Contacts of the strand formed by residues 507 - 512 (chain E) in PDB entry 3SRF
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 507 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422E CYS* 4.1 25.8 - - + +
423E LEU 5.9 0.4 + - - +
424E ALA* 3.4 5.3 - - - -
425E ALA* 2.8 31.8 + - - +
505E GLY 4.6 4.7 - - - +
506E ASP* 1.3 81.1 + - - +
508E VAL* 1.3 65.5 + - - +
526E VAL* 3.8 29.2 - - + -
527E VAL 4.0 5.2 - - - +
528E PRO* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E ALA* 4.3 1.3 - - - -
425E ALA* 4.1 1.3 - - + -
426E ALA* 3.5 28.3 - - + +
428E ILE* 3.9 15.7 - - + -
493E MET* 3.6 27.1 - - + -
502E PHE* 3.8 30.5 - - + -
507E VAL* 1.3 80.9 - - - +
509E ILE* 1.3 66.5 + - - +
510E VAL* 4.1 6.2 + - + -
525E ARG 3.6 0.7 - - - +
526E VAL* 3.7 3.5 - - - -
527E VAL* 3.1 40.9 + - + +
529E VAL* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 509 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E SER* 4.1 19.7 - - - +
418E ALA* 4.0 23.1 - - + +
419E SER* 4.1 15.7 - - - -
422E CYS* 4.2 5.6 - - - -
424E ALA* 3.9 19.1 - - + -
426E ALA 3.3 7.6 + - - +
427E LEU* 3.4 9.5 - - + +
428E ILE* 2.8 33.4 + - - +
508E VAL* 1.3 77.1 - - - +
510E VAL* 1.3 60.4 + - - +
511E LEU* 4.1 2.4 + - + +
524E MET* 3.7 30.3 - - + -
525E ARG 3.4 3.1 - - - +
526E VAL* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E ILE* 3.4 33.2 - - + +
489E VAL* 3.9 17.0 - - + -
493E MET* 5.7 0.2 - - - -
508E VAL* 4.4 2.7 - - + -
509E ILE* 1.3 77.6 - - - +
511E LEU* 1.3 63.2 + - - +
512E THR* 3.6 12.9 + - + +
523E THR 3.1 6.4 - - - +
524E MET* 3.3 1.8 - - - -
525E ARG* 2.7 69.0 + - + +
527E VAL* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 511 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E MET* 4.9 0.9 - - + -
411E MET* 3.5 33.9 - - + +
415E SER* 3.4 37.5 - - - +
427E LEU* 4.8 7.9 - - + -
428E ILE 2.6 15.1 + - - +
429E VAL* 3.7 24.5 - - + -
430E LEU* 3.0 26.9 + - - +
440E VAL* 3.8 15.5 - - + -
509E ILE* 5.4 3.1 - - + +
510E VAL* 1.3 73.2 - - - +
512E THR* 1.3 62.0 + - - +
521E THR* 3.0 29.7 + - + +
523E THR 3.3 3.6 - - - +
524E MET* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 512 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E LEU* 4.0 17.9 - - + -
485E VAL* 3.7 22.0 - - + +
489E VAL* 4.2 0.9 - - + -
510E VAL* 3.6 11.7 - - + -
511E LEU* 1.3 78.6 - - - +
513E GLY* 1.3 63.4 + - - +
514E TRP* 5.2 0.3 - - - -
521E THR* 2.7 19.0 + - - -
522E ASN 3.0 15.4 + - - -
523E THR* 2.9 28.6 + - - +
525E ARG* 3.4 41.2 + - - +
----------------------------------------------------------
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