Contacts of the strand formed by residues 434 - 440 (chain B) in PDB entry 3EPZ
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 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B VAL* 3.3 5.9 - - - +
413B TYR* 2.6 58.1 + + + -
414B CYS 4.5 0.4 - - - -
415B LYS* 3.7 31.9 - - + -
432B GLU* 3.6 41.7 - - + -
433B LEU* 1.3 76.1 - - - +
435B PHE* 1.3 60.9 + - - +
457B ASN* 3.9 18.8 - - + -
459B GLY* 3.6 24.9 - - - +
460B PRO* 3.9 18.8 - - + -
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Residues in contact with PHE 435 (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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407B LEU* 3.6 32.3 - - + -
410B PHE* 5.8 0.4 - - + -
411B SER 2.9 19.1 - - - +
412B VAL* 4.2 2.5 - - + -
413B TYR* 3.8 4.7 - - - -
434B PHE* 1.3 76.6 - - - +
436B SER* 1.3 59.1 + - - +
457B ASN 3.4 4.3 + - - -
458B LEU* 2.7 62.5 + - + +
459B GLY* 3.8 6.1 - - - +
461B ILE* 3.6 28.0 - - + -
479B PHE* 3.9 23.1 - + + -
481B THR* 3.6 22.4 - - + -
486B TYR* 3.6 33.2 - + - -
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Residues in contact with SER 436 (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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368B GLY* 6.1 0.2 - - - -
369B GLN 5.0 2.9 + - - -
370B HIS* 3.7 28.0 - - - -
407B LEU* 4.7 0.6 - - - +
409B CYS 3.7 1.1 + - - +
410B PHE* 3.0 7.5 - - - +
411B SER* 2.8 49.1 + - - -
413B TYR* 3.7 8.7 - - - -
435B PHE* 1.3 78.3 - - - +
437B GLY* 1.3 58.5 + - - +
455B GLY 3.6 14.1 - - - -
456B LYS* 4.0 1.6 - - - -
458B LEU* 4.0 5.2 - - - -
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Residues in contact with GLY 437 (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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380B MSE 3.1 6.2 - - - +
407B LEU* 3.9 6.7 - - - -
408B THR 3.3 11.4 - - - -
409B CYS* 3.7 8.1 - - - -
410B PHE* 4.3 0.2 - - - -
436B SER* 1.3 77.4 - - - +
438B SER* 1.3 59.2 + - - -
454B ASN* 3.5 9.8 - - - -
455B GLY 2.7 37.9 + - - +
458B LEU* 4.1 2.6 - - - +
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B MSE 3.8 0.4 - - - -
407B LEU* 3.3 5.4 - - - +
408B THR* 2.9 44.2 + - - -
409B CYS* 5.0 2.9 - - - +
437B GLY* 1.3 73.4 - - - -
439B ALA* 1.3 60.4 + - - +
440B LYS* 3.7 5.0 + - - +
450B GLU* 4.1 15.6 + - - -
452B GLY* 3.5 14.2 + - - -
453B VAL 3.2 26.2 + - - -
454B ASN* 3.6 18.1 + - - +
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Residues in contact with ALA 439 (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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380B MSE 3.1 29.0 - - + +
381B LEU* 5.6 1.6 - - + -
405B HIS* 4.6 14.8 - - + -
406B LYS 3.3 13.2 - - - +
407B LEU* 4.2 5.4 - - + -
438B SER* 1.3 70.1 - - - +
440B LYS* 1.3 61.9 + - - +
441B PRO* 4.7 1.0 - - - +
452B GLY* 4.0 0.7 - - - -
453B VAL* 2.7 37.2 + - + +
486B TYR* 4.8 5.6 - - + -
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Residues in contact with LYS 440 (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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405B HIS* 3.5 7.5 - - - +
406B LYS* 3.0 31.6 + - + +
408B THR* 4.8 7.4 - - - +
438B SER* 3.7 8.4 + - - +
439B ALA* 1.3 76.0 - - - +
441B PRO* 1.3 80.6 - - + +
444B ASP* 4.3 8.1 - - + +
445B ASP 3.4 27.1 - - - +
446B ASP* 4.9 7.6 - - - +
450B GLU* 5.4 5.2 - - - -
451B GLY 5.3 7.6 - - - +
452B GLY* 4.3 20.2 - - - +
489B MSE 4.7 8.7 - - - -
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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