Contacts of the helix formed by residues 47 - 65 (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 ASP 47 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P GLU* 5.3 7.2 - - - +
539P ARG* 5.3 1.7 + - - -
597P GLU* 4.7 1.6 - - - +
43Q LEU* 3.6 19.7 - - + +
44Q LEU* 2.9 25.4 + - + +
45Q SER 3.4 0.4 - - - -
46Q VAL* 1.3 79.1 - - - +
48Q PRO* 1.3 75.6 - - - +
49Q ARG* 2.6 56.8 + - - +
50Q PHE* 3.0 8.1 + - + +
51Q LEU* 2.9 19.9 + - - +
579Q PHE* 4.9 0.2 - - - -
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Residues in contact with PRO 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P GLU* 5.6 3.1 - - - +
534P SER* 3.2 35.9 - - - +
535P GLY* 4.9 3.6 - - - +
537P ARG* 3.5 25.8 + - - +
542P ARG* 5.7 2.0 - - - +
46Q VAL 3.1 6.5 - - - +
47Q ASP* 1.3 91.0 - - - +
49Q ARG* 1.3 64.2 + - - +
51Q LEU* 3.3 8.0 + - + +
52Q SER* 2.9 25.5 + - - -
259Q ASP* 5.8 11.0 - - + +
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Residues in contact with ARG 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537P ARG* 3.7 43.9 - - + +
539P ARG* 4.3 11.5 - - - +
542P ARG* 6.1 1.1 - - - +
597P GLU* 2.6 44.1 + - - -
600P ARG* 3.3 24.0 - - - +
601P TYR* 5.8 2.4 + - - -
43Q LEU* 5.8 1.4 - - - +
47Q ASP* 2.6 42.4 + - - +
48Q PRO* 1.3 74.1 - - - +
50Q PHE* 1.3 55.7 + - - +
52Q SER* 3.3 2.4 - - - -
53Q PHE* 2.8 29.1 + - - +
578Q ALA* 3.3 27.5 + - - +
579Q PHE* 3.4 29.1 - - + +
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Residues in contact with PHE 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q THR* 3.8 28.3 - - + -
40Q TYR* 5.7 0.9 - + - -
43Q LEU* 4.0 18.8 - - + -
44Q LEU 4.1 2.0 - - - -
45Q SER* 3.5 25.6 - - - -
47Q ASP* 3.0 21.9 + - + +
49Q ARG* 1.3 80.3 - - - +
51Q LEU* 1.3 52.2 + - - +
53Q PHE* 2.9 16.0 + + - +
54Q LYS* 2.7 50.5 + - + +
526Q PHE* 3.7 44.6 - + + -
575Q TRP* 3.9 19.5 - + - -
579Q PHE* 3.6 14.7 - + + -
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Residues in contact with LEU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q SER 3.2 24.7 - - - +
46Q VAL* 3.4 19.1 - - + +
47Q ASP 2.9 18.6 + - - +
48Q PRO* 3.9 7.4 - - + +
50Q PHE* 1.3 72.4 - - - +
52Q SER* 1.3 53.0 + - - +
54Q LYS* 3.0 14.6 + - + +
55Q ASN* 2.7 36.7 + - - +
89Q HIS 5.1 0.9 - - - +
90Q MET* 3.2 31.0 - - + -
259Q ASP* 4.0 9.4 - - - +
261Q PRO* 3.6 38.6 - - + -
264Q PHE* 3.6 11.7 - - + -
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Residues in contact with SER 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537P ARG* 3.5 22.5 + - - -
48Q PRO 2.9 18.5 + - - -
49Q ARG* 3.3 6.1 - - - -
51Q LEU* 1.3 77.3 - - - +
53Q PHE* 1.3 63.4 + - - -
55Q ASN* 3.1 9.3 + - - +
56Q GLU* 2.9 24.9 + - - +
261Q PRO* 5.7 0.6 - - - +
578Q ALA* 5.0 5.0 - - - +
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Residues in contact with PHE 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Q ARG 2.8 13.8 + - - +
50Q PHE* 3.1 23.3 - + - +
52Q SER* 1.3 77.0 + - - +
54Q LYS* 1.3 71.6 - - + +
56Q GLU* 3.2 4.8 + - - +
57Q LEU* 2.9 55.5 + - + +
526Q PHE* 3.6 41.3 - + + -
571Q ILE* 3.8 9.9 - - + -
574Q CYS* 3.5 31.4 - - + -
575Q TRP* 3.5 41.5 - + - -
578Q ALA* 3.6 14.3 - - + +
579Q PHE* 4.3 1.6 - - + -
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Residues in contact with LYS 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q SER 4.9 3.0 + - - -
50Q PHE* 2.7 33.0 + - + +
51Q LEU* 3.3 13.7 - - + +
53Q PHE* 1.3 85.2 - - + +
55Q ASN* 1.3 59.1 + - - +
57Q LEU* 4.7 0.2 - - - -
58Q SER* 2.9 31.4 + - - -
87Q MET* 3.1 50.8 + - + +
88Q ARG* 5.7 0.2 - - - -
89Q HIS 3.6 9.1 + - - -
91Q ASN* 3.1 31.5 - - - +
264Q PHE* 4.1 14.6 - - + -
526Q PHE* 3.1 26.3 + - + -
527Q SER* 3.4 6.7 + - - -
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Residues in contact with ASN 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q LEU 2.7 16.9 + - - +
52Q SER* 3.1 12.7 + - - +
54Q LYS* 1.3 74.2 - - - +
56Q GLU* 1.3 68.0 + - - +
58Q SER* 3.0 13.2 + - - -
59Q ARG* 3.1 34.4 + - - +
88Q ARG* 2.3 34.5 + - - +
261Q PRO* 5.9 2.8 - - + +
