Contacts of the helix formed by residues 47 - 65 (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 ASP 47 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P LEU* 3.6 20.9 - - + +
44P LEU* 2.9 25.0 + - + +
45P SER 3.4 0.2 - - - -
46P VAL* 1.3 78.8 - - - +
48P PRO* 1.3 75.1 - - - +
49P ARG* 2.6 57.0 + - - +
50P PHE* 3.0 9.2 + - + +
51P LEU* 2.9 19.8 + - - +
255Q GLN 4.6 10.3 - - - +
256Q TYR* 5.3 2.1 - - - -
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Residues in contact with PRO 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P VAL 3.1 7.6 - - - +
47P ASP* 1.3 90.7 - - - +
49P ARG* 1.3 65.6 + - + +
51P LEU* 3.3 7.9 + - + +
52P SER* 2.9 25.7 + - - -
259P ASP* 5.8 11.9 - - + +
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Residues in contact with ARG 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P LEU* 5.8 1.2 - - - +
47P ASP* 2.6 43.4 + - - +
48P PRO* 1.3 75.5 - - + +
50P PHE* 1.3 57.0 + - - +
52P SER* 3.3 7.3 - - - -
53P PHE* 2.8 29.3 + - - +
578P ALA* 3.3 28.7 + - - +
579P PHE* 3.4 37.0 - - + +
256Q TYR* 4.2 23.6 + - - -
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Residues in contact with PHE 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P THR* 3.8 27.6 - - + -
40P TYR* 5.7 1.1 - + - -
43P LEU* 4.0 17.7 - - + -
44P LEU 4.1 2.2 - - - +
45P SER* 3.5 24.0 - - - -
47P ASP* 3.0 22.3 + - + +
49P ARG* 1.3 78.4 - - - +
51P LEU* 1.3 51.9 + - - +
53P PHE* 2.9 16.3 + + - +
54P LYS* 2.7 51.6 + - + +
526P PHE* 3.7 44.6 - + + -
575P TRP* 3.9 20.0 - + - -
579P PHE* 3.6 14.5 - + + -
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Residues in contact with LEU 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P SER 3.2 24.7 - - - +
46P VAL* 3.4 18.8 - - + +
47P ASP 2.9 19.8 + - - +
48P PRO* 3.9 7.6 - - + +
50P PHE* 1.3 72.0 - - - +
52P SER* 1.3 53.5 + - - +
54P LYS* 3.0 13.3 + - + +
55P ASN* 2.7 36.7 + - - +
89P HIS 5.1 1.3 - - - +
90P MET* 3.2 32.3 - - + -
259P ASP 4.0 9.0 - - - +
261P PRO* 3.6 38.6 - - + -
264P PHE* 3.6 11.7 - - + -
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Residues in contact with SER 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P PRO 2.9 18.3 + - - -
49P ARG* 3.3 8.7 - - - -
51P LEU* 1.3 76.2 - - - +
53P PHE* 1.3 63.6 + - - -
55P ASN* 3.1 10.0 + - - +
56P GLU* 2.9 25.2 + - - +
261P PRO* 6.1 0.6 - - - +
578P ALA* 5.0 6.0 - - - +
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Residues in contact with PHE 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P ARG 2.8 12.9 + - - +
50P PHE* 3.1 23.3 - + - +
52P SER* 1.3 77.1 - - - +
54P LYS* 1.3 71.9 + - + +
56P GLU* 3.2 4.4 + - - +
57P LEU* 2.9 57.5 + - + +
87P MET* 5.7 0.2 - - - -
526P PHE* 3.6 40.4 - + + -
571P ILE* 3.8 10.1 - - + -
574P CYS* 3.5 32.8 - - + -
575P TRP* 3.5 41.1 - + - -
578P ALA* 3.6 15.2 - - + +
579P PHE* 4.3 1.1 - - + -
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Residues in contact with LYS 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P SER 4.9 3.2 + - - -
50P PHE* 2.7 33.6 + - + +
51P LEU* 3.3 13.0 - - + +
53P PHE* 1.3 84.2 - - + +
55P ASN* 1.3 57.7 + - - +
57P LEU* 4.7 0.2 - - - -
58P SER* 2.9 31.7 + - - -
87P MET* 3.1 50.8 + - + +
88P ARG* 5.7 0.2 - - - -
89P HIS 3.6 9.3 + - - -
91P ASN* 3.1 30.7 - - - +
264P PHE* 4.1 15.3 - - + -
526P PHE* 3.1 26.0 + - + -
527P SER* 3.4 6.7 + - - -
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Residues in contact with ASN 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P LEU 2.7 15.9 + - - +
52P SER* 3.4 12.3 + - - +
54P LYS* 1.3 74.2 - - - +
56P GLU* 1.3 69.3 + - - +
58P SER* 3.0 13.8 + - - -
59P ARG* 3.1 34.7 + - - +
88P ARG* 2.3 34.8 + - - +
261P PRO* 5.9 3.7 - - + +
262P ASP 4.6 2.9 - - - +
264P PHE* 3.9 12.7 - - + -
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Residues in contact with GLU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P SER 2.9 15.4 + - - +
