Contacts of the strand formed by residues 242 - 246 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I MET* 3.3 25.4 - - + +
218I LYS 3.5 5.9 + - - +
219I ALA* 3.5 18.5 - - + -
220I VAL* 3.2 20.3 + - - -
240I GLY 3.9 1.4 + - - -
241I LYS* 1.3 80.0 - - - +
243I CYS* 1.3 62.1 + - - +
469I ARG* 3.2 9.7 + - - +
470I PHE* 3.0 38.0 + - + +
472I THR 2.8 28.9 + - - -
473I LYS* 3.8 13.3 - - - +
233L TYR* 4.4 9.9 - - - +
458L GLY* 4.2 15.6 + - - +
459L ASP* 3.5 39.7 + - + +
461L HIS* 5.0 6.5 + - - -
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Residues in contact with CYS 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220I VAL* 3.3 16.2 - - - +
232I ILE* 4.3 14.6 - - - -
233I TYR* 3.5 51.0 - - + -
236I ALA* 4.0 16.8 - - + -
237I SER* 4.8 2.9 - - - +
241I LYS 4.4 1.3 - - - +
242I ARG* 1.3 79.9 - - - +
244I GLN* 1.3 74.0 + - - +
245I ALA* 4.2 4.7 - - - -
457I PHE 4.2 0.5 - - - +
458I GLY* 4.3 5.0 - - - -
470I PHE* 3.4 13.2 - - - -
233L TYR* 5.0 3.0 + - - -
459L ASP* 4.4 5.1 + - - +
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Residues in contact with GLN 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I MET* 5.5 0.5 - - - +
220I VAL 3.1 3.2 + - - +
221I SER* 2.5 33.3 + - - +
222I PHE 2.8 33.2 + - - +
243I CYS* 1.3 76.3 - - - +
245I ALA* 1.3 54.6 + - - +
246I LEU* 4.1 11.0 - - + -
456I LEU* 5.9 1.1 - - + -
457I PHE 3.6 7.4 - - - +
458I GLY* 5.5 1.6 - - - -
460I LEU 2.9 36.8 + - - +
461I HIS 3.2 20.9 + - - -
462I ALA* 4.7 8.7 - - - +
463I TYR 5.3 1.6 + - - -
467I ALA* 5.5 2.2 - - - +
470I PHE* 3.7 29.0 - - + +
471I TYR* 3.7 8.1 + - - -
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I PHE* 3.4 16.6 - - + -
229I ALA* 3.5 31.6 - - + +
233I TYR* 4.1 15.9 - - + +
243I CYS* 4.2 4.7 - - - -
244I GLN* 1.3 74.5 - - - +
246I LEU* 1.3 63.6 + - - +
456I LEU* 3.5 0.9 - - - -
457I PHE* 2.8 43.0 + - + +
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Residues in contact with LEU 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I TRP* 4.2 4.0 - - + -
222I PHE* 2.9 25.4 + - - +
223I VAL* 3.6 7.9 - - + -
224I GLY 3.0 26.3 + - - +
229I ALA* 4.1 0.9 - - - -
244I GLN* 4.4 14.4 - - + -
245I ALA* 1.3 83.3 - - - +
247I GLY* 1.3 60.1 + - - +
449I PHE* 3.7 18.6 - - + +
450I GLY* 4.3 5.4 - - - -
451I GLY 5.3 0.7 - - - +
455I SER 3.7 4.9 - - - +
456I LEU* 3.9 19.7 - - + +
461I HIS* 5.7 0.2 - - - -
462I ALA* 3.6 33.7 - - + +
501I NAD 3.1 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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