Contacts of the strand formed by residues 511 - 517 (chain B) in PDB entry 2O8F
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 ARG 511 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLY* 5.1 3.6 - - - -
412B LYS* 3.4 31.2 + - + +
416B ILE* 4.8 2.7 - - + +
427B TYR* 3.5 40.4 + - + +
428B LYS 2.8 21.6 + - - -
429B VAL* 3.7 15.8 - - - +
483B VAL* 4.0 11.0 - - + -
484B GLU 3.2 12.8 - - - +
485B GLN* 3.1 26.5 + - + +
508B VAL* 4.4 6.7 - - - +
509B VAL* 3.4 16.5 + - - +
510B ARG* 1.3 81.1 - - - +
512B GLU* 1.3 64.1 + - - +
11E G 3.2 19.6 + - - -
12E C 3.0 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 5.3 6.7 - - + -
483B VAL* 3.7 9.1 - - - +
484B GLU 3.0 29.7 + - - +
486B THR* 3.2 25.7 + - + +
510B ARG* 4.1 10.7 + - + -
511B ARG* 1.3 77.0 - - - +
513B ILE* 1.3 64.4 + - - +
514B CYS* 3.5 3.5 + - - -
838B PRO* 4.1 14.1 - - + +
841B ARG* 2.8 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 4.1 16.1 - - + +
420B ASN* 3.4 31.6 - - + +
481B ALA* 4.5 14.1 - - + -
482B ARG 3.7 4.5 - - - +
483B VAL* 3.8 18.2 - - + -
512B GLU* 1.3 74.1 - - - +
514B CYS* 1.3 61.8 + - - +
515B ARG 3.8 11.9 - - - +
516B ILE* 3.7 32.3 - - + -
693B LYS 5.5 0.2 - - - +
695B LEU* 3.3 20.4 - - + +
838B PRO* 3.9 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 3.0 16.4 + - - +
484B GLU* 3.7 25.8 - - + -
486B THR* 4.6 4.5 - - - -
512B GLU 3.7 14.6 - - - -
513B ILE* 1.3 74.3 - - - +
515B ARG* 1.3 65.4 + - - +
695B LEU* 3.6 11.6 - - - +
837B HIS* 3.7 20.6 - - - -
838B PRO* 3.4 33.9 - - - -
839B ASP* 3.7 23.5 - - - +
842B ALA* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL 3.9 0.3 - - - +
481B ALA* 3.7 1.2 - - - -
482B ARG* 2.8 61.0 + - + +
513B ILE* 3.6 4.2 - - - +
514B CYS* 1.3 83.5 - - - +
516B ILE* 1.3 88.4 + - - +
517B ILE* 3.6 23.3 - - + +
521B THR* 2.8 30.5 + - - -
522B GLN* 4.0 0.6 - - - +
523B THR* 3.1 25.3 + - - +
528B GLU* 2.9 28.1 + - - +
694B CYS* 3.7 9.2 + - - +
695B LEU* 4.6 0.9 - - - -
696B ILE* 3.5 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 3.7 42.8 - - + -
479B LYS* 5.0 0.4 - - + -
480B VAL 3.3 9.6 - - - +
481B ALA* 4.7 1.6 - - - -
513B ILE* 3.7 23.6 - - + -
515B ARG* 1.3 92.1 + - - +
517B ILE* 1.3 61.1 + - - +
518B THR* 4.4 9.6 - - - +
521B THR* 3.6 3.1 + - - -
690B TYR* 5.3 3.4 - - - +
693B LYS* 3.5 45.1 - - + +
694B CYS* 3.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 4.0 32.5 - - + -
470B SER* 4.6 9.4 - - - +
474B VAL* 3.8 24.2 - - + +
478B TYR 4.1 1.2 - - - +
479B LYS* 3.7 1.2 - - - -
480B VAL* 2.7 43.5 + - + +
482B ARG* 5.2 2.9 - - + +
515B ARG* 3.6 39.7 - - + +
516B ILE* 1.3 70.5 - - - +
518B THR* 1.3 73.2 + - - +
522B GLN* 4.6 7.6 - - + +
528B GLU* 4.1 25.8 - - + +
----------------------------------------------------------
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