Contacts of the strand formed by residues 252 - 259 (chain C) in PDB entry 5BZZ
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 ASP 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PRO 5.0 0.4 - - - -
97C GLN* 3.4 14.1 - - + +
98C LEU* 2.9 26.2 + - - +
174C TYR* 3.0 26.6 + - - +
188C TYR* 5.4 0.2 - - - -
219C GLN* 3.8 16.9 - - - +
220C LEU* 3.8 8.2 + - - +
250C CYS 3.5 2.0 + - - -
251C GLY* 1.3 70.3 - - - -
253C ILE* 1.3 65.4 + - - +
274C TRP* 4.0 16.1 - - + -
275C VAL 3.7 2.0 - - - -
276C ASN* 2.5 30.2 + - - +
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Residues in contact with ILE 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PHE* 5.5 4.0 - - + -
217C VAL* 3.9 25.4 - - + -
218C CYS 3.5 1.6 - - - +
219C GLN* 3.7 21.8 - - + +
224C ILE* 5.2 0.4 - - + -
249C VAL* 3.9 14.8 - - + -
250C CYS 3.7 24.2 - - - +
251C GLY 3.5 10.1 - - - +
252C ASP* 1.3 82.2 - - - +
254C LYS* 1.3 61.2 + - - +
255C VAL* 4.1 13.6 + - + -
273C PHE* 3.8 2.0 - - + +
274C TRP* 3.3 7.7 - - - -
275C VAL* 2.8 46.6 + - + +
277C THR* 3.7 14.8 - - + +
347C PHE* 6.2 3.6 - - + -
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASN* 3.4 23.6 + - - +
216C VAL 3.8 1.0 - - - +
217C VAL* 3.4 3.6 - - - +
218C CYS* 2.8 53.0 + - + +
253C ILE* 1.3 72.9 - - - +
255C VAL* 1.3 68.7 + - - +
256C GLU* 3.7 24.5 + - + +
272C HIS* 3.6 28.3 + - - -
273C PHE 3.4 8.3 - - - +
274C TRP* 3.6 37.4 - - + +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PHE* 4.2 18.6 - - + -
198C MET* 3.9 21.5 - - + -
215C PHE* 4.6 5.4 - - + -
216C VAL 3.5 7.4 - - - +
217C VAL* 4.3 6.7 - - + -
253C ILE* 4.1 16.6 - - + -
254C LYS* 1.3 78.5 - - - +
256C GLU* 1.3 64.8 + - - +
257C PHE* 4.0 11.4 - - + -
272C HIS* 3.2 3.9 - - - +
273C PHE* 2.9 72.3 + - + -
345C LEU* 5.6 0.2 - - + -
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 3.2 4.7 - - - +
216C VAL* 3.0 38.3 + - + +
254C LYS* 3.7 21.9 + - + +
255C VAL* 1.3 77.9 - - - +
257C PHE* 1.3 66.4 + - - +
258C PHE* 3.5 38.0 - - + -
269C LYS* 4.3 17.9 + - + +
271C PHE 3.7 5.2 - - - +
272C HIS* 3.7 22.8 - - + +
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C MET* 3.7 41.1 - - + -
200C PHE* 3.6 29.8 - + - -
213C PRO* 4.2 8.5 - - + -
214C GLN 3.3 13.2 - - - -
215C PHE* 3.6 13.0 - + + -
241C PHE* 3.8 24.5 - + - -
255C VAL* 4.0 9.9 - - + -
256C GLU* 1.3 78.3 - - - +
258C PHE* 1.3 65.9 + - - +
269C LYS* 3.9 1.0 - - - +
270C MET* 2.9 26.5 + - + -
271C PHE* 2.8 57.1 + + + +
273C PHE* 4.9 1.6 - + - -
343C VAL* 4.9 0.7 - - + -
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Residues in contact with PHE 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PRO* 3.2 6.2 - - - +
214C GLN* 2.7 59.2 + - + +
216C VAL* 3.8 24.2 - - + -
256C GLU* 3.5 45.8 - - + -
257C PHE* 1.3 78.5 - - - +
259C HIS* 1.3 61.5 + - - +
260C LYS 4.0 0.2 - - - -
267C LYS* 3.7 41.7 - - + -
268C ASP 3.2 15.5 - - - +
269C LYS* 3.9 24.2 - - + -
270C MET* 3.7 5.5 - - - +
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Residues in contact with HIS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C PHE* 3.7 22.0 - - + -
207C SER* 3.8 27.6 - - - -
211C CYS* 3.6 12.5 - - - +
212C ASN* 3.2 33.1 + - + -
258C PHE* 1.3 72.8 - - - +
260C LYS* 1.3 65.3 + - - +
261C GLN* 3.9 23.5 + - + +
267C LYS* 3.4 2.7 - - - -
268C ASP* 2.6 62.9 + - + +
270C MET* 3.5 19.7 - - + +
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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