Contacts of the strand formed by residues 269 - 273 (chain A) in PDB entry 4V0P
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 TYR 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO* 3.7 4.3 - - - +
218A GLU* 3.0 40.1 + - - +
219A GLU* 4.3 2.9 + - - +
258A TYR* 3.1 47.1 - + + +
259A ARG 3.3 4.5 - - - +
260A GLN* 3.6 33.7 + - + -
261A VAL* 3.9 4.8 - - - +
267A ALA* 3.7 33.6 - - + +
268A CYS* 1.3 77.7 - - - +
270A GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A CYS* 3.2 27.1 - - + -
216A ALA 3.2 18.6 - - - +
217A PRO* 4.2 2.6 - - + +
218A GLU 4.1 1.8 - - - +
257A GLU 3.9 0.3 - - - +
258A TYR* 3.6 5.8 - - - -
259A ARG* 2.8 76.9 + - + +
261A VAL* 3.6 26.3 - - + +
262A PRO* 3.6 12.6 - - - +
269A TYR* 1.3 74.3 - - - +
271A PHE* 1.3 66.7 + - - +
272A LEU* 4.8 1.0 - - + +
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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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205A VAL* 5.6 0.9 - - + -
209A ILE* 3.7 21.1 - - + +
215A CYS* 3.3 5.7 - - - +
216A ALA 2.8 34.4 + - - +
218A GLU* 3.9 14.6 - - + -
221A ILE* 3.7 24.2 - - + -
222A TRP* 3.8 20.2 - + - -
247A THR* 3.6 30.5 - - - -
251A VAL* 4.0 19.1 - - + -
256A LEU* 3.8 18.6 - - + -
257A GLU 3.4 11.9 - - - -
258A TYR* 3.5 32.1 - + + -
270A GLU* 1.3 73.7 - - - +
272A LEU* 1.3 61.3 - - - +
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Residues in contact with LEU 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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209A ILE* 4.1 10.5 - - - -
214A ASP 3.6 17.3 - - - +
215A CYS* 4.0 5.2 - - + -
256A LEU* 3.4 7.3 - - - +
257A GLU* 2.8 62.7 + - + +
259A ARG* 3.4 53.2 - - + +
270A GLU* 4.8 1.8 - - + +
271A PHE* 1.3 78.3 - - - +
273A TRP* 1.3 84.8 + - - +
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Residues in contact with TRP 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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206A LEU* 3.0 55.1 + - + +
209A ILE* 3.7 21.3 - - + +
210A ALA* 4.4 1.6 - - + -
214A ASP 4.7 1.4 + - - -
255A TYR 3.9 3.6 - - - -
256A LEU* 4.8 0.4 - - - -
257A GLU* 4.2 0.9 - - - +
272A LEU* 1.3 91.9 - - - +
274A GLY* 1.3 66.2 + - - +
277A ALA* 3.6 25.4 - - + -
278A LEU* 3.9 27.8 - - + +
281A THR* 3.7 17.3 - - + -
282A SER* 3.4 39.3 - - - -
283A TYR* 3.4 29.8 + + + +
286A VAL* 3.5 20.4 - - + -
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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