Contacts of the strand formed by residues 456 - 460 (chain D) in PDB entry 5MKE
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 GLN 456 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ALA 3.6 3.6 + - - +
653A ASN* 2.4 35.3 + - - +
654A ARG* 4.6 7.7 - - - +
379D HIS* 4.3 8.2 - - + +
438D VAL* 3.8 2.9 - - + +
440D ARG* 2.5 73.9 + - + +
441D LEU* 4.3 0.2 - - - +
442D LEU* 6.3 0.7 - - + -
455D TRP* 1.3 79.0 - - - +
457D PHE* 1.3 89.9 + - - +
458D GLN* 5.6 0.5 - - - +
556D ILE* 5.5 10.8 - - + +
1007D PX6 2.6 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 457 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR* 4.7 11.3 - - - +
622A GLN* 3.5 37.2 - - + +
653A ASN* 5.0 2.1 + - - +
250D THR* 5.7 4.7 - - + -
253D MET 5.4 0.9 - - - -
254D SER* 3.7 22.7 - - - -
257D PHE* 5.3 11.9 - + + -
258D LEU* 4.6 14.1 - - + -
437D CYS* 5.1 8.5 - - - -
438D VAL* 3.4 13.2 - - - -
439D VAL* 4.0 29.2 - - + -
441D LEU* 5.2 6.7 - - + -
455D TRP* 4.5 16.0 - + + -
456D GLN* 1.3 99.1 + - - +
458D GLN* 1.3 65.8 + - - +
459D PRO* 4.5 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 458 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR* 4.5 11.0 - - - +
653A ASN* 4.7 6.6 - - - +
437D CYS* 3.0 5.6 - - - -
438D VAL* 2.7 56.3 + - + +
456D GLN* 5.6 1.1 - - + +
457D PHE* 1.3 78.2 - - - +
459D PRO* 1.3 91.1 + - - +
552D ALA* 5.2 0.9 - - + +
555D GLN* 4.7 3.1 - - + -
556D ILE* 3.2 53.8 - - + +
559D ASN* 2.9 33.0 - - - +
560D ASN* 4.9 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 459 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A GLY 5.7 1.6 - - - +
621A THR* 4.8 11.7 - - + +
242D MET* 5.6 8.8 - - + +
246D VAL* 4.7 16.8 - - + -
249D TYR* 5.4 2.9 - - + -
250D THR* 5.2 14.4 - - + -
435D LEU* 3.8 18.4 - - + -
436D PHE 3.1 4.7 - - - +
437D CYS* 3.8 9.2 - - - -
457D PHE* 4.5 2.9 - - + +
458D GLN* 1.3 119.0 + - - +
460D LEU* 1.3 61.9 + - - +
555D GLN* 4.0 8.1 - - - +
559D ASN* 4.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D MET* 5.2 2.0 - - - -
435D LEU* 3.0 9.4 - - - +
436D PHE* 2.1 82.8 + - + +
437D CYS* 4.3 1.1 - - - +
438D VAL* 5.3 3.8 - - + -
458D GLN 5.1 0.2 - - - +
459D PRO* 1.3 73.4 - - - +
461D LYS* 1.3 73.9 + - - +
462D LEU* 3.5 17.3 - - + +
548D PHE* 3.4 38.6 - - + -
552D ALA* 6.0 0.4 - - + -
555D GLN* 3.1 44.0 - - + +
----------------------------------------------------------
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