Contacts of the strand formed by residues 363 - 368 (chain F) in PDB entry 1ZMD
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 GLU 363 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ARG* 2.8 34.1 + - - -
357F VAL* 5.1 0.2 - - + -
358F ILE 3.3 12.8 - - - +
359F TYR* 4.3 10.8 - - - +
360F THR 3.2 15.9 - - - +
361F HIS* 5.1 6.1 - - + -
362F PRO* 1.3 74.7 - - + +
364F VAL* 1.3 68.3 + - - +
421F LEU* 3.5 1.7 - - - +
422F GLY 2.9 36.4 + - - +
423F PRO* 5.1 0.6 - - + +
424F GLY* 3.7 11.1 - - - +
425F ALA* 3.4 13.3 + - + -
426F GLY* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F ILE* 4.2 5.4 - - + -
222F ILE* 3.6 30.5 - - + -
226F PHE* 3.4 46.2 - - + -
357F VAL* 3.3 1.9 - - - +
358F ILE* 2.7 43.1 + - + +
363F GLU* 1.3 81.2 - - - +
365F ALA* 1.3 67.9 + - - +
366F TRP* 4.0 18.6 - - + -
420F ILE 3.2 7.9 - - - +
421F LEU* 3.8 5.4 - - + -
425F ALA* 4.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 365 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F SER 3.1 13.5 - - - +
357F VAL* 3.9 8.3 - - + -
364F VAL* 1.3 79.3 - - - +
366F TRP* 1.3 65.4 + - - +
419F HIS* 3.6 0.2 - - - -
420F ILE* 2.7 42.4 + - + +
425F ALA* 3.4 32.9 - - + +
429F VAL* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F VAL* 5.8 2.5 - - + -
214F GLY 4.5 6.1 - - - -
216F VAL 3.9 9.4 - - - -
217F GLY* 3.7 17.6 + - - -
218F ILE* 3.6 50.9 - - + -
222F ILE* 5.7 0.9 - - + -
354F VAL 4.5 0.3 - - - +
355F PRO* 3.4 1.4 - - - +
356F SER* 2.9 60.6 + - - +
358F ILE* 4.1 20.9 - - + -
364F VAL* 4.0 18.8 - - + -
365F ALA* 1.3 85.6 - - - +
367F VAL* 1.3 68.4 + - - +
368F GLY 4.7 7.6 - - - -
418F ALA 3.2 13.2 - - - +
419F HIS* 3.3 27.4 - + + +
429F VAL* 3.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F ASN 3.8 0.9 - - - +
353F CYS* 3.6 37.5 - - - +
354F VAL 4.0 2.7 - - - -
355F PRO* 4.0 13.0 - - + -
366F TRP* 1.3 78.7 - - - +
368F GLY* 1.3 66.8 + - - +
417F GLY* 3.5 0.7 - - - -
418F ALA* 3.0 34.4 + - + +
419F HIS* 4.7 1.4 + - - -
429F VAL* 3.9 11.2 - - + -
432F ALA* 3.7 35.7 - - + -
433F ALA* 4.0 6.5 - - + +
436F LEU* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F ASN* 3.0 39.6 + - - +
366F TRP* 4.7 8.8 - - - -
367F VAL* 1.3 76.5 - - - +
369F LYS* 1.3 62.1 + - - -
373F GLN* 3.9 5.9 + - - +
416F LEU 3.4 10.3 - - - -
419F HIS* 5.1 0.2 - - - -
436F LEU* 3.6 9.9 - - - -
----------------------------------------------------------
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