Contacts of the helix formed by residues 549 - 559 (chain Q) in PDB entry 1HI0
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 549 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546Q PHE* 3.1 33.7 + - + +
548Q GLY* 1.3 70.9 - - - +
550Q ALA* 1.3 63.6 + - - +
551Q TRP 2.9 5.6 - - - -
552Q ALA* 2.8 22.9 + - - +
553Q SER* 3.6 4.0 + - - -
591Q LEU* 4.2 7.9 - - + -
594Q ASP* 4.0 15.9 - - + +
595Q THR* 4.0 24.7 - - - +
598Q LEU* 4.0 12.1 - - + -
611Q LEU* 4.2 13.5 - - + -
619Q LEU* 4.1 24.8 - - + +
622Q LEU* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525Q GLN* 5.7 4.0 - - + +
547Q PRO 3.4 13.3 + - - +
548Q GLY 3.2 0.8 - - - -
549Q LEU* 1.3 76.9 - - - +
551Q TRP* 1.3 60.9 + - - +
553Q SER* 3.4 11.8 + - - +
554Q MET* 3.0 23.6 + - - +
587Q ARG* 4.8 7.6 - - - +
619Q LEU 5.0 2.0 - - - -
620Q GLU* 4.1 11.9 - - - +
623Q ALA* 4.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 551 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525Q GLN* 4.0 8.5 - - - -
548Q GLY 3.3 15.9 + - - +
549Q LEU 2.8 0.8 + - - -
550Q ALA* 1.3 77.7 - - - +
552Q ALA* 1.3 62.7 + - - +
554Q MET* 3.3 56.8 + - + +
555Q LYS* 4.5 1.6 + - - +
568Q LEU* 4.1 11.9 - - + -
583Q TYR* 3.7 24.7 - + - -
584Q ARG* 4.2 24.9 - - + -
587Q ARG* 3.4 57.3 - - + +
588Q GLU* 3.6 21.4 + - + -
591Q LEU* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 552 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549Q LEU 2.8 8.6 + - - +
551Q TRP* 1.3 81.5 - - - +
553Q SER* 1.3 59.6 + - - +
554Q MET 3.6 0.3 + - - -
555Q LYS* 4.6 6.4 + - - +
556Q ASP* 5.0 3.1 + - - +
591Q LEU* 4.1 15.0 - - + +
611Q LEU* 4.1 20.6 - - + -
619Q LEU* 3.3 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549Q LEU 3.6 0.8 + - - -
550Q ALA* 3.4 12.8 + - - -
552Q ALA* 1.3 78.8 - - - +
554Q MET* 1.3 54.1 + - - +
555Q LYS 3.5 0.7 - - - -
556Q ASP* 3.2 9.5 + - - +
557Q THR* 2.7 35.3 + - - -
616Q PRO* 3.7 29.4 - - - -
619Q LEU* 3.8 14.2 - - - +
620Q GLU* 2.6 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 554 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521Q MET* 3.6 24.9 - - + +
525Q GLN* 3.4 24.7 - - - +
550Q ALA 3.0 13.8 + - - +
551Q TRP* 3.3 56.1 - - + +
552Q ALA 3.3 1.6 - - - -
553Q SER* 1.3 76.5 - - - +
555Q LYS* 1.3 57.1 + - + +
557Q THR* 3.2 1.1 + - - -
558Q TYR* 2.7 43.1 + - + -
559Q GLY 3.8 0.2 + - - -
564Q TYR* 3.3 17.7 + - - +
568Q LEU* 3.8 17.0 - - + -
620Q GLU* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 555 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551Q TRP 4.5 2.4 + - - +
552Q ALA 4.6 4.7 + - - +
553Q SER 3.5 0.4 - - - -
554Q MET* 1.3 78.1 - - + +
556Q ASP* 1.3 58.5 + - - +
559Q GLY* 2.6 40.0 + - - -
564Q TYR* 3.0 44.8 + - + +
565Q SER* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 556 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Q ARG* 5.0 12.1 + - - -
552Q ALA 5.0 1.5 + - - +
553Q SER* 3.2 12.5 + - - +
555Q LYS* 1.3 85.3 - - - +
557Q THR* 1.3 66.0 + - - +
559Q GLY 4.2 1.7 + - - -
560Q ALA* 5.2 2.3 + - - +
616Q PRO* 3.5 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 557 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Q ARG* 4.3 8.9 - - - +
499Q ASP* 5.1 0.7 - - - +
516Q GLY* 4.0 17.3 + - - -
553Q SER* 2.7 19.8 + - - -
556Q ASP* 1.3 77.7 + - - +
558Q TYR* 1.3 97.8 + - + +
560Q ALA* 5.4 0.7 + - - +
616Q PRO* 5.4 2.3 - - - +
620Q GLU* 3.2 30.8 + - - +
631Q LYS* 6.3 2.9 - - - -
632Q TRP* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 558 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516Q GLY* 4.7 3.1 - - - -
517Q ASN 3.2 38.1 - - - -
518Q ILE* 4.5 6.1 - - + -
520Q SER* 3.7 7.8 + - - -
521Q MET* 3.4 50.1 + - + -
524Q ASN* 3.6 19.9 + - - +
554Q MET* 2.7 27.1 + - + +
557Q THR* 1.3 101.6 - - + +
559Q GLY* 1.3 65.4 + - - +
560Q ALA* 3.1 3.1 - - - -
561Q CYS* 2.8 24.3 + - + +
564Q TYR* 3.7 19.3 - - + -
620Q GLU* 4.7 9.1 + - - -
627Q LYS* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 559 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554Q MET 3.8 0.4 + - - -
555Q LYS* 2.6 39.7 + - - -
556Q ASP 4.2 0.4 + - - -
557Q THR 3.8 0.6 - - - -
558Q TYR* 1.3 70.2 - - - +
560Q ALA* 1.3 60.7 + - - +
561Q CYS 3.1 8.8 + - - +
564Q TYR* 3.7 27.8 - - - +
----------------------------------------------------------
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