Contacts of the strand formed by residues 417 - 425 (chain B) in PDB entry 2ZL6
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 VAL 417 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B ILE* 3.8 28.9 - - + -
411B PRO* 5.0 4.0 - - - -
415B GLY 4.2 3.8 - - - +
416B GLU* 1.3 77.4 - - - +
418B LEU* 1.3 65.4 + - - +
419B VAL* 5.1 0.2 - - + -
482B THR* 3.1 24.7 - - - -
483B CYS* 2.9 23.9 + - - +
485B PRO* 3.8 31.4 - - + -
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Residues in contact with LEU 418 (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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254B GLY 4.0 3.6 - - - +
255B ILE* 4.1 6.2 - - - +
256B SER* 4.8 0.6 + - - +
261B GLN 4.0 13.5 - - - +
263B VAL* 4.7 3.6 - - + -
409B VAL* 4.0 29.2 - - + +
410B TYR 4.0 9.4 - - - +
411B PRO* 4.0 25.0 - - + +
417B VAL* 1.3 83.3 - - - +
419B VAL* 1.3 60.6 + - - +
420B PHE* 3.6 41.2 - - + -
436B LEU* 5.0 1.6 - - + -
480B PHE* 3.4 42.8 - - + -
481B LEU 3.7 2.9 - - - +
482B THR* 4.2 2.5 - - + -
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Residues in contact with VAL 419 (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* 3.9 29.6 - - + -
254B GLY 3.8 4.5 - - - +
417B VAL* 4.0 0.7 - - + +
418B LEU* 1.3 76.0 - - - +
420B PHE* 1.3 73.0 + - - +
421B PHE* 4.4 14.9 - - + -
436B LEU* 4.3 18.4 - - - +
473B PHE* 3.7 25.8 - - + -
481B LEU* 2.9 22.9 + - + +
482B THR* 3.8 4.5 - - - -
483B CYS* 3.8 28.3 - - - +
492B PRO* 4.4 7.6 - - + -
501B PHE* 5.3 0.2 - - + -
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Residues in contact with PHE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MET* 3.2 8.1 - - - +
254B GLY 2.8 39.2 + - - +
256B SER* 4.0 19.3 - - - -
263B VAL* 3.9 11.9 - - + -
265B PHE* 3.7 22.7 - + - -
390B TRP* 3.6 32.5 - + - -
418B LEU* 3.6 45.3 - - + -
419B VAL* 1.3 78.3 - - - +
421B PHE* 1.3 64.6 + - - +
422B MET* 3.9 17.5 - - - -
434B PRO* 3.9 3.1 - - + -
435B CYS 3.4 13.7 - - - +
436B LEU* 3.5 21.1 - - + -
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Residues in contact with PHE 421 (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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238B LEU* 3.7 32.5 - - + -
243B ASN* 3.5 5.5 + - - -
250B ILE* 3.7 25.4 - - + -
252B SER 3.8 2.7 - - - -
253B MET* 4.0 17.3 - - + -
419B VAL* 4.4 15.0 - - + -
420B PHE* 1.3 73.6 - - - +
422B MET* 1.3 60.3 + - - +
433B LEU 3.4 2.9 - - - +
434B PRO* 3.5 0.2 - - - +
435B CYS* 2.9 40.3 + - - -
436B LEU 3.2 30.7 - - - -
437B LEU* 4.0 3.6 - - + -
438B PRO* 3.7 25.6 - - + -
441B TYR* 5.3 2.2 - + - -
481B LEU* 4.2 15.9 - - + -
501B PHE* 3.9 20.6 - + - -
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Residues in contact with MET 422 (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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250B ILE* 3.4 3.7 - - - +
251B SER* 2.8 26.7 + - - -
252B SER* 2.8 37.7 + - - +
253B MET 4.0 0.7 - - - -
254B GLY* 3.9 19.7 - - - +
255B ILE 5.7 0.9 - - - +
390B TRP* 4.4 11.7 - - + -
420B PHE* 3.9 14.6 - - - +
421B PHE* 1.3 73.2 - - - +
423B SER* 1.3 64.8 + - - +
432B ASN* 3.6 35.0 - - + +
433B LEU 3.3 4.9 - - - -
434B PRO* 3.6 40.8 - - + -
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Residues in contact with SER 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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243B ASN* 2.9 33.5 + - - +
248B LEU* 3.4 23.1 + - - -
249B PRO 2.8 24.5 + - - -
250B ILE* 3.7 1.9 - - - +
251B SER* 3.6 5.2 - - - -
422B MET* 1.3 74.0 + - - +
424B LYS* 1.3 62.0 + - - +
425B MET 3.5 0.3 + - - -
432B ASN* 3.4 7.5 - - - -
433B LEU* 2.8 35.6 + - - +
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Residues in contact with LYS 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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291A ARG* 4.7 9.3 - - - +
335A PHE* 3.5 59.0 - - + +
520A ACT 4.9 1.6 - - - +
248B LEU* 3.5 19.0 - - - +
249B PRO 4.6 1.6 + - - -
251B SER* 3.6 21.9 + - - +
423B SER* 1.3 72.4 - - - +
425B MET* 1.3 59.0 + - - +
431B TYR 3.4 9.2 - - - +
432B ASN* 4.5 9.9 - - - +
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Residues in contact with MET 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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335A PHE* 4.2 5.3 - - - -
246B ALA* 3.8 18.8 - - + -
248B LEU* 3.7 23.6 - - + -
323B LEU* 4.0 12.3 - - + -
373B LEU* 3.8 21.3 - - + +
374B SER 4.2 12.8 - - - +
375B TRP* 4.2 6.3 - - - -
376B ILE* 3.7 24.7 - - + -
389B LEU* 5.0 1.1 - - + -
423B SER 3.5 2.8 + - - +
424B LYS* 1.3 72.3 - - - +
426B PRO* 1.3 90.6 - - - +
429B GLY 4.5 2.6 - - - +
431B TYR* 3.0 35.7 + - + +
433B LEU* 4.3 9.6 - - + -
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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