Contacts of the strand formed by residues 242 - 246 (chain L) in PDB entry 4ZZ7
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 ARG 242 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I TYR* 4.3 9.2 - - - +
458I GLY* 4.0 16.0 + - - +
459I ASP* 3.6 44.8 + - + +
461I HIS* 4.8 6.7 + - - -
139L MET* 3.3 21.8 - - + +
218L LYS 3.6 6.1 + - - +
219L ALA* 3.5 20.1 - - + -
220L VAL* 3.1 21.8 + - - +
240L GLY 3.9 1.2 + - - -
241L LYS* 1.3 79.5 - - - +
243L CYS* 1.3 61.3 + - - +
469L ARG 3.1 7.3 + - - -
470L PHE* 2.9 33.6 + - + +
472L THR 2.8 28.9 + - - -
473L LYS* 3.7 18.4 - - - +
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Residues in contact with CYS 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I TYR* 4.8 4.0 + - - +
459I ASP* 4.4 5.1 + - - +
220L VAL* 3.3 15.9 - - + +
232L ILE* 4.3 13.0 - - - -
233L TYR* 3.4 52.8 + - + +
236L ALA* 3.7 24.0 - - + -
237L SER* 5.2 1.6 - - - +
241L LYS 3.9 1.1 + - - +
242L ARG* 1.3 79.9 - - - +
244L GLN* 1.3 71.7 + - - +
245L ALA* 4.2 1.8 - - - -
458L GLY* 4.2 6.1 - - - -
470L PHE* 3.5 10.1 - - - -
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Residues in contact with GLN 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158L MET* 5.7 0.4 - - - +
220L VAL 3.0 7.4 + - - +
221L SER* 2.8 32.4 + - - +
222L PHE* 2.8 27.8 + - - +
243L CYS* 1.3 75.7 - - - +
245L ALA* 1.3 60.0 + - - +
246L LEU* 4.2 10.6 - - + +
456L LEU* 6.0 0.4 - - + -
457L PHE 3.6 7.6 - - - +
458L GLY* 5.5 0.9 - - - -
460L LEU 2.9 28.6 - - - +
461L HIS 3.0 20.9 + - - +
462L ALA* 3.7 9.1 + - - +
463L TYR 5.4 1.8 - - - +
467L ALA* 5.5 1.0 - - - +
470L PHE* 3.4 29.0 - - + +
471L TYR* 3.8 9.5 + - - -
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Residues in contact with ALA 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L PHE* 3.4 14.4 - - + -
229L ALA* 3.6 35.4 - - + +
233L TYR* 4.2 14.4 - - + +
243L CYS* 4.2 4.7 - - - -
244L GLN* 1.3 73.7 - - - +
246L LEU* 1.3 64.0 - - - +
456L LEU* 3.5 0.7 - - - -
457L PHE* 2.8 44.1 + - + -
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Residues in contact with LEU 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L TRP* 4.3 3.8 - - + -
222L PHE* 3.0 24.7 + - - +
223L VAL* 3.7 9.9 - - + -
224L GLY 3.0 26.5 + - - +
229L ALA* 3.9 2.1 - - - +
244L GLN* 4.5 14.6 - - + +
245L ALA* 1.3 83.4 - - - +
247L GLY* 1.3 58.7 + - - +
449L PHE* 3.6 28.5 - - + +
450L GLY* 4.3 4.5 - - - -
451L GLY 5.2 0.2 - - - +
455L SER 3.8 4.0 - - - +
456L LEU* 3.8 21.1 - - + +
462L ALA* 3.8 22.4 - - + -
501L NAD 2.9 31.0 - - - +
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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