Contacts of the strand formed by residues 310 - 317 (chain B) in PDB entry 5IZL
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 HIS 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER 4.3 0.2 - - - -
309B LEU* 1.3 73.5 - - - +
311B THR* 1.3 60.3 + - - +
312B VAL* 2.8 36.4 - - + +
420B VAL 3.9 1.0 - - - +
421B THR* 3.7 0.6 - - - -
422B CYS* 3.1 31.7 + - - +
423B PRO 3.7 17.3 - - - -
424B ARG* 3.0 52.6 + - + +
450B LEU* 4.0 9.5 - - + +
453B GLY* 3.8 18.3 + - - -
455B GLU* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PRO* 5.9 2.0 - - + -
309B LEU 4.2 1.8 + - - +
310B HIS* 1.3 71.1 - - - +
312B VAL* 1.3 65.1 + - - +
313B HIS* 5.5 5.2 - - - -
419B PRO* 5.4 5.1 - - - +
420B VAL 3.2 11.4 - - - -
421B THR* 3.3 31.4 - - + +
455B GLU* 3.3 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 2.8 43.1 - - + +
311B THR* 1.3 76.8 - - - +
313B HIS* 1.3 63.2 + - - +
314B ALA 3.6 13.0 - - - +
416B PHE* 3.8 23.1 - - + -
419B PRO* 3.5 3.8 - - - +
420B VAL* 2.8 38.1 + - + +
422B CYS* 4.2 14.1 - - - -
450B LEU* 4.8 6.3 - - + -
453B GLY* 3.6 13.2 - - - -
454B LEU 3.4 9.9 - - - +
455B GLU* 4.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B THR* 5.5 4.7 - - - -
312B VAL* 1.3 73.0 - - - +
314B ALA* 1.3 61.8 + - - +
415B GLU* 3.9 1.4 - - - -
416B PHE* 3.1 39.1 + - - +
418B LYS 5.3 0.7 - - - -
419B PRO* 3.5 37.2 - - + +
454B LEU 3.0 7.0 + - - +
455B GLU 3.8 14.8 + - - -
456B ASP 4.2 0.2 + - - -
457B ARG* 3.8 35.4 - - + +
459B TYR* 3.8 25.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 3.5 6.2 - - - +
313B HIS* 1.3 78.4 - - - +
315B ALA* 1.3 63.8 + - - +
413B LEU* 4.3 4.3 - - + -
414B VAL 3.0 21.5 - - - +
416B PHE* 3.7 6.6 - - - -
454B LEU* 2.8 45.1 + - + -
459B TYR* 3.6 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 5.0 0.7 - - + -
314B ALA* 1.3 79.0 - - - +
316B LEU* 1.3 63.0 + - - +
317B ILE* 3.9 7.6 + - + -
412B ALA 3.8 0.3 - - - +
413B LEU* 3.5 7.3 - - - +
414B VAL* 3.3 27.8 + - + +
416B PHE* 4.5 11.1 - - + -
450B LEU* 3.7 33.9 - - + -
452B HIS 3.1 14.6 - - - +
453B GLY* 4.4 0.9 - - - -
454B LEU* 3.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA* 1.3 74.4 - - - +
317B ILE* 1.3 52.4 + - - +
351B PHE* 4.6 4.5 - - + -
367B PHE* 3.5 50.7 - - + -
369B PHE* 3.9 15.3 - - + -
411B TRP* 5.8 1.3 - - + -
412B ALA 3.6 11.2 - - - +
413B LEU* 3.8 29.4 - - + -
451B LEU* 2.7 36.6 + - + +
452B HIS* 2.9 22.0 + - + +
454B LEU* 5.3 5.4 - - + -
463B PHE* 5.6 3.4 - - + -
464B LEU* 6.0 0.7 - - + -
467B LEU* 3.8 20.6 - - + -
584B TYR* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA* 4.1 7.9 - - + +
316B LEU* 1.3 76.4 - - - +
318B SER* 1.3 76.2 + - - +
319B VAL* 3.2 20.9 - - + +
411B TRP* 4.5 2.4 - - - +
412B ALA* 3.3 18.8 + - + +
414B VAL* 4.2 25.6 - - + -
428B VAL* 3.6 33.9 - - + -
446B PHE* 4.4 11.2 - - + -
448B GLY* 5.0 1.1 - - - -
449B ILE 2.8 8.7 - - - +
450B LEU* 2.8 44.9 - - + +
451B LEU* 4.1 1.8 - - - +
----------------------------------------------------------
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