Contacts of the helix formed by residues 545 - 558 (chain D) in PDB entry 3F7F
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 THR 545 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D SER 5.0 2.7 - - - +
544D MET* 1.3 76.1 - - - +
546D THR* 1.3 65.4 - - - +
547D VAL* 3.4 10.2 + - - +
548D GLU* 2.7 62.3 + - - +
549D LYS* 3.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D MET 4.0 0.8 + - - -
545D THR* 1.3 72.5 - - - +
547D VAL* 1.3 63.4 + - - +
549D LYS* 3.1 18.0 + - + +
550D PHE* 3.0 48.7 + - + -
644D THR* 2.9 39.3 + - + +
651D ILE* 4.4 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D THR* 3.1 8.2 - - - +
546D THR* 1.3 76.6 - - - +
548D GLU* 1.3 53.5 + - + +
550D PHE* 4.0 7.2 - - - +
551D THR* 2.4 43.3 + - - +
644D THR* 4.0 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D SER 4.7 0.5 - - - +
544D MET* 3.6 21.6 - - + +
545D THR* 2.7 66.5 + - + +
547D VAL* 1.3 71.6 - - + +
549D LYS* 1.3 54.5 + - - +
551D THR* 3.1 8.8 + - - +
552D ASP* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D ILE* 4.0 48.6 + - + +
540D LEU* 4.5 9.6 + - + +
541D PRO 3.7 17.7 + - - -
542D ASP* 4.6 13.9 + - - +
544D MET* 3.4 45.6 + - + -
545D THR 3.1 10.0 + - - +
546D THR* 3.7 15.4 + - + +
548D GLU* 1.3 72.3 - - - +
550D PHE* 1.3 63.9 + - + +
552D ASP* 3.1 8.8 + - - +
553D ILE* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D PHE* 4.9 4.3 - + - -
535D ILE* 4.2 19.1 - - + -
546D THR* 3.0 27.3 + - + +
547D VAL* 4.0 7.2 - - - +
549D LYS* 1.3 81.6 - - + +
551D THR* 1.3 57.2 + - - +
553D ILE* 3.8 7.0 - - + +
554D PHE* 3.0 28.8 + - - +
634D LEU* 5.2 5.2 - - + -
637D PHE* 3.0 44.6 - - + -
638D VAL* 3.5 35.0 - - + +
644D THR* 4.9 2.9 - - - -
651D ILE* 3.7 36.3 - - + -
655D LEU* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D VAL* 2.4 28.8 + - - +
548D GLU* 3.2 12.4 - - - -
549D LYS 3.1 0.2 - - - -
550D PHE* 1.3 75.4 - - - +
552D ASP* 1.3 65.2 + - - +
554D PHE* 3.3 6.8 + - + +
555D LYS* 3.1 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D LYS* 3.3 18.1 + - - +
540D LEU* 3.8 21.7 - - + +
544D MET* 5.2 5.3 - - - +
548D GLU 2.8 13.0 + - - +
549D LYS* 3.4 12.1 - - - +
551D THR* 1.3 78.6 - - - +
553D ILE* 1.3 64.0 + - - +
555D LYS* 3.5 3.3 + - - +
556D ASN* 2.7 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D ILE* 4.5 12.1 - - + -
531D LYS* 3.3 37.9 - - + -
532D PHE* 3.4 37.9 - - + -
535D ILE* 4.2 16.2 - - + -
540D LEU* 4.5 3.8 - - + -
549D LYS 2.8 24.6 + - - +
550D PHE* 3.8 10.3 - - + +
552D ASP* 1.3 74.8 - - - +
554D PHE* 1.3 55.4 + - - +
557D CYS* 2.7 49.8 + - + +
558D LEU* 5.2 1.1 - - + -
638D VAL* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 554 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D PHE 3.0 18.8 + - - +
551D THR* 3.5 7.2 - - + +
552D ASP 3.3 0.2 - - - -
553D ILE* 1.3 78.4 - - - +
555D LYS* 1.3 75.2 + - + +
558D LEU* 2.8 44.3 + - + +
559D GLU* 2.9 41.2 + - + -
562D PHE* 4.2 18.8 - + - -
638D VAL* 4.6 11.0 - - + +
639D LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D THR* 3.1 35.9 + - + +
552D ASP* 4.1 3.8 - - - +
554D PHE* 1.3 87.8 - - + +
556D ASN* 1.3 65.5 + - - +
559D GLU* 3.5 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D SER* 5.7 0.3 - - - -
531D LYS* 4.1 12.2 - - - +
552D ASP* 2.7 50.4 + - - +
553D ILE 4.2 1.1 - - - +
555D LYS* 1.3 81.4 - - - +
557D CYS* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D VAL* 3.7 12.2 - - - +
527D SER* 3.4 46.3 + - - +
528D ILE* 3.6 17.7 - - + -
531D LYS* 3.8 18.4 - - - -
553D ILE* 2.7 24.2 + - + +
554D PHE 3.2 0.4 + - - -
555D LYS 5.1 0.2 - - - -
556D ASN* 1.3 85.7 - - - +
558D LEU* 1.3 59.0 + - - +
559D GLU 3.8 1.1 - - - -
561D GLN* 3.3 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D PHE* 5.6 1.3 - - + -
520D LEU* 3.9 26.9 - - + -
524D VAL* 4.1 7.0 - - + -
528D ILE* 3.3 30.1 - - + -
553D ILE* 3.7 1.1 + - + -
554D PHE* 2.8 28.7 + - + +
557D CYS* 1.3 73.4 - - + +
559D GLU* 1.3 66.8 + - - +
560D ASN 3.2 0.7 + - - -
561D GLN* 2.8 17.9 + - - +
562D PHE* 3.4 20.4 - - + -
635D LEU* 3.4 25.6 - - + -
638D VAL* 3.7 23.1 - - + -
639D LEU* 4.1 13.9 - - + -
----------------------------------------------------------
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