Contacts of the strand formed by residues 271 - 275 (chain B) in PDB entry 4X61
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 LEU 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B VAL* 3.9 34.1 - - + -
237B VAL* 4.2 9.6 - - + -
261B LEU* 3.9 16.6 - - + -
262B VAL 3.7 31.2 - - - +
263B PHE* 3.7 31.2 - - + -
270B PHE* 1.3 73.6 - - - +
272B ALA* 1.3 64.0 + - - +
273B SER 3.8 0.3 + - - -
281B ALA 3.5 0.5 - - - +
282B VAL* 3.3 6.2 - - - -
283B LEU* 2.9 52.0 + - + +
284B ASP 5.2 2.5 - - - +
287B LEU* 4.2 12.3 - - + -
305B TRP* 4.8 2.0 - - - -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLY 3.9 0.5 - - - +
261B LEU* 3.3 10.2 - - - +
262B VAL* 2.8 42.9 + - + +
270B PHE 4.2 0.4 - - - -
271B LEU* 1.3 72.8 - - - +
273B SER* 1.3 59.4 + - - +
274B LEU* 4.2 1.7 - - - +
280B LEU* 4.3 2.7 - - + -
281B ALA 3.4 4.5 - - - -
282B VAL* 4.6 2.2 - - - -
303B ALA* 4.2 18.2 - - + -
305B TRP* 3.9 15.3 - - + +
313B LEU* 4.0 21.3 - - + -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 3.8 10.9 - - - +
253B VAL* 3.7 7.6 - - - +
254B HIS* 2.8 40.3 + - - -
258B VAL* 4.2 1.9 - - - +
260B GLY 3.8 4.0 - - - -
261B LEU* 4.0 10.8 - - - +
272B ALA* 1.3 74.0 - - - +
274B LEU* 1.3 59.9 + - - +
280B LEU* 3.6 4.1 - - - +
281B ALA* 2.8 40.8 + - - -
283B LEU* 4.3 12.3 - - - -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B HIS* 4.0 0.7 - - - -
258B VAL* 3.5 6.4 - - - +
259B THR* 2.7 31.7 + - - -
260B GLY* 3.2 42.6 + - - +
261B LEU* 5.0 0.7 - - - -
262B VAL* 5.3 3.8 - - + +
272B ALA* 4.6 6.3 - - + +
273B SER* 1.3 74.3 + - - +
275B SER* 1.3 55.1 + - - +
279B SER 3.9 3.6 - - - -
280B LEU* 4.9 3.1 - - + +
300B VAL* 3.7 26.2 - - + +
301B ARG 3.4 36.1 - - - +
302B ASP* 3.5 5.2 - - - +
303B ALA* 3.6 35.2 - - + +
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Residues in contact with SER 275 (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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254B HIS* 3.2 35.7 - - - -
256B GLN 2.8 22.9 + - - -
257B CYS 2.9 8.6 + - - -
259B THR* 3.8 7.4 - - - -
274B LEU* 1.3 74.0 - - - +
276B GLU* 1.3 67.9 + - - +
277B ASP* 3.2 20.8 + - - -
278B CYS 3.6 4.2 + - - -
279B SER 3.5 6.3 + - - -
300B VAL* 3.5 25.5 + - - +
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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
------------------------------------------------------------
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