Contacts of the helix formed by residues 517 - 527 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P ARG* 3.8 33.3 + - - +
498P GLY* 3.5 20.0 + - - +
500P ILE* 4.0 23.8 - - + +
516P GLY* 1.3 71.4 - - - -
518P ILE* 1.3 64.7 + - - +
519P ASN* 2.7 25.3 + - - +
520P SER* 3.1 30.4 + - - +
558P TYR* 3.2 19.5 - - - -
666P GTP 4.1 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 518 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P GLY 5.0 3.6 + - - +
80P VAL* 4.3 23.6 - - + -
84P PHE* 4.1 17.7 - - + -
516P GLY 3.5 5.5 + - - -
517P ASN* 1.3 71.9 + - - +
519P ASN* 1.3 74.0 + - + +
521P MET* 2.9 47.1 + - + +
522P LEU* 3.1 12.6 + - + +
558P TYR* 4.5 4.5 - - + -
561P CYS* 3.2 34.6 - - + -
563P ILE* 4.4 5.4 - - + -
564P TYR* 4.3 19.1 - - + +
567P VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 519 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P VAL* 5.8 0.2 - - - +
81P ARG* 6.3 1.6 - - + -
82P THR* 4.4 14.4 - - + +
83P ASN 3.4 18.3 + - - +
84P PHE* 3.1 32.3 - - - +
86P GLY* 5.4 5.9 - - - -
517P ASN* 2.7 20.7 + - - +
518P ILE* 1.3 79.2 - - + +
520P SER* 1.3 50.2 + - - +
522P LEU* 3.1 10.3 + - - +
523P ASN* 2.7 64.3 + - - +
666P GTP 5.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 520 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498P GLY* 5.0 3.0 + - - -
517P ASN* 3.1 33.2 + - - +
518P ILE 3.1 0.6 - - - -
519P ASN* 1.3 76.7 - - - +
521P MET* 1.3 64.9 - - - +
523P ASN* 3.9 10.1 - - - +
524P ASN* 2.9 33.4 + - - +
558P TYR* 3.8 10.1 - - - -
666P GTP 3.9 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 521 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518P ILE* 2.9 30.9 + - + +
520P SER* 1.3 78.4 - - - +
522P LEU* 1.3 70.9 + - + +
524P ASN* 3.8 1.9 - - - +
525P GLN* 3.0 39.4 + - + +
554P MET* 3.6 31.9 - - - +
558P TYR* 3.4 46.0 - - + -
564P TYR* 4.0 13.5 - - + -
567P VAL* 3.6 24.0 - - + -
568P LEU* 4.9 3.4 - - + -
571P ILE* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU* 4.1 13.5 - - + -
61P LEU* 3.6 14.4 - - + -
84P PHE* 3.3 37.2 - - + -
87P MET* 4.2 17.1 - - + +
518P ILE 3.1 9.6 + - - +
519P ASN* 3.1 10.0 + - - +
521P MET* 1.3 78.5 - - + +
523P ASN* 1.3 65.9 + - - +
525P GLN* 6.0 0.2 - - - -
526P PHE* 3.0 54.4 + - + +
527P SER* 5.2 0.2 - - - -
567P VAL* 4.1 15.5 - - + -
571P ILE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 523 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P GLY* 4.8 3.8 - - - -
87P MET* 4.9 3.4 + - - +
207P SER* 5.7 0.2 - - - +
208P THR* 3.0 43.6 + - + +
519P ASN* 2.7 45.5 + - - +
520P SER* 3.7 9.4 - - - +
522P LEU* 1.3 72.4 - - - +
524P ASN* 1.3 65.9 + - - +
527P SER* 2.8 38.8 + - - +
666P GTP 4.4 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 524 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P TYR* 4.4 2.4 + - - -
520P SER* 2.9 27.5 + - - +
521P MET 3.8 2.9 - - - +
523P ASN* 1.3 81.7 - - - +
525P GLN* 1.3 64.4 + - + +
526P PHE 3.5 0.2 + - - -
527P SER 5.1 0.9 - - - -
528P PRO* 3.9 20.3 - - - +
544P ARG* 5.3 1.6 + - - -
558P TYR* 3.6 15.8 + - - +
620P GLU* 5.1 2.4 - - - +
627P LYS* 3.2 27.4 + - - +
666P GTP 4.8 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 525 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P THR* 4.5 0.9 - - - +
40P TYR* 2.9 39.1 + - - +
521P MET* 3.0 32.8 + - + +
524P ASN* 1.3 79.5 - - + +
526P PHE* 1.3 77.6 + - + +
528P PRO* 4.6 0.7 - - - -
550P ALA* 5.7 4.7 - - + +
551P TRP* 4.0 10.6 - - - -
554P MET* 3.4 29.2 - - - +
568P LEU* 5.7 0.2 - - - +
571P ILE* 4.5 6.0 - - - +
583P TYR* 2.7 42.7 + - - +
587P ARG* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 526 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P THR* 4.9 0.2 - - - -
40P TYR* 5.0 1.8 - + - -
50P PHE* 3.7 23.3 - + + -
53P PHE* 3.6 36.8 - + + -
54P LYS* 3.1 35.3 + - + -
57P LEU* 4.7 2.2 - - + -
87P MET* 5.0 7.9 - - + -
91P ASN* 3.5 4.3 + - - -
522P LEU* 3.0 33.0 + - + +
525P GLN* 1.3 92.7 - - + +
527P SER* 1.3 61.5 + - - +
528P PRO* 3.4 7.3 - - - +
571P ILE* 3.6 27.6 - - + -
575P TRP* 3.9 3.1 - + - -
583P TYR* 3.4 44.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 527 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P LYS* 3.4 17.0 + - - -
87P MET* 3.8 10.3 + - - -
91P ASN* 3.6 10.3 + - - +
207P SER* 2.5 35.8 + - - -
208P THR* 3.5 29.4 - - - +
522P LEU 4.2 0.4 + - - -
523P ASN* 2.8 20.2 + - - +
526P PHE* 1.3 84.2 + - - +
528P PRO* 1.3 62.2 - - - +
529P GLU* 4.8 0.3 - - - +
----------------------------------------------------------
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