Contacts of the strand formed by residues 275 - 279 (chain A) in PDB entry 3SMQ
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 VAL 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A LYS* 1.3 70.8 - - - +
276A VAL* 1.3 64.3 + - - +
296A LYS* 3.8 22.9 - - - +
297A LYS* 3.4 27.6 - - + +
299A LEU* 4.7 3.4 - - + -
337A VAL* 4.3 17.0 - - + -
339A LYS 4.3 6.1 - - - +
340A VAL* 3.7 25.1 - - + +
341A ASP* 2.8 49.6 + - - +
342A VAL 3.2 6.9 + - - -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.8 27.6 - - + -
274A LYS* 4.1 7.4 - - + +
275A VAL* 1.3 76.7 - - - +
277A LEU* 1.3 58.4 + - - +
290A ALA* 4.3 4.5 - - + -
295A ALA* 3.9 22.0 - - + -
297A LYS 2.8 11.5 + - - +
298A VAL* 3.3 15.2 - - + -
299A LEU* 2.7 35.7 + - - +
340A VAL* 4.7 2.7 - - - -
342A VAL* 3.3 16.8 - - + +
344A ILE* 3.9 32.8 - - + -
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Residues in contact with LEU 277 (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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276A VAL* 1.3 77.1 - - - +
278A ASP* 1.3 62.9 + - - +
279A VAL* 3.8 9.8 + - + -
299A LEU* 3.5 23.8 - - + +
301A VAL* 3.9 24.5 - - + -
330A ILE* 4.1 13.2 - - + -
335A LEU* 4.6 16.2 - - + -
340A VAL* 4.0 24.0 - - + +
342A VAL 2.8 10.1 + - - +
343A ILE* 3.3 13.7 - - + +
344A ILE* 2.9 26.3 + - - +
364A ALA* 3.9 27.1 - - + -
368A TYR* 4.6 5.8 - - + -
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Residues in contact with ASP 278 (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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276A VAL 4.1 0.8 - - - -
277A LEU* 1.3 70.8 - - - +
279A VAL* 1.3 66.0 + - - +
280A GLY 3.5 2.4 + - - +
281A CYS* 3.3 27.3 - - - +
284A GLY 4.9 0.2 - - - -
286A LEU* 3.5 24.2 + - - +
287A SER* 2.9 40.0 + - - +
298A VAL* 4.6 3.1 - - + +
299A LEU 2.7 12.8 + - - +
300A GLY* 3.6 0.6 - - - -
301A VAL* 3.1 27.0 + - - +
344A ILE* 3.3 20.9 - - + +
345A SER* 4.3 0.7 - - - -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.9 24.0 - - + -
278A ASP* 1.3 67.9 - - - +
280A GLY* 1.3 68.7 + - - +
301A VAL* 4.2 3.8 - - + -
330A ILE* 4.6 12.8 - - + -
343A ILE* 3.9 15.5 - - + -
344A ILE 3.1 6.7 + - - -
345A SER* 2.8 35.3 + - - +
346A GLU 4.5 0.2 + - - -
357A MET* 3.6 8.4 - - + +
360A SER* 4.3 15.7 - - - +
361A VAL* 4.2 26.0 - - + +
364A ALA* 3.9 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