Contacts of the helix formed by residues 517 - 527 (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 ASN 517 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q GLY 5.4 0.3 - - - +
81Q ARG* 3.8 33.3 + - - +
498Q GLY* 3.5 20.9 + - - +
500Q ILE* 4.0 22.7 - - + +
516Q GLY* 1.3 70.8 - - - -
518Q ILE* 1.3 65.3 + - - +
519Q ASN* 2.7 25.4 + - - +
520Q SER* 3.1 29.8 + - - +
558Q TYR* 3.2 20.3 - - - -
666Q GTP 4.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 518 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q GLY 5.0 3.4 + - - +
80Q VAL* 4.3 23.6 - - + +
84Q PHE* 4.1 16.8 - - + -
516Q GLY 3.5 4.9 + - - -
517Q ASN* 1.3 71.3 + - - +
519Q ASN* 1.3 73.2 + - + +
521Q MET* 2.9 47.2 + - + +
522Q LEU* 3.1 13.7 + - + +
558Q TYR* 4.5 4.9 - - + -
561Q CYS* 3.2 33.9 - - + -
563Q ILE* 4.4 5.4 - - + -
564Q TYR* 4.3 18.8 - - + -
567Q VAL* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 519 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q VAL* 5.8 0.2 - - - +
81Q ARG* 6.3 1.3 - - + -
82Q THR* 4.4 15.2 - - + +
83Q ASN 3.4 17.9 + - - +
84Q PHE* 3.1 33.2 - - - +
86Q GLY* 5.4 5.9 - - - -
517Q ASN* 2.7 20.5 + - - +
518Q ILE* 1.3 79.1 - - + +
520Q SER* 1.3 51.7 + - - +
522Q LEU* 3.1 10.7 + - - +
523Q ASN* 2.7 62.9 + - - +
666Q GTP 5.7 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 520 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498Q GLY* 5.0 3.5 + - - -
517Q ASN* 3.1 31.6 + - - +
518Q ILE 3.1 0.4 - - - -
519Q ASN* 1.3 76.3 - - - +
521Q MET* 1.3 66.0 + - - +
523Q ASN* 3.9 10.1 - - - +
524Q ASN* 2.9 33.8 + - - -
558Q TYR* 3.8 11.2 - - - -
666Q GTP 3.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 521 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518Q ILE* 2.9 30.3 + - + +
520Q SER* 1.3 78.3 - - - +
522Q LEU* 1.3 71.2 + - + +
524Q ASN* 3.8 1.4 - - - +
525Q GLN* 3.0 40.7 + - + +
554Q MET* 3.6 32.1 - - + +
558Q TYR* 3.4 45.8 - - + -
564Q TYR* 4.0 13.2 - - + -
567Q VAL* 3.6 24.5 - - + -
568Q LEU* 4.9 4.3 - - + -
571Q ILE* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU* 4.1 13.7 - - + -
61Q LEU* 3.6 14.6 - - + -
84Q PHE* 3.3 37.9 - - + -
87Q MET* 4.2 16.4 - - + +
518Q ILE 3.1 8.9 + - - +
519Q ASN* 3.1 10.4 + - - +
521Q MET* 1.3 80.1 - - + +
523Q ASN* 1.3 64.4 + - - +
525Q GLN* 6.0 0.2 - - - -
526Q PHE* 3.0 54.1 + - + +
527Q SER 4.2 0.2 + - - -
567Q VAL* 4.1 15.5 - - + -
571Q ILE* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 523 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q GLY* 4.8 3.8 - - - -
87Q MET* 4.9 2.8 + - - +
207Q SER* 5.7 0.9 - - - +
208Q THR* 3.0 43.4 + - + +
519Q ASN* 2.7 45.9 + - - +
520Q SER* 3.7 9.5 - - - +
521Q MET 3.4 0.2 - - - -
522Q LEU* 1.3 73.3 - - - +
524Q ASN* 1.3 64.5 + - - +
527Q SER* 2.8 39.4 + - - +
666Q GTP 4.4 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 524 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Q TYR* 4.4 2.4 + - - -
520Q SER* 2.9 27.1 + - - +
521Q MET* 3.8 3.1 - - - +
523Q ASN* 1.3 82.0 - - - +
525Q GLN* 1.3 64.8 + - + +
526Q PHE 3.5 0.2 + - - -
527Q SER 5.2 0.7 - - - -
528Q PRO* 3.9 20.3 - - - +
544Q ARG* 5.3 1.6 + - - -
558Q TYR* 3.6 15.1 + - - +
620Q GLU* 5.1 2.3 - - - +
627Q LYS* 3.2 28.6 + - - +
666Q GTP 4.8 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 525 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q THR* 4.5 1.2 - - - +
40Q TYR* 2.9 39.1 + - - +
521Q MET* 3.0 31.5 + - + +
524Q ASN* 1.3 78.1 - - + +
526Q PHE* 1.3 78.4 + - + +
528Q PRO* 4.6 0.8 - - - +
550Q ALA* 5.7 4.3 - - + +
551Q TRP* 4.0 10.8 - - - -
554Q MET* 3.4 28.5 - - - +
568Q LEU* 5.7 0.2 - - - +
571Q ILE* 4.5 6.4 - - - +
583Q TYR* 2.7 44.0 + - - +
587Q ARG* 4.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 526 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q THR* 4.9 0.2 - - - -
40Q TYR* 5.0 2.5 - + - -
50Q PHE* 3.7 24.1 - + + -
53Q PHE* 3.6 37.2 - + + -
54Q LYS* 3.1 34.6 + - + -
57Q LEU* 4.4 3.1 - - + -
87Q MET* 5.0 8.1 - - + -
91Q ASN* 3.5 4.2 + - - -
522Q LEU* 3.0 31.5 + - + +
525Q GLN* 1.3 92.8 - - + +
527Q SER* 1.3 60.3 + - - +
528Q PRO* 3.4 7.7 - - - +
571Q ILE* 3.6 28.3 - - + -
575Q TRP* 3.9 2.9 - + - -
583Q TYR* 3.4 43.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 527 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q LYS* 3.4 17.2 + - - -
87Q MET* 3.8 9.9 + - - -
91Q ASN* 3.6 11.0 + - - +
207Q SER* 2.5 36.5 + - - -
208Q THR* 3.5 28.7 - - - +
522Q LEU 5.2 0.2 - - - -
523Q ASN* 2.8 20.4 + - - +
524Q ASN* 5.2 0.2 - - - -
526Q PHE* 1.3 84.4 + - - +
528Q PRO* 1.3 62.1 - - - +
529Q GLU* 4.8 0.2 - - - +
----------------------------------------------------------
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