262Q ASP 4.6 3.1 - - - +
264Q PHE* 3.9 12.7 - - + -
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Residues in contact with GLU 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q SER 2.9 15.0 + - - +
53Q PHE* 3.8 3.1 - - - +
55Q ASN* 1.3 85.1 - - - +
57Q LEU* 1.3 58.0 + - - +
59Q ARG* 3.8 4.0 - - - +
60Q TYR* 3.0 34.6 + - + +
573Q ARG* 3.7 11.6 + - - +
574Q CYS* 3.4 27.4 - - - +
577Q ASN* 3.0 36.6 + - - +
578Q ALA* 5.8 0.3 - - - +
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Residues in contact with LEU 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q PHE* 2.9 50.3 + - + +
54Q LYS 4.1 2.0 - - - +
56Q GLU* 1.3 70.1 - - - +
58Q SER* 1.3 67.0 + - - +
60Q TYR* 4.6 1.6 - - + -
61Q LEU* 3.0 46.7 + - + +
87Q MET* 4.1 20.2 - - + -
522Q LEU* 4.1 8.1 - - + -
526Q PHE* 4.4 1.8 - - + -
570Q ALA* 3.9 29.6 - - + -
571Q ILE* 3.7 17.9 - - + +
574Q CYS* 3.9 14.7 - - + -
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Residues in contact with SER 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q LYS 2.9 23.4 + - - -
55Q ASN 3.0 5.9 + - - -
57Q LEU* 1.3 78.0 - - - +
59Q ARG* 1.3 68.1 + - - +
61Q LEU* 4.0 0.7 - - - +
62Q THR* 2.7 33.2 + - - -
84Q PHE* 3.4 26.2 - - - +
85Q PHE* 4.0 11.1 - - - -
87Q MET* 3.6 16.3 - - - -
88Q ARG* 3.3 20.1 + - - +
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Residues in contact with ARG 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q ASN* 3.1 44.7 + - - +
56Q GLU* 3.8 4.3 - - - +
58Q SER* 1.3 82.6 + - - +
60Q TYR* 1.3 63.1 + - - +
62Q THR* 3.3 2.1 + - - -
63Q ASP* 2.9 25.0 + - - +
85Q PHE* 3.9 16.5 - - + -
88Q ARG* 3.2 6.7 - - - +
213Q LEU* 4.4 12.7 - - + +
218Q GLY 5.4 4.2 + - - -
220Q PHE* 3.4 30.8 - - + -
262Q ASP* 5.2 6.5 + - - +
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Residues in contact with TYR 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q GLU* 3.0 22.2 + - + +
57Q LEU* 3.9 4.0 - - + +
59Q ARG* 1.3 76.3 - - - +
61Q LEU* 1.3 79.9 + - + +
63Q ASP* 3.0 5.9 + - - -
64Q HIS* 2.8 72.9 + + + +
65Q PHE* 4.6 5.8 - + - -
570Q ALA* 3.9 18.8 - - + -
573Q ARG* 3.1 37.3 + - - +
574Q CYS* 5.2 0.7 - - - -
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Residues in contact with LEU 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU* 3.0 41.8 + - + +
58Q SER 4.0 0.4 - - - +
60Q TYR* 1.3 77.8 - - + +
62Q THR* 1.3 58.8 + - - +
65Q PHE* 2.8 64.1 + - + +
84Q PHE* 3.6 21.5 - - + -
87Q MET* 5.3 0.2 - - + -
522Q LEU* 3.6 31.2 - - + -
567Q VAL* 4.0 25.4 - - + -
570Q ALA* 4.0 16.2 - - + -
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Residues in contact with THR 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Q SER 2.7 21.9 + - - -
59Q ARG 3.6 4.0 - - - -
61Q LEU* 1.3 77.2 - - - +
63Q ASP* 1.3 63.5 + - - +
65Q PHE 3.9 0.8 - - - -
66Q PRO* 3.8 19.7 - - + +
83Q ASN* 3.2 27.6 - - + +
84Q PHE* 3.0 27.7 + - - -
85Q PHE* 3.2 29.0 - - + -
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Residues in contact with ASP 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Q ARG 2.9 17.3 + - - +
60Q TYR* 3.0 6.0 + - - +
62Q THR* 1.3 81.1 - - - +
64Q HIS* 1.3 77.9 + - + +
65Q PHE 3.5 0.2 + - - -
66Q PRO* 3.8 9.0 - - - +
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Residues in contact with HIS 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q TYR* 2.8 64.5 + + + +
63Q ASP* 1.3 89.2 - - + +
65Q PHE* 1.3 90.5 + - + +
66Q PRO* 3.5 6.3 - - - +
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Residues in contact with PHE 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q TYR* 4.6 8.1 - + - -
61Q LEU* 2.8 45.6 + - + +
62Q THR* 3.9 2.2 - - - +
63Q ASP 3.3 0.2 - - - -
64Q HIS* 1.3 102.3 - - + +
66Q PRO* 1.3 69.8 - - - +
78Q ASN* 3.8 8.3 - - + +
80Q VAL* 3.4 29.7 - - + +
82Q THR 4.8 0.3 - - - +
83Q ASN* 5.7 0.5 - - - -
84Q PHE* 3.5 11.0 - - + -
563Q ILE* 3.3 39.5 - - + -
566Q ASP* 3.6 32.5 - - + -
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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