Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 3HVK
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.5 32.6 + - + +
62A PRO 3.3 0.8 - - - -
63A GLY* 1.3 77.6 - - - +
65A PRO* 1.3 64.8 - - - +
66A GLN* 3.3 11.4 + - - +
67A SER* 2.6 53.7 + - - +
68A VAL* 3.2 11.5 + - - +
149A ALA 3.9 1.5 + - - -
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Residues in contact with PRO 65 (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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63A GLY 3.3 13.0 - - - +
64A ASP* 1.3 84.2 - - - +
66A GLN* 1.3 61.9 + - - +
68A VAL* 3.1 8.8 + - + +
69A LEU* 3.0 27.3 + - - +
117A VAL* 3.9 17.4 - - + +
121A ARG* 3.9 26.7 - - + -
149A ALA* 3.6 16.2 - - + +
151A LEU* 3.8 20.0 - - + -
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.2 8.8 + - - +
65A PRO* 1.3 79.6 - - - +
67A SER* 1.3 58.0 + - - +
69A LEU* 3.2 14.1 + - - +
70A GLU* 2.9 60.1 + - - +
87A ASP* 5.9 1.0 + - - -
118A ARG* 5.6 2.4 + - - +
121A ARG* 3.6 30.2 + - - +
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Residues in contact with SER 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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60A ALA* 3.9 5.4 - - - +
61A LYS* 3.5 24.7 + - - -
64A ASP* 2.6 47.1 + - - +
66A GLN* 1.3 77.6 - - - +
68A VAL* 1.3 57.0 + - - +
70A GLU* 3.5 14.4 + - - +
71A ALA* 3.0 29.1 + - - +
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Residues in contact with VAL 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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56A VAL* 4.4 3.8 - - + +
60A ALA* 4.3 6.5 - - + -
61A LYS 4.4 0.4 - - - +
64A ASP 3.2 13.4 + - - +
65A PRO* 3.1 10.3 + - + +
67A SER* 1.3 74.0 + - - +
69A LEU* 1.3 67.0 + - - +
71A ALA* 3.2 3.7 + - - +
72A ILE* 3.0 30.1 + - + +
117A VAL* 4.4 14.6 - - + -
145A MET* 3.9 33.2 - - + -
148A PHE* 3.6 35.9 - - + -
149A ALA* 4.2 14.1 - - + +
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Residues in contact with LEU 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 PRO 3.0 18.0 + - - +
66A GLN* 3.2 17.5 + - - +
68A VAL* 1.3 75.9 - - - +
70A GLU* 1.3 57.4 + - - +
72A ILE* 3.2 3.0 + - + +
73A ASP* 2.9 36.0 + - - +
114A TYR* 3.5 45.8 - - + +
117A VAL* 3.7 15.0 - - + -
118A ARG* 3.6 34.3 - - + +
121A ARG* 4.0 32.1 - - - +
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Residues in contact with GLU 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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66A GLN* 2.9 48.9 + - - +
67A SER* 3.8 12.3 - - - +
69A LEU* 1.3 76.5 - - - +
71A ALA* 1.3 58.7 + - - +
73A ASP* 3.3 7.6 + - - +
74A THR* 2.9 34.9 + - - +
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Residues in contact with ALA 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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55A TYR* 3.6 19.9 - - + -
56A VAL* 4.3 12.8 - - + -
59A ASN* 4.9 2.9 - - + -
60A ALA* 4.0 21.3 - - + +
67A SER 3.0 17.6 + - - +
68A VAL 3.2 4.0 + - - +
70A GLU* 1.3 78.9 - - - +
72A ILE* 1.3 57.3 + - - +
74A THR* 3.4 3.3 + - - -
75A TYR* 2.9 29.8 + - - +
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Residues in contact with ILE 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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52A ILE* 4.3 13.0 - - + -
56A VAL* 3.6 17.7 - - + -
68A VAL* 3.0 27.6 + - + +
69A LEU* 3.2 4.2 + - + +
71A ALA* 1.3 74.8 - - - +
73A ASP* 1.3 63.7 + - - +
75A TYR* 3.2 5.5 + - - +
76A CYS* 2.9 27.4 + - - -
84A ASN* 3.3 30.1 - - - +
112A CYS* 5.9 1.1 - - + -
114A TYR* 3.7 35.4 - - + +
145A MET* 3.9 30.5 - - + -
243A TYR* 4.1 1.8 - - - +
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Residues in contact with ASP 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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69A LEU* 2.9 22.5 + - - +
70A GLU* 3.7 7.2 - - - +
72A ILE* 1.3 76.8 - - - +
74A THR* 1.3 62.1 + - - +
76A CYS* 3.3 1.4 + - - +
77A THR* 2.8 31.3 + - - +
87A ASP* 3.6 23.1 + - + +
114A TYR* 2.8 30.7 + - - -
118A ARG* 4.6 1.6 + - - -
243A TYR* 2.9 30.5 + - + -
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Residues in contact with THR 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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55A TYR* 3.9 17.3 - - - +
70A GLU* 2.9 19.9 + - - +
71A ALA* 3.7 6.7 - - - -
73A ASP* 1.3 75.5 - - - +
75A TYR* 1.3 66.2 + - - +
77A THR* 3.2 4.4 + - - -
78A GLN* 2.9 54.9 + - - +
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Residues in contact with TYR 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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51A ARG* 3.6 19.9 - - - +
52A ILE* 3.7 32.5 - - + -
55A TYR* 3.3 48.9 - + + -
56A VAL* 6.4 0.2 - - + -
71A ALA 2.9 17.1 + - - +
72A ILE* 3.7 6.3 - - - +
74A THR* 1.3 77.3 - - - +
76A CYS* 1.3 60.5 + - - +
79A LYS* 2.8 52.2 + - + +
80A GLU* 2.5 56.8 + - + +
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Residues in contact with CYS 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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52A ILE* 4.2 10.1 - - - -
72A ILE* 2.9 24.0 + - - +
74A THR 3.2 0.2 - - - -
75A TYR* 1.3 81.4 - - - +
77A THR* 1.3 60.5 + - - +
80A GLU 3.2 18.1 + - - +
81A TRP* 3.6 19.6 + - - +
82A ALA* 3.8 15.7 - - - +
84A ASN* 3.3 25.4 - - - -
243A TYR* 3.4 34.3 - - + +
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Residues in contact with THR 77 (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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73A ASP* 2.8 22.9 + - - +
74A THR* 3.8 4.5 - - - -
76A CYS* 1.3 80.7 - - - +
78A GLN* 1.3 67.5 + - + +
79A LYS 5.5 0.2 - - - -
243A TYR* 3.6 22.1 - - + +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 5.0 2.9 + - - -
74A THR* 2.9 41.1 + - + +
77A THR* 1.3 87.6 - - + +
79A LYS* 1.3 87.2 + - + +
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Residues in contact with LYS 79 (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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55A TYR* 5.3 7.2 - - + -
75A TYR* 2.8 54.3 + - + +
76A CYS 5.2 0.4 - - - -
77A THR 5.5 0.2 - - - -
78A GLN* 1.3 99.4 + - + +
80A GLU* 1.3 65.9 + - + +
266A NHE 4.2 11.5 + - - -
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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
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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