Contacts of the strand formed by residues 246 - 249 (chain A) in PDB entry 1ITU
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A VAL 3.0 7.3 + - - +
216A ILE* 3.0 13.2 - - + +
217A PHE* 2.9 28.0 + - - -
240A VAL* 4.6 0.4 - - - -
245A SER* 1.3 82.2 - - - +
247A VAL* 1.3 63.3 + - - +
248A MET* 3.8 19.3 - - + -
282A ALA* 3.5 12.1 - - - +
283A VAL 3.4 35.7 - - - +
284A GLY* 3.8 4.0 - - - +
329A ASN* 3.8 13.2 - - + +
330A LEU* 3.5 46.7 - - + +
332A ARG* 5.0 0.2 - - - +
333A VAL* 3.8 12.1 - - + -
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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
----------------------------------------------------------
217A PHE* 3.9 26.7 - - + -
220A SER 3.3 26.7 - - - +
221A SER 4.8 0.4 - - - +
232A VAL* 4.3 10.1 - - + -
237A LEU* 3.9 24.0 - - + -
240A VAL* 4.1 16.6 - - + -
246A LEU* 1.3 74.4 - - - +
248A MET* 1.3 60.7 + - - +
249A VAL* 3.6 4.7 + - - +
274A ILE* 3.8 24.6 - - + +
282A ALA 2.9 16.3 + - - +
283A VAL* 3.7 1.9 - - - +
284A GLY 3.2 20.0 + - - +
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Residues in contact with MET 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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17A ILE 3.8 12.1 - - - +
18A ASP 4.4 0.7 - - - -
19A GLY* 3.7 23.6 - - - +
64A PHE* 5.7 0.2 - - - -
216A ILE* 4.4 10.1 - - - -
217A PHE 2.7 18.2 + - - +
218A SER* 3.4 18.2 - - - +
219A HIS* 3.1 5.5 - - - -
220A SER 3.0 25.9 + - - -
246A LEU* 3.8 24.2 - - + +
247A VAL* 1.3 72.2 - - - +
249A VAL* 1.3 62.4 + - - +
284A GLY* 3.6 7.9 - - - -
285A PHE 3.4 34.1 - - - +
286A GLY 3.7 1.6 - - - -
330A LEU* 3.9 34.1 - - + -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A SER 3.5 4.9 - - - +
221A SER* 3.6 12.1 - - - +
247A VAL 4.4 2.5 - - - +
248A MET* 1.3 69.4 - - - +
250A ASN* 1.3 69.5 + - - +
251A PHE* 3.5 10.3 - - + -
256A ILE* 4.5 0.4 - - + -
267A VAL* 4.1 24.0 - - + -
270A HIS* 4.4 11.2 - - + -
271A LEU* 3.6 26.7 - - + +
274A ILE* 3.2 34.8 - - + -
283A VAL* 4.8 0.7 - - + -
284A GLY 3.0 13.5 + - - +
285A PHE* 3.9 0.6 - - + -
286A GLY 2.9 23.0 + - - -
287A GLY 3.4 2.1 + - - -
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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