Contacts of the strand formed by residues 270 - 275 (chain A) in PDB entry 3U8Z
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 GLU 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG 5.0 0.2 - - - +
226A ASN 5.1 0.2 - - - -
227A LYS* 3.3 39.5 + - - +
265A SER 4.0 0.3 - - - +
266A TYR* 3.5 5.9 - - - -
267A SER* 2.9 36.0 + - - +
268A ASP 3.2 4.4 + - - +
269A LYS* 1.4 76.8 - - - +
271A PHE* 1.4 65.6 - - - +
272A THR* 4.8 4.7 + - - +
284A LYS* 3.7 7.7 - - + -
285A PHE* 3.3 31.3 + - - +
286A ASN* 3.2 27.5 + - - +
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Residues in contact with PHE 271 (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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264A ILE* 4.7 7.9 - - + -
265A SER 3.4 6.5 - - - +
266A TYR* 3.6 28.0 - + + -
269A LYS 4.3 2.9 - - - -
270A GLU* 1.4 72.8 - - - +
272A THR* 1.3 65.2 + - - +
273A ILE* 4.2 0.7 - - + -
283A PHE 3.7 0.8 - - - +
284A LYS* 3.2 6.1 - - - +
285A PHE* 2.7 78.6 + + + +
287A SER* 4.0 10.5 - - - -
293A ASN* 3.6 40.6 - - + -
296A ILE* 3.6 27.4 - - + -
297A LEU* 3.7 28.7 - - + -
300A CYS* 6.1 0.7 - - - -
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Residues in contact with THR 272 (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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263A ASN* 4.9 0.3 - - - +
264A ILE* 3.3 7.6 - - - +
265A SER* 2.9 47.1 + - - +
270A GLU* 4.8 5.2 + - - +
271A PHE* 1.3 76.9 + - - +
273A ILE* 1.3 62.3 + - - +
274A LYS* 3.8 26.2 + - + -
282A VAL* 4.5 7.9 - - + -
283A PHE 3.5 3.6 - - - +
284A LYS* 3.5 42.8 - - + +
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Residues in contact with ILE 273 (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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234A LEU* 4.9 0.2 - - + -
241A LEU* 3.8 26.7 - - + -
243A ILE* 4.7 4.3 - - + -
256A PHE* 4.0 39.5 - - + -
261A ILE* 4.0 34.1 - - + -
263A ASN 4.0 1.8 - - - -
264A ILE* 4.5 6.1 - - + -
271A PHE* 5.7 0.2 - - + -
272A THR* 1.3 72.6 - - - +
274A LYS* 1.3 62.6 + - - +
275A PRO* 3.4 6.8 - - - +
282A VAL* 3.5 2.8 - - - +
283A PHE* 2.8 47.5 + - + +
285A PHE* 3.6 30.3 - - + -
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Residues in contact with LYS 274 (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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261A ILE* 3.7 2.3 - - - +
262A ARG* 2.8 36.4 + - + +
263A ASN* 2.9 46.8 + - - +
265A SER* 4.4 11.2 - - - -
272A THR* 4.1 15.5 - - + +
273A ILE* 1.3 74.2 - - - +
275A PRO* 1.4 65.0 - - + +
282A VAL* 4.0 17.0 - - + -
284A LYS* 6.0 0.9 - - - +
181C PRO* 4.1 17.6 - - - +
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Residues in contact with PRO 275 (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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256A PHE* 4.3 17.7 - - + -
260A GLU 3.5 11.4 - - - +
261A ILE* 4.5 1.1 - - - -
262A ARG* 3.7 10.5 - - - +
273A ILE* 3.4 10.5 - - + +
274A LYS* 1.4 88.1 - - + +
276A LEU* 1.3 63.9 + - - +
277A ASP 3.7 15.9 - - - +
278A LYS* 5.4 2.9 - - - +
280A ILE* 3.8 29.2 - - + +
281A ASP 3.4 24.7 - - - +
282A VAL* 3.9 11.2 - - + -
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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