Contacts of the helix formed by residues 68 - 86 (chain A) in PDB entry 3HPD
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 5.3 4.7 - - - -
66A THR 4.9 2.3 - - - +
67A LEU* 1.3 75.7 - - - +
69A SER* 1.3 66.1 + - - +
70A GLY* 2.9 17.4 + - - -
71A TRP* 2.9 31.5 + - - +
72A ARG* 2.9 22.5 + - - +
101A PHE* 4.0 14.1 - - - -
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Residues in contact with SER 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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68A ASP* 1.3 75.2 - - - +
70A GLY* 1.3 64.6 + - - +
72A ARG* 3.5 13.7 + - - +
73A ARG* 3.2 38.0 + - - +
101A PHE* 4.1 9.4 - - - -
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Residues in contact with GLY 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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45A HIS* 6.4 0.4 - - - -
47A GLU* 4.4 1.0 - - - +
68A ASP* 2.9 8.9 + - - -
69A SER* 1.3 84.0 + - - +
71A TRP* 1.3 63.1 + - - -
73A ARG* 3.3 24.2 + - - +
74A SER* 3.3 21.6 + - - -
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Residues in contact with TRP 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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21A ILE* 4.1 13.5 - - + -
22A THR 3.3 30.1 - - - -
24A PHE* 3.6 34.6 - + - -
27A MET* 3.7 22.9 - - + -
44A ALA 5.7 0.7 - - - -
45A HIS* 3.6 57.4 + + + -
66A THR 5.1 3.4 - - - -
67A LEU* 4.4 4.5 - - - -
68A ASP* 2.9 47.5 + - - +
70A GLY* 1.3 75.2 - - - +
72A ARG* 1.3 61.4 + - - +
74A SER* 3.2 6.9 + - - -
75A MET* 2.8 49.6 + - + +
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Residues in contact with ARG 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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67A LEU* 5.0 2.4 - - + +
68A ASP 2.9 18.3 + - - +
69A SER* 3.6 11.8 + - - +
71A TRP* 1.3 77.8 - - - +
73A ARG* 1.3 73.9 + - - +
75A MET* 3.2 10.5 + - - +
76A VAL* 2.9 38.2 + - + +
101A PHE* 4.2 13.7 - - + -
104A ARG* 6.1 1.6 - - - +
105A VAL* 3.5 42.4 - - + -
108A GLU* 2.6 39.2 + - - -
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Residues in contact with ARG 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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47A GLU* 3.1 31.9 + - - +
69A SER* 3.2 30.4 + - - +
70A GLY* 3.4 23.6 - - - +
72A ARG* 1.3 91.7 - - - +
74A SER* 1.3 61.6 + - - +
76A VAL* 4.0 4.5 - - - +
77A LYS* 3.0 27.1 + - + +
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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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21A ILE* 4.7 5.8 - - - -
45A HIS* 2.6 42.8 + - - +
47A GLU* 3.8 13.1 + - - +
50A LEU* 3.5 14.0 - - - +
70A GLY 3.3 9.8 + - - -
71A TRP* 3.2 12.3 + - - -
73A ARG* 1.3 79.6 - - - +
75A MET* 1.3 56.6 + - - +
77A LYS 3.4 0.2 + - - -
78A ALA* 2.8 31.5 + - - +
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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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21A ILE* 3.6 25.1 - - + +
22A THR 4.8 1.3 - - - +
62A ILE* 3.7 19.9 - - + +
63A ASN 3.3 25.4 - - - +
64A ILE* 3.8 28.3 - - - -
66A THR 6.1 0.4 - - - -
67A LEU* 4.5 8.5 - - + -
71A TRP* 2.8 52.2 + - + +
72A ARG* 3.7 8.3 - - - +
74A SER* 1.3 70.6 - - - +
76A VAL* 1.3 59.1 + - - +
78A ALA* 3.4 7.0 + - - +
79A THR* 2.9 32.9 + - - -
105A VAL* 5.2 2.5 - - + -
109A ILE* 4.2 9.6 - - + -
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Residues in contact with VAL 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 ARG* 2.9 32.9 + - + +
73A ARG* 4.0 4.3 - - - +
75A MET* 1.3 73.3 - - - +
77A LYS* 1.3 66.1 + - - +
79A THR* 3.3 8.3 + - - -
80A GLU* 3.1 32.9 + - - +
105A VAL* 5.2 0.4 - - + -
108A GLU* 3.6 28.9 - - + +
109A ILE* 4.4 15.0 - - + -
112A ARG* 3.4 35.9 - - - +
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Residues in contact with LYS 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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47A GLU* 5.2 9.0 - - + +
