Contacts of the strand formed by residues 353 - 358 (chain E) in PDB entry 1D00
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 353 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D TYR* 4.1 13.1 + - + -
349E THR* 2.8 29.5 + - - +
351E ASP* 3.1 25.6 - - - +
352E GLY* 1.3 79.8 - - - +
354E PHE* 1.3 66.8 + - - +
355E ILE* 5.1 1.1 - - + -
493E LYS* 4.1 26.2 - - - +
494E ALA 3.5 4.5 - - - +
495E ILE* 4.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D TYR* 3.4 15.7 - - - -
347E ALA* 3.4 26.7 - - + -
349E THR* 4.2 2.2 - - - -
353E VAL* 1.3 76.4 - - - +
355E ILE* 1.3 70.2 + - - +
356E TRP* 3.7 24.9 - - + -
378E SER* 3.7 19.5 - - - -
379E PRO* 3.7 33.2 - - + -
380E ALA 4.6 1.8 - - - -
381E PHE* 3.4 52.3 - + + -
392E LEU* 4.4 9.9 - - + -
492E ILE 3.9 0.3 - - - +
493E LYS* 3.2 5.2 - - - +
494E ALA* 2.7 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D TYR* 3.1 60.3 + - + -
418D ASN* 4.1 11.2 - - - +
421D LEU* 4.6 16.4 - - + -
353E VAL* 5.1 1.1 - - + -
354E PHE* 1.3 86.6 - - - +
356E TRP* 1.3 62.5 + - - +
357E LYS 3.9 2.7 + - - +
435E LEU* 4.9 3.6 - - + -
491E PHE* 4.0 27.4 - - + -
492E ILE 3.4 5.8 - - - +
493E LYS* 3.8 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E PHE* 3.7 14.1 - + + -
355E ILE* 1.3 73.0 - - - +
357E LYS* 1.3 70.6 + - - +
358E ILE* 3.5 29.2 + - + +
376E ILE* 3.5 31.9 - - + -
377E PHE 3.6 8.5 + - - -
378E SER* 3.2 35.9 - - - +
379E PRO* 3.8 20.1 - - + +
392E LEU* 4.2 19.7 - - + -
394E ILE* 3.6 32.5 - - + -
409E LEU* 5.3 1.3 - - + -
490E ILE 3.6 0.2 - - - +
491E PHE* 3.5 3.7 - - - -
492E ILE* 2.6 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D GLY 5.4 0.2 + - - -
417D PRO* 3.3 40.2 + - + +
418D ASN* 5.2 2.2 - - - +
355E ILE* 3.9 4.2 + - + -
356E TRP* 1.3 78.2 + - - +
358E ILE* 1.3 63.5 + - - +
359E SER* 3.6 22.0 + - - +
489E ALA* 4.4 13.0 - - + -
490E ILE 3.6 5.8 - - - +
491E PHE* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E TRP* 3.8 55.2 - - + +
357E LYS* 1.3 70.7 - - - +
359E SER* 1.3 68.1 - - - +
361E PHE* 4.2 13.1 - - + +
364E LYS* 4.0 20.6 - - + +
376E ILE* 5.5 3.6 - - + -
394E ILE* 4.2 14.6 - - + -
396E LEU* 5.1 8.1 - - + -
489E ALA* 3.2 5.6 - - - -
490E ILE* 2.8 59.2 + - + +
492E ILE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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