Contacts of the strand formed by residues 548 - 553 (chain A) in PDB entry 1QFM
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 548 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA* 3.8 21.5 - - + +
470A LEU* 4.1 15.9 - - + -
534A ALA* 3.6 31.2 - - + +
537A LEU* 4.5 4.7 - - + -
538A ILE* 4.4 9.2 - - + -
543A THR* 4.2 11.2 - - + +
544A SER 3.1 8.2 + - - +
545A PRO 3.2 11.4 + - - +
546A LYS 3.5 0.6 - - - -
547A ARG* 1.3 78.4 - - - +
549A THR* 1.3 78.5 + - - +
550A ILE* 4.5 1.1 - - + -
570A LEU 3.5 19.5 - - - +
571A PHE* 3.8 12.3 - - + -
572A GLY* 2.8 27.9 + - - -
573A CYS 3.1 6.5 + - - +
704A LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA 2.9 15.8 + - - +
469A PHE* 4.1 13.0 - - + -
470A LEU 2.9 25.3 + - - -
491A PHE* 5.9 0.7 - - - -
547A ARG 3.9 0.2 + - - -
548A LEU* 1.3 77.5 - - - +
550A ILE* 1.3 73.4 + - - +
573A CYS* 3.1 31.3 - - + +
575A ILE* 4.5 5.6 - - + -
700A ILE* 3.7 45.3 - - + +
704A LEU* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A LEU* 3.2 21.3 - - + +
530A PHE* 3.7 20.2 - - + -
548A LEU* 4.3 2.7 - - + -
549A THR* 1.3 80.1 - - - +
551A ASN* 1.3 62.2 + - - +
560A VAL* 3.8 32.5 - - + +
563A CYS* 4.0 6.1 - - + -
571A PHE* 3.6 54.7 - - + -
573A CYS 3.0 9.3 + - - +
574A VAL* 3.5 18.1 - - + +
575A ILE 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE* 3.3 40.2 - - + -
470A LEU 3.0 6.3 + - - +
471A TYR* 3.3 25.6 - - + -
472A GLY 3.3 22.3 + - - -
488A ARG* 4.9 0.9 + - - -
550A ILE* 1.3 77.7 - - - +
552A GLY* 1.3 64.7 + - - +
560A VAL* 3.6 9.1 - - - +
575A ILE* 2.9 36.2 + - + +
577A GLN* 3.0 27.9 + - - +
696A MET* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A TYR* 4.1 7.4 - - - -
472A GLY 3.6 11.0 - - - -
551A ASN* 1.3 82.8 + - - +
553A GLY* 1.3 57.3 - - - -
556A GLY 3.3 22.2 - - - -
557A GLY* 3.6 4.9 - - - -
560A VAL* 3.7 2.6 - - - +
575A ILE 3.5 5.0 + - - +
577A GLN* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A TYR* 4.6 10.2 + - - -
472A GLY 4.7 0.2 + - - -
473A TYR* 3.5 11.1 - - - -
552A GLY* 1.3 74.1 - - - -
554A SER* 1.3 65.2 + - - -
555A ASN 3.2 0.3 + - - -
556A GLY* 2.8 19.3 + - - -
557A GLY 3.3 3.0 - - - +
577A GLN* 3.1 18.6 + - - -
578A VAL* 4.5 2.9 - - - -
----------------------------------------------------------
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