Contacts of the strand formed by residues 242 - 248 (chain A) in PDB entry 1SHZ
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 ALA 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A VAL* 5.4 0.4 - - + -
50A LYS 3.1 4.6 + - - +
51A LEU* 3.1 15.1 - - + -
52A LEU 3.0 21.4 + - - -
240A VAL* 3.2 7.0 - - - +
241A THR* 1.3 82.6 - - + +
243A ILE* 1.3 65.8 + - - +
284A THR* 3.7 1.6 - - - -
285A SER* 3.3 14.4 - - - +
287A ILE* 4.2 11.4 - - + -
365A ILE* 4.0 29.6 - - + -
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Residues in contact with ILE 243 (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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52A LEU* 3.5 17.7 - - + +
54A LEU* 3.7 23.1 - - + -
240A VAL* 3.6 12.3 - - + -
242A ALA* 1.3 79.8 - - - +
244A ILE* 1.3 65.8 + - - +
245A PHE* 4.0 13.5 - - + +
275A ILE* 4.1 16.2 - - + -
281A PHE* 3.7 49.1 - - + -
284A THR* 4.2 4.0 - - + -
285A SER 3.0 8.8 + - - +
286A ILE* 3.8 10.9 - - + -
287A ILE* 2.9 29.7 + - - +
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Residues in contact with ILE 244 (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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51A LEU* 3.8 29.8 - - + +
52A LEU 2.9 10.5 + - - -
53A LEU* 3.6 21.6 - - + -
54A LEU 3.1 20.1 + - - +
64A PHE* 6.3 0.7 - - + -
220A MET* 4.8 2.7 - - + -
243A ILE* 1.3 73.4 - - - +
245A PHE* 1.3 59.6 + - - +
246A CYS* 3.5 9.0 + - - -
287A ILE* 3.4 25.1 - - + +
289A PHE* 3.6 47.8 - - + -
358A PHE* 4.8 11.0 - - + -
361A VAL* 4.5 12.3 - - + -
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Residues in contact with PHE 245 (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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54A LEU* 4.0 5.6 - - + +
55A GLY* 3.7 21.1 - - - -
243A ILE* 3.8 8.1 - - + +
244A ILE* 1.3 69.8 - - - +
246A CYS* 1.3 63.8 + - - +
247A VAL* 3.5 26.7 - - + -
268A SER* 3.6 22.9 - - - -
271A LEU* 3.8 17.0 - - + -
272A PHE* 3.6 47.8 - + + -
275A ILE* 3.4 35.9 - - + -
286A ILE* 5.4 1.8 - - + -
287A ILE 3.0 12.3 + - - +
288A LEU* 3.6 4.8 - - + +
289A PHE 2.9 25.3 + - - +
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Residues in contact with CYS 246 (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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53A LEU* 4.4 6.5 - - - -
54A LEU 3.0 17.1 + - - +
55A GLY* 3.5 13.2 - - - -
56A ALA 4.4 1.4 + - - -
59A SER* 3.5 33.1 + - - +
61A LYS* 4.3 10.8 - - + -
64A PHE* 4.0 30.7 - - + -
244A ILE* 3.8 23.8 - - - -
245A PHE* 1.3 74.5 - - - +
247A VAL* 1.3 65.5 + - - +
268A SER* 4.4 0.5 + - - -
289A PHE* 3.5 7.9 - - + +
291A ASN* 5.2 0.9 - - + -
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Residues in contact with VAL 247 (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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59A SER* 4.1 5.8 - - - -
245A PHE* 3.5 27.1 - - + -
246A CYS* 1.3 80.5 - - - +
248A ALA* 1.3 70.8 + - - +
249A LEU* 4.0 2.2 - - + +
265A MET* 4.4 5.4 - - - -
268A SER* 3.2 22.2 - - - +
288A LEU* 4.3 9.2 - - + -
289A PHE 2.8 12.9 + - - +
290A LEU* 4.3 11.0 - - + -
291A ASN* 2.6 37.0 + - - +
329A PHE* 3.7 30.1 - - + -
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Residues in contact with ALA 248 (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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58A GLU 4.2 0.7 - - - +
59A SER* 4.0 12.2 - - - -
247A VAL* 1.3 82.5 - - - +
249A LEU* 1.3 61.7 + - - +
250A SER* 4.4 2.0 - - - +
251A ASP* 2.7 44.5 + - - +
265A MET* 4.2 5.0 - - - +
268A SER* 4.9 0.8 + - - -
291A ASN 3.5 5.2 - - - -
292A LYS* 3.3 32.8 - - + +
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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