Contacts of the strand formed by residues 420 - 425 (chain A) 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 PHE 420 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A MET* 3.2 7.6 - - - +
254A GLY 2.8 36.6 + - - +
256A SER* 3.7 27.8 - - - -
263A VAL* 3.9 16.6 - - + -
265A PHE* 3.7 22.4 - + - -
390A TRP* 3.7 27.6 - + + -
418A LEU* 3.6 40.8 - - + -
419A VAL* 1.3 75.2 - - - +
421A PHE* 1.3 64.0 + - - +
422A MET* 3.9 17.9 - - - -
434A PRO* 4.0 3.6 - - + -
435A CYS 3.4 12.6 - - - +
436A LEU* 3.6 21.5 - - + -
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LEU* 3.8 33.7 - - + -
243A ASN* 3.6 3.8 + - - -
250A ILE* 3.8 25.8 - - + -
252A SER 3.7 2.9 - - - -
253A MET* 3.9 15.7 - - + -
419A VAL* 4.4 14.8 - - + -
420A PHE* 1.3 73.0 - - - +
422A MET* 1.3 59.0 + - - +
435A CYS* 2.9 46.3 + - - -
436A LEU 3.2 30.1 - - - -
437A LEU* 4.1 3.1 - - + -
438A PRO* 3.8 27.6 - - + -
441A TYR* 5.3 2.0 - + - -
481A LEU* 4.2 15.3 - - + -
501A PHE* 3.9 20.4 - + - -
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Residues in contact with MET 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE* 3.5 3.5 - - - +
251A SER* 2.8 33.8 + - - +
252A SER* 2.8 36.0 + - - +
253A MET 4.2 0.2 - - - -
254A GLY* 4.0 18.4 - - - +
255A ILE 5.6 0.4 - - - +
390A TRP* 4.2 13.7 - - + -
420A PHE* 3.9 15.0 - - - -
421A PHE* 1.3 72.8 - - - +
423A SER* 1.3 60.3 + - - +
432A ASN* 3.9 26.9 - - + +
433A LEU 3.3 7.0 - - - -
434A PRO* 3.7 41.1 - - + -
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Residues in contact with SER 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASN* 2.9 31.4 + - - +
248A LEU* 3.5 23.5 + - - -
249A PRO 2.7 23.8 + - - -
250A ILE* 3.6 1.6 - - - +
251A SER* 3.5 7.2 - - - -
422A MET* 1.3 73.1 + - - +
424A LYS* 1.3 65.3 + - - +
432A ASN* 3.5 5.4 - - - +
433A LEU* 2.8 32.7 + - - -
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.5 17.0 - - - +
249A PRO 4.7 0.8 + - - -
251A SER* 4.0 18.7 + - - +
423A SER* 1.3 73.0 - - - +
425A MET* 1.3 59.2 + - - +
426A PRO* 3.8 1.6 - - - +
430A ALA* 5.0 11.8 - - - +
431A TYR 3.4 8.5 - - - +
432A ASN* 2.8 33.5 + - - +
335B PHE* 3.4 31.1 - - + -
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Residues in contact with MET 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ALA* 3.7 29.6 - - + -
248A LEU* 3.7 13.5 - - + -
323A LEU* 4.0 10.5 - - + -
373A LEU* 3.8 21.8 - - + +
374A SER 4.3 11.9 - - - +
375A TRP* 4.4 1.3 - - - -
376A ILE* 3.6 30.1 - - + -
389A LEU* 4.7 7.4 - - + -
423A SER 3.9 0.8 + - - -
424A LYS* 1.3 71.5 - - - +
426A PRO* 1.3 93.1 - - - +
427A GLY 3.7 0.7 + - - -
429A GLY 4.6 2.9 - - - +
431A TYR* 3.0 34.6 + - + +
433A LEU* 4.2 5.2 - - + -
335B PHE* 4.3 5.0 - - - -
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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