Contacts of the strand formed by residues 276 - 279 (chain B) in PDB entry 4LDR
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 PHE 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B VAL* 3.6 32.3 - - + -
245B VAL* 3.5 21.1 - - + -
262B THR* 3.8 20.0 - - + -
265B LEU* 3.9 9.2 - - + -
266B ALA* 3.6 36.6 - - + +
269B ALA* 4.4 9.4 - - + -
275B PRO* 1.3 73.9 - - - +
277B TYR* 1.3 60.2 + - - +
278B VAL* 3.8 22.2 - - + -
328B THR* 4.4 8.7 - - + -
332B LEU 3.5 23.8 - - - +
333B ILE* 3.7 10.0 - - + +
334B THR* 3.1 13.0 + - - +
335B GLY* 2.7 23.4 + - - +
336B GLY 3.5 2.6 + - - -
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLY 5.1 0.2 - - - -
150B HIS* 3.0 30.8 + + + -
151B LEU* 3.3 45.9 - - + -
154B ARG* 3.5 16.6 - - - +
242B ALA* 4.9 0.7 - - + -
243B VAL 2.7 20.3 + - - +
244B VAL* 3.5 7.4 - - + -
245B VAL* 3.0 31.2 + - - +
275B PRO* 3.9 17.7 - - + -
276B PHE* 1.3 78.2 - - - +
278B VAL* 1.3 61.3 + - - +
335B GLY* 3.3 35.6 + - - -
336B GLY* 3.4 7.4 - - - -
338B ILE* 3.8 31.4 - - + -
343B VAL* 4.4 3.4 - - + -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 3.5 9.4 - - + -
246B GLY 3.9 4.5 - - - +
247B ALA* 3.6 30.7 - - + -
250B VAL* 4.2 7.6 - - + -
256B THR* 3.9 27.4 - - + +
262B THR* 5.8 0.2 - - + -
276B PHE* 3.8 22.0 + - + -
277B TYR* 1.3 76.4 - - - +
279B ALA* 1.3 58.0 + - - +
280B ALA* 4.4 0.9 - - + -
328B THR* 6.0 0.2 - - - -
333B ILE* 4.2 16.1 - - + +
336B GLY 3.0 9.4 + - - +
337B ILE* 3.3 10.8 - - + +
338B ILE* 2.6 34.9 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 4.0 12.3 - - + -
180B THR* 3.8 15.3 + - - +
181B ALA* 3.6 29.8 - - + +
184B VAL* 4.6 0.4 - - + -
244B VAL* 4.3 7.4 - - + +
245B VAL 2.8 14.7 + - - +
246B GLY* 3.4 19.6 - - - -
247B ALA 3.7 2.1 + - - -
277B TYR 4.1 0.4 - - - -
278B VAL* 1.3 70.3 - - - +
280B ALA* 1.3 62.7 + - - +
281B PRO* 4.7 0.2 - - - +
338B ILE* 3.5 13.2 - - + -
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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