53P PHE* 3.8 3.2 - - - +
55P ASN* 1.3 84.9 - - - +
57P LEU* 1.3 58.8 + - - +
59P ARG* 3.8 3.8 - - - +
60P TYR* 3.0 35.0 + - + +
573P ARG* 3.7 12.2 + - - +
574P CYS* 3.4 27.5 - - - +
577P ASN* 3.0 36.6 + - - +
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 2.9 48.8 + - + +
54P LYS 4.1 2.0 - - - +
56P GLU* 1.3 70.0 - - - +
58P SER* 1.3 67.0 + - - +
60P TYR* 4.6 1.6 - - + -
61P LEU* 3.0 47.3 + - + +
87P MET* 4.1 19.1 - - + -
522P LEU* 4.1 8.7 - - + -
526P PHE* 4.4 1.3 - - + -
570P ALA* 3.9 30.1 - - + -
571P ILE* 3.7 18.2 - - + +
574P CYS* 3.9 13.6 - - + -
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Residues in contact with SER 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P LYS 2.9 23.0 + - - -
55P ASN 3.0 6.6 + - - -
57P LEU* 1.3 78.4 - - - +
59P ARG* 1.3 66.0 + - - +
61P LEU* 4.0 0.7 - - - +
62P THR* 2.7 33.9 + - - -
84P PHE* 3.4 26.4 - - - +
85P PHE* 4.0 10.7 - - - -
87P MET* 3.6 16.1 - - - -
88P ARG* 3.3 19.9 + - - +
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Residues in contact with ARG 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P ASN* 3.1 45.0 + - - +
56P GLU* 3.8 4.5 - - - +
58P SER* 1.3 82.8 + - - +
60P TYR* 1.3 64.3 + - - +
62P THR* 3.3 2.4 + - - -
63P ASP* 2.9 25.0 + - - +
85P PHE* 3.9 17.0 - - + -
88P ARG* 3.2 7.0 - - - +
213P LEU* 4.4 12.7 - - + +
218P GLY 5.4 4.2 + - - -
220P PHE* 3.4 30.3 - - + -
262P ASP* 5.2 6.7 + - - +
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Residues in contact with TYR 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P GLU* 3.0 21.0 + - + +
57P LEU* 3.9 4.0 - - + +
59P ARG* 1.3 76.7 - - - +
61P LEU* 1.3 79.3 + - + +
63P ASP* 3.0 5.9 + - - -
64P HIS* 2.8 73.7 + + + +
65P PHE* 4.6 5.4 - + - -
570P ALA* 3.9 19.1 - - + -
573P ARG* 3.1 36.8 + - - +
574P CYS* 5.2 1.1 - - - -
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Residues in contact with LEU 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU* 3.0 42.9 + - + +
58P SER 4.0 0.2 - - - +
60P TYR* 1.3 77.7 - - + +
62P THR* 1.3 58.1 + - - +
65P PHE* 2.8 64.8 + - + +
84P PHE* 3.6 22.0 - - + -
87P MET* 5.3 0.2 - - + -
522P LEU* 3.6 31.4 - - + -
567P VAL* 4.0 25.8 - - + -
570P ALA* 4.0 16.4 - - + -
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Residues in contact with THR 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P SER 2.7 21.9 + - - -
59P ARG 3.6 4.3 - - - -
61P LEU* 1.3 78.5 - - - +
63P ASP* 1.3 61.9 + - - +
65P PHE 3.9 0.8 - - - -
66P PRO* 3.8 19.6 - - + +
83P ASN* 3.2 27.1 - - + +
84P PHE* 3.0 27.8 + - - -
85P PHE* 3.2 28.1 - - + -
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Residues in contact with ASP 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P ARG 2.9 16.9 + - - +
60P TYR* 3.4 6.3 - - - +
62P THR* 1.3 81.3 - - - +
64P HIS* 1.3 78.7 + - + +
65P PHE 3.5 0.7 + - - -
66P PRO* 3.8 8.3 - - - +
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Residues in contact with HIS 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P TYR* 2.8 64.2 + + + +
63P ASP* 1.3 88.1 - - + +
65P PHE* 1.3 90.6 - - + +
66P PRO* 3.5 6.1 - - - +
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Residues in contact with PHE 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P TYR* 4.6 8.1 - + - -
61P LEU* 2.8 44.5 + - + +
62P THR* 3.9 2.5 - - - +
64P HIS* 1.3 102.8 - - + +
66P PRO* 1.3 69.6 - - - +
78P ASN* 3.8 8.5 - - + +
80P VAL* 3.4 29.7 - - + +
82P THR 4.8 0.3 - - - +
83P ASN* 5.7 0.3 - - - -
84P PHE* 3.5 10.1 - - + -
563P ILE* 3.3 40.8 - - + -
566P ASP* 3.6 32.3 - - + -
567P VAL* 5.5 0.2 - - + -
570P ALA* 5.9 0.2 - - + -
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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) + - + + + + + -
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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