Contacts of the strand formed by residues 369 - 375 (chain D) in PDB entry 3HYW
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 ARG 369 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ARG* 5.4 0.4 - - - +
359D PHE* 4.6 13.4 - - + -
360D ALA* 3.8 0.2 - - - -
361D ASP* 2.9 44.9 + - + +
367D ARG* 3.5 2.9 - - - +
368D GLU* 1.3 95.8 + - + +
370D VAL* 1.3 70.5 + - - +
371D ILE* 5.8 6.5 - - + -
411D LEU 4.5 9.3 + - - -
412D LYS* 3.6 42.5 + - - +
431D SO4 3.0 49.0 + - - +
172F LYS* 3.5 21.7 + - - +
212F GLU 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ILE* 3.8 18.6 - - + -
200D GLY* 3.9 26.2 - - - +
359D PHE* 3.1 14.8 - - - +
360D ALA* 4.1 0.9 - - - -
367D ARG* 3.6 29.8 - - + +
369D ARG* 1.3 82.7 - - - +
371D ILE* 1.3 73.6 + - - +
372D THR* 5.4 0.7 - - - +
211F ALA 4.6 1.8 - - - +
212F GLU* 3.3 31.7 + - + +
214F ASN* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ILE* 4.5 0.2 - - - +
357D PHE* 3.5 12.5 - - + +
358D PHE* 3.4 4.3 - - - -
359D PHE* 2.8 51.8 + - + +
369D ARG* 5.8 7.9 - - + -
370D VAL* 1.3 80.2 - - - +
372D THR* 1.3 65.9 + - - +
373D LYS* 3.9 36.8 - - + +
410D PHE 5.7 0.4 - - - +
411D LEU* 3.6 32.3 - - + -
600D LMT 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ILE* 3.0 33.1 + - - +
200D GLY* 4.4 2.3 + - - -
201D ALA* 4.7 14.6 - - + +
205D LEU* 3.5 32.3 - - + +
357D PHE 3.4 3.1 - - - -
358D PHE* 3.9 17.4 - - + -
370D VAL* 5.2 1.0 - - - +
371D ILE* 1.3 77.5 + - - +
373D LYS* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C LMT 4.8 4.0 + - - -
205D LEU* 4.5 6.5 - - - +
356D GLY* 3.6 1.9 - - - -
357D PHE* 2.7 43.1 + - + +
358D PHE* 5.6 0.2 - - - -
371D ILE* 3.9 20.5 - - + +
372D THR* 1.3 80.7 - - - +
374D MET* 1.3 61.4 - - - +
377D TRP* 3.9 16.8 - - + +
600D LMT 2.7 70.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LEU* 4.4 17.0 - - + -
209D LEU* 3.6 33.4 - - + -
212D GLU* 5.9 0.7 - - - +
213D ARG* 3.6 12.8 - - - +
351D PHE* 4.4 8.7 - - + -
354D ASP* 3.4 32.1 - - + +
355D ALA 3.4 19.5 - - - +
356D GLY* 4.4 1.1 - - - -
357D PHE 4.7 0.2 - - - +
373D LYS* 1.3 77.6 - - - +
375D GLY* 1.3 58.2 + - - +
377D TRP* 4.2 8.0 + - - -
378D ALA* 5.4 0.4 - - - -
434D SO4 3.5 9.0 + - - -
600D LMT 4.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D ASP* 3.7 8.5 - - - -
355D ALA 3.1 25.1 + - - +
374D MET* 1.3 77.5 - - - +
376D LYS* 1.3 66.4 + - - -
377D TRP* 3.2 10.6 - - - +
378D ALA* 3.2 10.6 + - - +
434D SO4 3.3 17.9 - - - -
----------------------------------------------------------
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