Contacts of the strand formed by residues 415 - 422 (chain G) 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 VAL 415 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406G ILE* 4.2 9.2 - - + -
407G LEU 3.7 4.7 - - - +
408G GLY* 4.3 2.0 - - - -
413G ASP 3.4 0.2 + - - -
414G ARG* 1.3 82.6 + - - +
416G LEU* 1.3 62.4 + - - +
417G GLY 3.8 22.0 - - - +
418G ALA* 5.0 6.5 - - + +
435G ALA* 5.7 2.2 - - + -
436G LEU* 3.2 28.8 - - + +
439G GLY 6.0 0.2 - - - -
440G ALA* 2.9 24.1 + - + +
441G SER 3.7 2.7 - - - -
442G CYS* 3.6 17.9 - - - +
445G ILE* 3.7 15.9 - - + -
459G PHE* 6.1 0.9 - - + -
463G ASN* 3.6 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352G ASN* 4.7 3.3 + - - -
368G GLY* 3.5 6.1 - - - -
369G LYS* 2.9 25.0 + - + +
374G LEU* 3.8 30.7 - - + -
379G ILE* 3.7 29.2 - - + -
381G TYR* 4.4 1.6 - - + -
407G LEU 2.6 15.5 + - - +
408G GLY 4.0 2.9 - - - +
409G GLN* 3.6 29.8 - - + +
414G ARG* 3.6 20.6 - - + +
415G VAL* 1.3 80.2 - - - +
417G GLY* 1.3 56.2 + - - +
436G LEU* 4.3 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G VAL 3.5 10.8 - - - -
368G GLY* 4.1 0.2 - - - -
369G LYS 3.6 18.2 - - - -
406G ILE* 3.6 2.6 - - - -
407G LEU* 3.0 32.1 + - - +
415G VAL* 3.7 8.5 - - - +
416G LEU* 1.3 80.3 - - - +
418G ALA* 1.3 61.0 + - - +
419G HIS* 4.1 4.7 - - - -
436G LEU* 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G TRP* 3.1 5.9 - - - +
367G VAL* 3.0 33.9 + - + +
405G LYS 3.6 5.4 - - - -
406G ILE* 3.7 17.9 - - + -
415G VAL* 5.0 4.9 - - + -
417G GLY* 1.3 75.7 - - - +
419G HIS* 1.3 62.7 + - - +
420G ILE* 5.0 5.2 - - + -
429G VAL* 5.0 0.7 - - - +
432G ALA* 3.8 28.9 - - + -
436G LEU* 5.5 1.5 - - + +
459G PHE* 4.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ASP* 3.6 23.0 + - + +
222G ILE* 3.6 25.8 - - + +
365G ALA 3.5 4.0 - - - -
366G TRP* 3.3 34.3 - + + +
367G VAL 4.9 2.0 - - - -
369G LYS 2.7 31.2 + - - -
370G SER* 3.6 18.3 - - - -
403G MET 4.0 0.5 - - - +
404G VAL* 3.4 1.9 - - - +
405G LYS* 2.7 51.2 + - + +
406G ILE* 4.9 0.4 - - - +
407G LEU* 3.9 12.8 - - + +
417G GLY 4.1 2.2 - - - -
418G ALA* 1.3 83.3 + - - +
420G ILE* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G ILE* 4.5 2.6 - - - +
364G VAL* 3.3 7.4 - - - +
365G ALA 2.8 41.3 + - - +
388G PHE* 4.0 19.1 - - + -
403G MET 3.6 3.6 - - - -
404G VAL* 4.3 12.8 - - + -
418G ALA 5.0 1.6 - - - +
419G HIS* 1.3 83.4 - - - +
421G LEU* 1.3 62.2 + - - +
422G GLY 4.1 0.4 - - - +
425G ALA* 3.6 25.4 - - + +
428G MET* 4.0 31.6 - - + +
429G VAL* 3.8 40.8 - - + +
432G ALA* 5.1 4.5 - - + -
459G PHE* 5.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G ILE* 4.0 20.4 - - + +
225G ASN* 3.4 36.8 - - + +
226G PHE* 3.8 26.5 - - + +
229G ILE* 3.9 11.2 - - + -
362G PRO* 4.1 11.4 - - + -
363G GLU 3.6 11.4 - - - +
364G VAL* 3.9 18.4 - - + -
388G PHE* 3.2 5.5 - - - -
402G GLY* 3.0 15.3 - - - -
403G MET* 2.7 44.0 + - + +
420G ILE* 1.3 73.6 - - - +
422G GLY* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 422 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G PRO* 3.4 19.5 - - - +
363G GLU 2.9 27.3 + - - +
388G PHE* 3.9 4.3 - - - -
401G ASP 3.7 5.4 - - - -
420G ILE 4.1 0.6 - - - -
421G LEU* 1.3 75.3 - - - +
423G PRO* 1.3 77.3 - - - +
424G GLY 3.6 1.6 + - - -
425G ALA* 3.6 8.7 + - - +
----------------------------------------------------------
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