + +
435D LEU* 4.2 1.7 + - + -
436D PHE* 1.3 73.8 - - - +
438D VAL* 1.3 69.4 - - - +
439D VAL* 5.1 6.1 - - - -
457D PHE* 4.9 6.3 - - - -
458D GLN 3.1 29.8 - - - +
459D PRO* 3.7 9.4 - - + -
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Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D PHE 4.8 0.2 - - - +
427D SER* 3.2 20.9 - - - +
436D PHE* 4.8 1.6 - - + +
437D CYS* 1.3 74.8 - - - +
439D VAL* 1.3 69.0 + - - +
440D ARG* 5.9 4.3 - - + -
456D GLN 4.1 0.6 - - - +
457D PHE* 3.9 2.3 - - - -
458D GLN* 3.0 48.7 + - + +
460D LEU* 6.1 0.9 - - + -
548D PHE* 3.5 37.2 - - + -
549D GLU* 5.1 14.4 - - + -
552D ALA* 4.9 9.0 - - + -
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Residues in contact with VAL 439 (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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253D MET* 4.0 14.1 - - + -
424D ILE 4.9 0.4 - - - +
425D ASP* 3.4 17.2 - - - +
426D PHE* 3.1 67.4 + - + +
427D SER* 5.2 1.3 - - - -
428D VAL* 5.6 0.9 - - + -
437D CYS* 5.1 4.7 - - - +
438D VAL* 1.3 82.6 - - - +
440D ARG* 1.3 66.4 + - - +
441D LEU* 4.0 15.5 - - + -
456D GLN 3.9 2.5 - - - -
457D PHE* 3.7 31.0 - - + -
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Residues in contact with ARG 440 (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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322D ARG* 3.7 7.1 - - - +
378D SER 4.7 4.4 + - - -
379D HIS* 3.0 45.7 - - - +
423D PHE* 3.1 39.0 - - + -
425D ASP* 3.1 25.6 + - - +
438D VAL* 4.3 4.7 - - + -
439D VAL* 1.3 76.6 - - - +
441D LEU* 1.3 63.5 + - - +
442D LEU* 3.9 6.3 + - + +
455D TRP 3.7 0.9 - - - -
456D GLN* 2.9 52.6 + - + +
549D GLU* 2.9 47.7 + - + -
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Residues in contact with LEU 441 (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* 5.4 6.7 - - + +
258D LEU* 5.0 5.2 - - + -
270D PHE* 4.8 13.9 - - + -
282D PHE* 4.6 15.3 - - + -
287D LEU* 3.7 31.9 - - + -
422D THR 3.5 1.4 - - - +
423D PHE* 3.4 4.2 - - - -
424D ILE* 2.9 48.9 + - + +
425D ASP* 4.0 0.2 + - - -
426D PHE* 4.8 1.3 - - + -
439D VAL* 4.0 14.4 - - + -
440D ARG* 1.3 75.6 - - - +
442D LEU* 1.3 61.0 + - - +
443D VAL* 4.1 3.0 + - + +
454D SER 4.1 4.5 - - - +
455D TRP* 3.6 28.0 - - + -
457D PHE* 4.3 17.0 - - + -
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Residues in contact with LEU 442 (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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654A ARG* 6.0 2.5 - - - +
379D HIS* 3.3 36.6 - - + +
381D GLY* 4.5 7.0 - - - -
382D ILE* 5.5 0.7 - - + +
386D TYR* 5.7 1.6 - - + -
422D THR 3.3 4.9 - - - -
423D PHE* 3.4 24.5 - - + -
440D ARG* 3.9 7.6 + - + +
441D LEU* 1.3 72.9 - - - +
443D VAL* 1.3 60.5 + - - +
444D GLU* 3.6 35.2 - - + +
454D SER* 2.9 54.6 + - - +
455D TRP* 5.4 2.9 - - - +
456D GLN* 6.0 3.4 - - + -
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Residues in contact with VAL 443 (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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270D PHE* 4.0 25.6 - - + -
273D LEU* 5.6 2.2 - - + -
279D PHE* 3.3 42.2 - - + -
420D ARG 3.6 1.6 - - - +
422D THR* 2.9 37.0 + - + +
424D ILE* 5.9 2.0 - - + -
441D LEU* 5.0 4.0 - - + +
442D LEU* 1.3 77.0 - - - +
444D GLU* 1.3 65.3 + - - +
445D PHE* 3.9 8.7 - - + -
451D VAL* 3.7 27.8 - - + -
452D ILE 3.6 5.4 - - - +
453D PRO* 4.9 3.1 - - + -
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Residues in contact with GLU 444 (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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381D GLY* 4.0 3.5 - - - -
382D ILE* 3.0 48.1 + - - +
383D ILE* 3.2 27.5 + - + +
384D ALA 4.6 0.2 - - - +
386D TYR* 4.0 24.5 + - + +
420D ARG 3.7 4.5 - - - -
421D ALA* 5.0 1.1 - - - +
442D LEU* 3.6 24.8 - - + +
443D VAL* 1.3 75.2 - - - +
445D PHE* 1.3 71.8 + - - +
451D VAL* 3.5 1.4 - - - +
452D ILE* 2.8 45.8 + - + +
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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