Contacts of the strand formed by residues 277 - 281 (chain A) in PDB entry 4O5A
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 SER 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.4 1.8 - - - -
188A HIS* 3.3 18.7 + - - -
248A THR 2.8 8.6 + - - -
249A ALA* 3.1 9.5 - - - -
250A ILE 2.9 25.9 + - - -
273A PRO 4.2 4.3 + - - -
276A LEU* 1.3 75.8 - - - +
278A ILE* 1.3 63.5 + - - +
336A SER 3.2 8.7 + - - -
337A THR* 3.9 12.3 - - - -
338A ALA 3.1 36.0 + - - -
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.4 3.8 - - + +
252A TYR* 3.7 31.0 - - + +
258A ALA* 4.0 17.0 - - + +
261A GLY 4.2 2.0 - - - -
262A GLU* 3.6 41.1 - - + +
272A VAL* 3.9 17.5 - - + -
276A LEU* 4.0 18.6 + - + -
277A SER* 1.3 79.2 - - - +
279A ILE* 1.3 67.9 + - - +
294A ILE* 4.1 10.3 - - + -
295A THR* 3.9 1.4 + - - +
336A SER* 2.7 40.2 + - - +
337A THR* 3.5 8.0 - - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MSE 3.8 36.6 - - + +
182A HIS* 4.1 11.9 - - + -
183A LEU* 3.7 38.4 - - + -
250A ILE 3.1 6.7 + - - +
251A ILE* 3.5 15.4 - - + +
252A TYR* 2.9 30.5 + - - -
278A ILE* 1.3 77.2 - - - +
280A SER* 1.3 70.6 + - - +
295A THR* 3.3 19.5 - - + +
331A LEU* 4.5 5.2 - - + -
337A THR* 3.5 23.3 - - + -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR 3.8 3.6 - - - -
254A ASN 3.6 0.2 - - - -
255A ASP* 3.3 22.7 + - - -
258A ALA* 3.9 14.6 - - - -
279A ILE* 1.3 75.2 - - - +
281A TRP* 1.3 60.2 + - - +
282A GLY 2.7 25.3 + - - -
287A ASN* 3.5 22.1 + - - -
294A ILE* 4.0 2.3 - - - +
295A THR 2.9 11.8 + - - -
296A ALA* 3.2 1.2 - - - -
297A LEU 2.9 25.8 + - - -
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Residues in contact with TRP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.9 23.4 + - - -
175A ALA* 4.2 5.5 - - + +
176A SER* 3.4 20.2 - - - -
179A MSE 3.5 30.7 - - + -
193A ARG* 4.0 10.1 - - - -
206A ARG* 3.5 57.0 - - + +
210A PHE* 3.7 14.4 - + - -
251A ILE* 4.5 6.5 - - + +
252A TYR 2.8 21.0 + - - +
253A ASP* 3.1 38.7 - - - +
254A ASN* 3.7 6.1 - - - -
279A ILE* 4.1 0.6 + - - +
280A SER* 1.3 68.7 + - - +
282A GLY* 1.3 61.1 + - - +
297A LEU* 4.1 27.5 - - + +
299A ARG* 5.8 6.9 - - + +
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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