50A LEU* 4.0 12.6 - - + -
73A ARG* 3.0 19.8 + - + +
74A SER 3.8 3.4 - - - +
76A VAL* 1.3 78.1 - - - +
78A ALA* 1.3 58.3 + - - +
80A GLU* 3.2 21.4 + - + +
81A ILE* 2.9 57.1 + - + +
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Residues in contact with ALA 78 (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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21A ILE* 3.2 36.1 - - + -
50A LEU* 4.2 5.1 - - + +
54A ILE* 3.6 22.9 - - + +
60A VAL* 4.8 4.0 - - + -
62A ILE* 4.8 4.3 - - + -
74A SER 2.8 12.9 + - - +
75A MET 3.6 4.5 - - - +
76A VAL 3.3 0.2 - - - -
77A LYS* 1.3 78.2 - - - +
79A THR* 1.3 56.6 + - - +
81A ILE* 3.3 0.4 + - - -
82A ALA* 2.8 34.1 + - - +
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Residues in contact with THR 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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62A ILE* 3.1 19.1 - - - +
75A MET 2.9 19.0 + - - -
76A VAL* 3.5 10.5 - - - -
77A LYS 3.2 0.2 - - - -
78A ALA* 1.3 76.8 - - - +
80A GLU* 1.3 60.9 + - - +
83A ASN* 3.0 46.2 + - - +
89A ILE* 3.6 12.5 - - + +
109A ILE* 3.5 21.7 - - + +
112A ARG* 3.9 20.0 - - + -
113A GLY 3.7 11.0 - - - +
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Residues in contact with GLU 80 (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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76A VAL* 3.1 19.7 + - - +
77A LYS* 3.2 27.1 + - + +
79A THR* 1.3 78.0 - - - +
81A ILE* 1.3 59.1 + - + +
83A ASN* 3.5 4.9 + - - +
84A GLU* 2.9 37.4 + - + +
112A ARG* 2.7 42.2 + - + -
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Residues in contact with ILE 81 (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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50A LEU* 4.0 11.4 - - + -
51A GLU* 3.9 45.8 - - + +
54A ILE* 3.8 17.7 - - + -
77A LYS* 2.9 48.3 + - + +
78A ALA 3.7 3.8 - - - +
80A GLU* 1.3 74.3 - - + +
82A ALA* 1.3 66.8 + - - +
84A GLU* 3.2 15.0 + - - +
85A LEU* 3.1 41.9 + - + +
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Residues in contact with ALA 82 (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 ILE* 3.9 20.6 - - + +
60A VAL* 4.1 10.5 - - + -
78A ALA 2.8 21.5 + - - +
81A ILE* 1.3 73.8 - - - +
83A ASN* 1.3 58.1 + - - +
85A LEU* 3.3 1.5 + - - -
86A GLY 2.8 24.9 + - - -
87A LYS* 2.9 20.2 + - + +
89A ILE* 3.5 27.6 - - + -
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Residues in contact with ASN 83 (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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79A THR* 3.0 28.5 + - - +
80A GLU* 3.9 4.6 - - - +
81A ILE 3.3 0.2 - - - -
82A ALA* 1.3 73.4 - - - +
84A GLU* 1.3 67.0 + - + +
86A GLY* 3.3 11.6 + - - +
87A LYS 5.0 1.4 - - - +
89A ILE* 3.6 9.1 - - - +
112A ARG* 3.4 20.3 + - - +
113A GLY* 2.8 30.9 + - - +
114A VAL 5.7 0.2 - - - -
115A ASP* 4.8 6.1 - - - +
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Residues in contact with GLU 84 (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 GLU* 5.1 5.9 - - - +
80A GLU* 2.9 28.3 + - + +
81A ILE* 3.2 15.0 + - - +
83A ASN* 1.3 77.9 - - + +
85A LEU* 1.3 64.5 + - + +
86A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 85 (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 GLU* 5.7 2.9 - - - +
54A ILE* 4.1 10.3 - - + +
55A ARG* 3.8 44.2 - - + +
81A ILE* 3.1 34.7 + - + +
82A ALA 3.9 3.1 - - - +
84A GLU* 1.3 79.9 - - + +
86A GLY* 1.3 62.2 + - - +
87A LYS* 4.0 19.5 - - + +
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Residues in contact with GLY 86 (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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82A ALA 2.8 6.0 + - - -
83A ASN* 3.3 11.7 + - - -
84A GLU 3.4 0.2 - - - -
85A LEU* 1.3 80.9 - - - +
87A LYS* 1.3 64.7 - - - +
88A PRO* 3.6 6.8 - - - +
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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