Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 5HK5
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 THR 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PRO* 1.3 74.6 - - - +
64A ASN* 1.3 66.7 + - - +
65A HIS* 3.8 9.1 + - - +
66A ALA* 2.9 39.9 + - - +
67A VAL* 2.9 12.2 + - - +
120A ARG* 3.6 36.0 + - - +
87C PRO* 6.1 0.5 - - - +
90C LEU* 4.8 12.6 - - + +
111C ASP* 4.0 26.0 - - + +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO 3.7 2.2 + - - +
63A THR* 1.3 70.2 - - - +
65A HIS* 1.3 62.3 + - - +
67A VAL* 3.2 12.4 + - - +
68A ILE* 3.0 28.0 + - - +
109C TYR* 4.0 20.3 - - - +
110C GLU* 2.7 49.8 + - - +
111C ASP* 3.5 4.2 + - - +
112C MET* 3.5 17.0 - - - -
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.0 5.1 - - - +
64A ASN* 1.3 76.4 - - - +
66A ALA* 1.3 58.1 + - - +
68A ILE* 3.2 8.5 + - + +
69A GLN* 2.9 54.7 + - + +
120A ARG 4.6 2.2 + - - -
24C LEU* 4.7 2.5 - - + +
43C TYR* 4.8 0.7 - - - -
45C ALA* 3.4 18.3 + - + +
46C PHE 2.7 29.4 + - - -
47C HIS* 4.4 2.0 - - - -
87C PRO* 4.5 9.4 - - + +
90C LEU* 3.9 12.3 - - + -
111C ASP 2.8 19.7 + - - +
112C MET* 3.4 25.1 - - - +
114C VAL* 3.5 19.5 - - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 4.5 2.5 - - + -
62A PRO* 4.1 4.9 - - + -
63A THR* 2.9 27.8 + - - +
65A HIS* 1.3 76.5 + - - +
67A VAL* 1.3 63.6 + - - +
70A THR* 2.6 34.1 + - - +
83A THR* 3.5 19.4 - - + +
119A CYS* 3.5 24.2 - - + +
120A ARG* 4.0 6.3 - - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 4.3 10.1 - - + -
62A PRO* 3.8 25.4 - - + +
63A THR 2.9 16.2 + - - +
64A ASN* 3.4 13.5 - - - +
66A ALA* 1.3 77.6 - - - +
68A ILE* 1.3 64.1 + - + +
70A THR* 3.7 2.1 - - - -
71A LEU* 3.0 24.3 + - + +
33C TRP* 4.7 18.4 - - + -
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASN* 3.0 17.6 + - + +
65A HIS* 3.2 8.0 + - + +
67A VAL* 1.3 78.0 - - + +
69A GLN* 1.3 57.2 + - - +
71A LEU* 3.3 4.5 + - - +
72A MET* 3.0 30.8 + - - +
24C LEU* 5.7 1.3 - - + -
26C VAL* 3.7 33.2 - - + -
28C PHE* 4.1 8.1 - - + -
31C MET* 3.7 17.0 - - + -
33C TRP* 4.0 27.4 - - + -
43C TYR* 3.7 11.4 - - + +
45C ALA* 5.7 0.2 - - + -
112C MET* 3.7 31.6 - - + -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 2.9 40.9 + - + +
68A ILE* 1.3 75.0 - - - +
70A THR* 1.3 60.9 + - - +
72A MET* 3.4 6.2 + - - +
73A ASN* 2.9 28.1 + - - +
80A THR* 3.8 10.7 - - + +
81A PRO* 3.1 33.5 + - - +
82A PRO 3.8 10.9 + - - -
83A THR* 4.0 19.3 - - + +
120A ARG 4.4 4.5 - - - +
24C LEU* 4.3 9.0 - - + -
47C HIS* 4.0 22.8 - - - +
48C CYS 4.9 4.9 + - - -
87C PRO* 5.7 0.9 - - - +
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A CYS 3.8 13.2 + - - +
53A GLU* 4.7 0.7 - - - -
54A PHE* 3.8 25.7 - - + +
56A LEU* 3.7 30.6 - - + +
66A ALA 2.6 23.1 + - - -
67A VAL 3.7 3.4 - - - -
69A GLN* 1.3 73.1 - - - +
71A LEU* 1.3 66.7 + - - +
73A ASN* 3.3 9.9 + - + +
74A SER* 3.0 23.0 + - - -
82A PRO* 5.6 0.4 - - - -
83A THR* 3.2 24.2 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 4.3 23.1 - - + -
67A VAL* 3.0 15.7 + - + +
68A ILE* 3.5 9.2 - - - +
69A GLN 3.3 0.2 - - - -
70A THR* 1.3 77.3 - - - +
72A MET* 1.3 61.6 + - - +
74A SER* 2.7 29.7 + - - +
75A MET* 3.3 22.0 + - + +
31C MET* 3.7 17.0 - - + +
33C TRP* 3.4 42.4 - - + +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.0 31.9 + - - +
69A GLN 3.7 4.5 - - - +
70A THR 3.4 0.2 - - - -
71A LEU* 1.3 74.6 - - - +
73A ASN* 1.3 61.9 + - - +
75A MET* 3.4 25.2 + - + +
76A ASP* 3.2 24.1 + - - +
80A THR* 3.6 26.8 + - + +
24C LEU* 3.8 30.3 - - + -
25C HIS 3.7 20.2 - - - +
26C VAL* 4.3 12.8 - - - -
27C ASN 5.4 0.9 - - - +
31C MET* 4.1 12.6 - - + +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 4.8 13.3 - - - +
54A PHE 5.1 1.7 + - - -
69A GLN 2.9 17.3 + - - +
70A THR* 3.4 7.6 - - - +
71A LEU 3.3 0.2 - - - -
72A MET* 1.3 77.8 - - - +
74A SER* 1.3 63.9 + - - +
76A ASP 4.4 0.4 - - - -
77A PRO* 3.1 40.6 + - - +
80A THR* 2.8 32.1 + - - +
81A PRO* 3.4 6.2 - - - +
82A PRO* 3.2 37.3 - - + +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 3.5 43.0 - - - -
70A THR 3.0 8.4 + - - -
71A LEU* 2.7 27.5 + - - +
73A ASN* 1.3 78.4 - - - +
75A MET* 1.3 65.3 + - - +
77A PRO* 4.5 7.4 - - - +
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.3 18.4 + - + +
72A MET* 3.7 25.4 - - + +
73A ASN 3.2 0.4 - - - -
74A SER* 1.3 83.5 - - - +
76A ASP* 1.3 62.2 + - + +
77A PRO* 4.0 3.1 - - - +
30C ASP* 3.8 27.4 - - + +
31C MET* 3.6 37.0 - - + +
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET 3.2 9.4 + - - +
73A ASN 3.5 2.2 - - - -
75A MET* 1.3 83.8 - - + +
77A PRO* 1.4 65.3 - - - +
78A GLU* 3.2 26.6 + - - +
79A SER* 2.8 36.2 + - - +
80A THR 3.3 10.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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