Contacts of the strand formed by residues 427 - 433 (chain B) in PDB entry 4UM8
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 LEU 427 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.6 7.0 - - + -
89B PRO* 3.3 41.3 - - + +
90B GLN* 3.2 7.6 - - - +
92B LEU* 4.1 9.4 - - + -
104B LEU* 5.5 1.1 - - + -
106B VAL* 3.8 33.4 - - + -
417B ILE* 3.4 4.2 - - - -
418B ILE* 2.6 51.0 + - + +
426B ALA* 1.3 72.7 - - - +
428B GLU* 1.3 79.7 + - - +
429B LEU* 3.6 26.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 5.3 6.1 + - - -
90B GLN 2.6 15.2 + - - +
91B SER* 4.6 14.0 + - - +
92B LEU 3.0 26.9 + - - +
416B ILE 3.7 4.3 - - - +
417B ILE* 4.6 17.1 - - + +
426B ALA* 5.3 5.4 - - + +
427B LEU* 1.3 79.8 - - - +
429B LEU* 1.3 60.7 + - - +
430B LEU 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.7 21.3 - - + +
94B LEU* 4.9 7.9 - - + -
104B LEU* 3.7 26.7 - - + -
404B VAL* 5.0 9.6 - - + -
414B ARG 3.6 1.9 - - - +
415B HIS* 3.6 7.2 - - - +
416B ILE* 2.7 58.7 + - + +
418B ILE* 3.6 31.0 - - + -
427B LEU* 3.6 26.5 - - + +
428B GLU* 1.3 72.4 - - - +
430B LEU* 1.3 60.1 + - - +
431B VAL* 3.7 11.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 2.9 9.6 + - - +
93B ILE* 3.5 40.9 - - + +
94B LEU 2.6 31.0 + - - +
413B SER* 3.7 28.9 - - - +
414B ARG 4.2 2.0 - - - +
415B HIS* 4.0 33.2 - - + +
428B GLU 4.2 0.4 - - - -
429B LEU* 1.3 71.3 - - - +
431B VAL* 1.3 58.1 + - - +
432B SER* 3.5 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.2 25.6 - - + +
96B LEU* 4.2 16.8 - - + -
369B LEU* 4.9 3.6 - - + -
404B VAL* 4.7 6.5 - - + -
406B ILE* 3.7 29.6 - - + -
410B GLU* 5.2 0.3 - - - +
413B SER* 3.2 4.2 - - - -
414B ARG* 3.2 41.2 + - + +
416B ILE* 3.8 27.6 - - + -
429B LEU* 4.5 10.1 - - + -
430B LEU* 1.3 72.1 - - - +
432B SER* 1.3 59.3 + - - +
433B PRO* 3.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.7 5.2 - - - +
94B LEU 2.9 10.7 + - - -
95B LYS* 3.3 27.0 - - - +
96B LEU 3.2 20.2 + - - -
413B SER* 3.6 18.4 - - - -
430B LEU* 3.5 7.6 + - - -
431B VAL* 1.3 73.7 - - - +
433B PRO* 1.3 69.6 - - - +
434B GLU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU 3.4 10.5 - - - +
98B PRO* 5.6 3.1 - - + -
406B ILE* 4.3 12.8 - - + -
409B CYS* 3.3 28.7 - - - +
410B GLU* 3.8 24.0 - - + +
411B ARG 5.2 0.9 - - - -
412B ARG* 4.0 23.1 - - - +
413B SER 4.1 0.2 - - - +
431B VAL 3.8 7.6 - - - +
432B SER* 1.3 91.9 - - - +
434B GLU* 1.3 63.1 + - - +
435B CYS* 5.2 1.1 - - - -
----------------------------------------------------------
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