Contacts of the strand formed by residues 407 - 412 (chain F) in PDB entry 2HU4
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 SER 407 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F LYS* 2.9 25.5 + - - +
351F GLY* 3.2 21.8 - - - +
352F PHE* 3.7 8.1 - - - -
363F GLY 5.1 1.0 - - - -
374F PHE* 3.4 40.3 - - - -
405F GLY 4.6 0.7 + - - -
406F TYR* 1.3 77.6 - - - +
408F GLY* 1.3 59.2 + - - +
423F TRP* 3.3 20.9 - - - -
424F VAL* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F SER* 4.8 0.9 - - - -
279F SER* 3.8 10.8 - - - -
350F LYS* 4.5 1.6 - - - -
352F PHE* 4.0 7.4 - - - -
407F SER* 1.3 75.4 - - - +
409F SER* 1.3 60.0 + - - -
422F PHE* 3.3 2.9 - - - +
423F TRP* 2.8 60.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F SER* 4.8 6.1 + - - -
229F GLU* 3.9 12.5 + - - +
279F SER* 3.8 22.0 + - - -
280F CYS 4.3 9.9 + - - +
281F TYR* 4.5 6.4 - - - +
352F PHE* 3.8 20.3 - - - +
353F SER 5.6 0.4 - - - -
354F PHE* 3.5 29.1 - - - -
408F GLY* 1.3 74.4 - - - -
410F PHE* 1.3 64.7 + - - +
421F CYS 3.6 5.2 - - - -
422F PHE* 4.2 2.5 - - - +
423F TRP* 4.3 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F TYR* 4.2 14.6 - + - -
122F ILE* 3.2 51.6 - - + +
123F SER* 4.8 0.7 - - - -
124F CYS* 4.1 15.0 - - - -
229F GLU* 3.0 11.4 - - - +
354F PHE* 4.6 1.0 - - - -
409F SER* 1.3 74.9 - - - +
411F VAL* 1.3 72.0 + - - +
412F GLN* 4.4 3.8 - - - -
420F PRO* 4.2 0.2 - - - +
421F CYS* 2.7 67.7 + - + +
422F PHE* 3.5 32.3 - - - -
423F TRP* 4.0 11.0 - + + -
445F SER* 3.8 18.4 - - - -
447F CYS* 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 5.5 1.1 - - + -
124F CYS* 4.0 14.4 + - - +
229F GLU* 3.0 15.1 + - - +
281F TYR* 3.6 18.8 - - + -
282F PRO* 3.5 26.9 - - + -
354F PHE* 5.4 4.3 - - + -
410F PHE* 1.3 85.6 - - - +
412F GLN* 1.3 103.5 - - - +
418F ILE* 2.9 36.1 - - + -
419F ARG 3.4 7.6 - - - +
420F PRO* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F TYR* 4.6 13.1 + - - -
124F CYS* 4.8 9.9 - - - -
129F CYS* 5.2 2.2 - - - -
410F PHE* 4.4 5.2 - - + -
411F VAL* 1.3 89.4 - - - +
412F HIS* 1.1 74.5 + - - +
413F THR* 3.6 19.2 + - - +
417F CYS 5.2 0.4 - - - -
418F ILE* 3.4 3.3 - - - -
419F ARG* 2.3 71.3 + - + +
421F CYS* 2.7 7.9 - - - -
447F CYS* 2.6 33.7 - - - -
210H ILE* 5.2 7.8 - - - +
211H ILE* 6.2 0.2 - - - +
----------------------------------------------------------
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