Contacts of the strand formed by residues 346 - 353 (chain E) in PDB entry 1KYZ
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 GLY 346 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E ALA* 4.6 2.5 - - - +
340E LYS* 6.3 1.6 - - - -
344E PHE* 4.1 6.6 - - - +
345E GLN* 1.3 80.9 - - - +
347E PHE* 1.3 62.1 + - - +
361E PHE* 3.7 3.8 - - - -
362E LEU* 2.9 43.0 + - - +
364E LYS* 6.0 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E GLN* 3.9 27.4 - - + -
335E PHE* 4.1 0.4 - - + -
336E GLU* 3.7 53.8 - - + -
339E ALA* 4.2 6.3 - - + -
340E LYS* 6.3 1.8 - - + -
346E GLY* 1.3 75.0 - - - +
348E LYS* 1.3 67.8 + - - +
349E VAL* 3.5 33.0 - - + -
359E MET* 3.8 22.9 - - + -
360E GLU 3.4 3.8 - - - -
361E PHE* 3.6 35.9 - + - -
362E LEU* 5.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E PHE* 1.3 83.1 - - - +
349E VAL* 1.3 82.3 + - - +
350E HIS* 3.4 34.6 + - + +
359E MET* 3.2 4.3 - - - +
360E GLU* 2.8 42.3 + - + +
362E LEU* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E ILE* 4.3 9.9 - - + -
332E GLN* 3.7 26.9 - - + +
347E PHE* 3.5 33.0 - - + -
348E LYS* 1.3 91.2 - - - +
350E HIS* 1.3 74.3 + - - +
357E TYR* 3.9 22.0 - - + -
358E ILE 3.8 5.4 - - - +
359E MET* 4.1 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E TYR* 3.9 19.6 - + + -
197E GLY* 6.0 0.7 - - - -
348E LYS* 3.4 41.1 + - + +
349E VAL* 1.3 87.9 - - - +
351E CYS* 1.3 73.5 + - - +
357E TYR* 4.1 3.6 - - - -
358E ILE* 2.7 24.9 + - + +
360E GLU* 3.2 45.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E ILE* 6.3 0.2 - - - -
194E THR* 3.3 33.7 - - - +
195E TYR* 3.7 28.5 - - - -
350E HIS* 1.3 93.5 - - - +
352E ASN* 1.3 64.6 + - - +
357E TYR* 3.7 1.7 - - - -
358E ILE* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E LYS* 5.6 0.7 - - - +
194E THR* 5.2 4.0 + - - +
351E CYS* 1.3 80.6 - - - +
353E ALA* 1.3 59.1 + - - +
354E PHE* 3.9 2.3 + - - +
355E ASN* 3.8 22.2 + - - +
356E THR 3.1 9.9 - - - +
357E TYR* 3.5 41.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E THR* 4.1 4.2 - - - +
190E LYS* 3.3 28.7 - - + +
191E ILE* 3.4 37.9 - - + +
194E THR* 4.9 3.6 - - - +
351E CYS* 4.3 0.4 - - - -
352E ASN* 1.3 71.4 - - - +
354E PHE* 1.3 73.2 + - - +
355E ASN 3.3 0.4 - - - -
356E THR* 2.7 27.7 + - - +
358E ILE* 5.6 2.1 - - + +
----------------------------------------------------------
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