Contacts of the strand formed by residues 248 - 251 (chain A) in PDB entry 1IEW
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 THR 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 2.6 30.7 + - + +
202A ALA* 5.2 0.4 - - + -
203A ALA 2.8 18.6 + - - +
204A CYS* 3.2 7.0 - - - +
205A ALA 3.2 18.2 + - - -
246A VAL* 3.5 7.3 - - - +
247A SER* 1.3 89.3 - - - +
249A VAL* 1.3 71.8 + - - +
278A PHE* 3.8 1.3 - - - -
281A PHE* 3.2 51.6 - - + -
283A ILE* 4.9 0.4 - - - -
352A VAL* 4.7 1.3 - - + -
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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
----------------------------------------------------------
204A CYS* 4.1 0.2 - - - -
205A ALA* 3.4 22.2 - - + +
208A PHE* 3.7 27.4 - - + -
238A TYR* 4.3 6.1 - - + -
242A MET* 4.3 15.3 - - + -
246A VAL* 4.4 0.4 - - + -
248A THR* 1.3 83.3 - - - +
250A MET* 1.3 62.9 + - - +
251A ILE* 4.5 2.5 - - + -
272A LEU* 3.9 18.8 - - + -
278A PHE* 3.8 27.8 - - + -
281A PHE 3.2 4.2 + - - -
282A VAL* 3.3 6.1 - - - +
283A ILE* 2.8 27.6 + - - +
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Residues in contact with MET 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.6 42.2 - - + -
204A CYS* 3.5 16.0 - - - -
205A ALA 3.2 7.2 + - - +
206A LYS* 3.8 9.9 - - + -
207A HIS* 3.5 10.3 - - + -
208A PHE* 2.9 24.4 + - - +
249A VAL* 1.3 74.0 - - - +
251A ILE* 1.3 73.4 + - - +
283A ILE* 3.2 12.3 - - + +
284A SER 3.6 20.4 - - - +
285A ASP* 3.7 25.6 - - - +
316A MET* 5.0 2.0 - - - -
620A G2F 3.8 23.3 - - - +
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Residues in contact with ILE 251 (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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207A HIS* 4.2 0.9 - - - -
208A PHE* 3.5 37.7 - - + +
249A VAL* 4.5 2.9 - - + -
250A MET* 1.3 77.8 - - - +
252A SER* 1.3 64.5 + - - +
261A MET* 3.5 35.0 - - + +
262A HIS* 3.2 32.0 + - + +
268A VAL* 4.1 9.6 - - + -
272A LEU* 5.0 0.7 - - + -
282A VAL* 3.4 32.5 - - + -
283A ILE 3.0 10.0 + - - +
285A ASP* 3.6 16.1 - - - +
312A LEU* 4.0 15.0 - - + -
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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