Contacts of the strand formed by residues 246 - 251 (chain I) in PDB entry 1DZG
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 246 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I LEU* 4.0 19.9 - - - +
239I PHE 3.3 9.6 - - - -
240I TYR* 3.8 25.1 - - - -
241I LYS* 3.9 6.6 - - - +
245I GLU* 1.3 80.9 - - - +
247I CYS* 1.3 67.2 + - - +
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Residues in contact with CYS 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I GLU 3.4 0.2 - - - +
238I LEU* 3.3 13.1 - - - +
239I PHE* 2.7 44.4 + - + +
241I LYS* 4.1 13.2 - - + -
246I SER* 1.3 81.0 - - - +
248I SER* 1.3 59.9 + - - +
249I ALA 3.5 0.6 + - - -
428I ASN* 3.4 11.9 - - - -
430I CYS* 2.0 49.8 - - - -
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Residues in contact with SER 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I LYS* 3.4 39.3 + - - +
237I GLU 3.8 5.6 + - - -
238I LEU* 5.2 3.1 - - - -
247I CYS* 1.3 74.1 - - - +
249I ALA* 1.3 59.6 + - - +
430I CYS* 3.3 16.8 - - - +
431I VAL 4.5 5.5 + - - +
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Residues in contact with ALA 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I LYS* 3.4 4.7 - - - -
237I GLU* 2.8 40.9 + - - +
239I PHE* 3.9 24.2 - - + -
247I CYS 3.5 1.0 + - - -
248I SER* 1.3 75.6 - - - +
250I SER* 1.3 60.5 + - - +
251I MET* 3.2 7.4 + - + -
321I PRO* 4.3 11.7 - - + -
322I ARG 5.7 0.4 - - - +
429I PRO* 4.0 20.2 - - + -
430I CYS* 4.3 8.3 - - - +
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Residues in contact with SER 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234I THR* 4.1 9.0 - - - -
236I LYS* 4.4 20.8 - - - +
248I SER 4.3 0.4 + - - -
249I ALA* 1.3 69.8 - - - +
251I MET* 1.3 62.4 + - - +
321I PRO* 4.2 2.0 - - - +
322I ARG* 3.0 63.7 + - - +
430I CYS* 5.7 0.2 - - - +
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Residues in contact with MET 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I ASN 4.5 0.5 - - - +
234I THR* 3.2 3.5 - - - +
235I ARG* 2.9 49.5 + - + +
237I GLU* 3.2 35.2 - - + +
238I LEU 4.8 4.3 - - - +
239I PHE* 5.0 1.6 - - + -
249I ALA* 3.2 14.7 + - + +
250I SER* 1.3 71.4 - - - +
252I MET* 1.3 60.5 + - - +
253I TYR* 5.2 0.3 - - - +
319I HIS* 3.8 24.5 - - + -
320I MET 3.7 11.4 - - - -
321I PRO* 3.5 31.9 - - + -
403I LYS* 5.6 0.2 - - - -
404I ALA 3.6 18.2 - - - +
405I ASN* 4.2 14.1 - - + -
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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