Contacts of the strand formed by residues 363 - 368 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C VAL* 5.0 0.7 - - + -
358C ILE 3.3 14.4 - - - +
359C TYR* 4.3 10.1 - - - +
360C THR 3.2 15.7 - - - +
361C HIS* 5.2 4.0 + - - +
362C PRO* 1.3 77.5 - - - +
364C VAL* 1.3 63.0 + - - +
421C LEU* 3.6 1.4 - - - +
422C GLY 2.9 35.7 + - - +
423C PRO* 5.2 0.9 - - + +
424C GLY* 3.7 10.5 - - - +
425C ALA* 3.3 15.1 + - + -
426C GLY* 2.9 28.0 + - - +
427C GLU 4.7 0.2 + - - -
393D ARG* 2.7 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ILE* 4.2 6.3 - - + -
222C ILE* 3.7 26.5 - - + -
226C PHE* 3.5 48.5 - - + -
357C VAL* 3.3 2.9 - - - +
358C ILE* 2.8 41.6 + - + +
360C THR* 4.2 0.2 - - - +
363C GLU* 1.3 79.5 - - - +
365C ALA* 1.3 67.4 + - - +
366C TRP* 3.9 20.4 - - + -
420C ILE 3.1 11.0 - - - +
421C LEU* 3.9 3.6 - - + -
425C ALA* 4.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C SER 3.1 13.5 - - - +
357C VAL* 4.0 5.2 - - + -
364C VAL* 1.3 78.1 - - - +
366C TRP* 1.3 67.5 + - - +
419C HIS* 3.6 0.2 - - - -
420C ILE* 2.7 39.9 + - + +
425C ALA* 3.3 33.7 - - + +
429C VAL* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 5.4 2.9 - - + -
214C GLY 4.1 12.6 - - - -
216C VAL 4.1 9.0 - - - -
217C GLY* 3.4 21.6 + - - -
218C ILE* 3.7 46.0 - - + -
222C ILE* 5.7 1.3 - - + -
354C VAL 4.5 0.3 - - - +
355C PRO* 3.3 3.3 - - - +
356C SER* 2.9 63.6 + - - -
358C ILE* 4.0 17.5 - - + -
364C VAL* 3.9 21.3 - - + -
365C ALA* 1.3 83.7 - - - +
367C VAL* 1.3 66.7 + - - +
368C GLY 4.7 6.5 - - - -
418C ALA 3.1 7.0 - - - +
419C HIS* 3.2 33.0 - + + +
429C VAL* 3.7 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ASN 3.8 2.5 - - - +
353C CYS 3.5 33.2 - - - +
354C VAL 3.9 3.1 - - - -
355C PRO* 3.8 16.2 - - + -
366C TRP* 1.3 80.4 - - - +
368C GLY* 1.3 66.7 + - - +
417C GLY* 3.6 0.5 - - - -
418C ALA* 3.0 34.9 + - + +
419C HIS* 4.7 1.4 + - - -
429C VAL* 3.9 7.4 - - + -
432C ALA* 3.7 30.5 - - + +
433C ALA* 4.0 12.6 - - - +
436C LEU* 3.9 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLY 5.7 0.7 - - - +
352C ASN* 3.2 37.4 + - - +
354C VAL 5.3 0.4 + - - -
366C TRP* 4.7 9.4 - - - -
367C VAL* 1.3 76.0 - - - +
369C LYS* 1.3 62.2 + - - -
370C SER 4.1 0.2 + - - -
373C GLN* 4.0 5.9 + - - +
416C LEU 3.4 9.4 - - - -
419C HIS* 5.1 0.2 - - - -
436C LEU* 3.6 9.0 - - - -
----------------------------------------------------------
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