Contacts of the helix formed by residues 74 - 94 (chain A) in PDB entry 4HNE
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 SER 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PRO* 3.0 39.1 + - - +
73A GLY* 1.3 79.3 - - - +
75A PRO* 1.4 74.0 - - - +
76A GLU* 3.3 7.5 + - - +
77A PHE* 3.0 14.9 + - - +
78A ALA* 3.2 21.3 + - - +
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Residues in contact with PRO 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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73A GLY 4.8 0.2 - - - +
74A SER* 1.4 87.8 - - - +
76A GLU* 1.3 66.5 + - + +
78A ALA* 3.3 7.8 + - + +
79A ALA* 3.1 24.8 + - - +
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Residues in contact with GLU 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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71A PRO* 4.6 13.6 - - + +
74A SER* 3.3 9.2 + - - +
75A PRO* 1.3 82.8 - - + +
77A PHE* 1.3 56.6 + - - +
79A ALA* 3.5 6.1 + - - +
80A GLN* 3.1 33.2 + - - +
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Residues in contact with PHE 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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71A PRO* 2.7 36.6 - - + +
72A LEU* 4.4 15.0 - - - -
73A GLY* 5.5 0.4 - - - -
74A SER* 3.0 10.3 + - - +
76A GLU* 1.3 73.2 - - - +
78A ALA* 1.3 59.5 + - - +
79A ALA 3.1 1.3 - - - -
80A GLN* 3.0 22.6 + - + +
81A ALA* 2.8 47.3 + - + +
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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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74A SER 3.2 17.0 + - - +
75A PRO* 3.3 9.1 + - + +
77A PHE* 1.3 81.6 - - - +
79A ALA* 1.3 59.7 + - - +
81A ALA* 3.6 8.2 + - - +
82A GLN* 3.3 33.8 + - - +
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Residues in contact with ALA 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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75A PRO 3.1 15.9 + - - +
76A GLU* 3.7 6.1 - - - +
78A ALA* 1.3 75.6 - - - +
80A GLN* 1.3 60.0 + - - +
82A GLN* 3.4 8.5 + - - +
83A ALA* 3.0 27.5 + - - +
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 4.6 9.7 - - - +
76A GLU* 3.1 17.1 + - - +
77A PHE* 3.0 36.1 + - + +
79A ALA* 1.3 76.8 - - - +
81A ALA* 1.3 55.9 + - - +
83A ALA* 3.3 9.1 - - - +
84A LEU* 3.2 25.6 + - - +
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Residues in contact with ALA 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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77A PHE* 2.8 37.7 + - + +
78A ALA* 3.8 8.5 - - - +
79A ALA 3.3 0.2 - - - -
80A GLN* 1.3 73.2 - - - +
82A GLN* 1.3 57.7 + - + +
84A LEU* 3.5 6.6 + - - +
85A ALA* 3.0 26.6 + - - +
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Residues in contact with GLN 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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78A ALA* 3.3 21.2 + - - +
79A ALA* 3.9 8.0 - - - +
80A GLN 3.3 0.2 - - - -
81A ALA* 1.3 75.0 - - + +
83A ALA* 1.3 65.2 + - - +
84A LEU 3.2 0.2 - - - -
85A ALA* 3.6 9.3 - - + +
86A ALA* 3.1 27.7 + - - +
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Residues in contact with ALA 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 ALA 3.0 15.2 + - - +
80A GLN* 3.3 15.7 - - - +
81A ALA 3.3 0.2 - - - -
82A GLN* 1.3 78.9 - - - +
84A LEU* 1.3 58.3 + - - +
86A ALA* 4.8 1.5 - - - +
87A GLN* 3.3 29.9 + - - +
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Residues in contact with LEU 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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80A GLN 3.2 12.9 + - - +
81A ALA* 3.9 9.0 - - - +
82A GLN 3.2 0.2 - - - -
83A ALA* 1.3 77.1 - - - +
85A ALA* 1.3 58.5 + - - +
86A ALA 3.3 0.2 - - - -
87A GLN* 3.3 26.6 - - + +
88A ALA* 2.9 39.2 + - + +
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Residues in contact with ALA 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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81A ALA 3.0 19.0 + - - +
82A GLN* 3.3 10.9 + - + +
84A LEU* 1.3 76.9 - - - +
86A ALA* 1.3 57.2 + - - +
88A ALA* 3.8 5.4 + - - +
89A ALA* 3.3 25.6 + - - +
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Residues in contact with ALA 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 GLN 3.1 17.0 + - - +
83A ALA* 4.8 1.6 - - - +
85A ALA* 1.3 74.7 - - - +
87A GLN* 1.3 60.8 + - - +
88A ALA 3.3 0.2 - - - -
89A ALA* 3.5 5.3 + - - +
90A ALA* 3.0 27.2 + - - +
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Residues in contact with GLN 87 (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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83A ALA* 3.3 21.7 + - - +
84A LEU* 3.3 32.5 - - + +
86A ALA* 1.3 76.1 - - - +
88A ALA* 1.3 64.3 + - + +
90A ALA* 3.9 7.0 - - - +
91A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 2.9 24.7 + - + +
85A ALA* 4.1 5.6 - - - +
87A GLN* 1.3 77.2 - - + +
89A ALA* 1.3 59.1 + - - +
91A ALA* 3.7 7.3 - - - +
92A ALA* 3.3 24.1 + - - +
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Residues in contact with ALA 89 (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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85A ALA 3.3 19.8 + - - +
86A ALA* 3.8 6.7 - - - +
87A GLN 3.3 0.2 - - - -
88A ALA* 1.3 76.7 - - - +
90A ALA* 1.3 62.8 + - - +
92A ALA* 3.6 7.1 + - - +
93A HIS* 3.2 21.7 + - - +
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Residues in contact with ALA 90 (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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86A ALA 3.0 17.9 + - - +
87A GLN* 3.9 7.2 - - - +
89A ALA* 1.3 74.0 - - - +
91A ALA* 1.3 65.9 + - - +
93A HIS* 3.1 8.4 + - - +
94A ALA* 3.0 26.2 + - - +
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Residues in contact with ALA 91 (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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87A GLN 3.0 19.1 + - - +
88A ALA* 3.7 10.1 - - - +
90A ALA* 1.3 77.0 - - - +
92A ALA* 1.3 60.3 + - - +
94A ALA* 3.3 6.6 + - - +
95A ALA* 3.3 21.8 + - - +
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Residues in contact with ALA 92 (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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88A ALA 3.3 14.9 + - - +
89A ALA* 3.9 6.7 - - - +
90A ALA 3.2 0.6 - - - -
91A ALA* 1.3 76.2 - - - +
93A HIS* 1.3 63.3 + - - +
95A ALA* 3.7 17.8 - - - +
96A GLN 5.1 0.3 + - - -
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Residues in contact with HIS 93 (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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89A ALA 3.2 13.6 + - - +
90A ALA* 3.1 12.5 + - - +
92A ALA* 1.3 77.6 - - - +
94A ALA* 1.3 59.3 + - + +
95A ALA 3.3 3.8 + - - -
96A GLN* 4.5 6.8 + - - +
97A ALA* 5.2 1.0 + - - +
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Residues in contact with ALA 94 (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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90A ALA 3.0 15.6 + - - +
91A ALA* 3.3 6.9 + - - +
93A HIS* 1.3 78.4 - - + +
95A ALA* 1.3 56.3 + - - +
96A GLN 3.5 2.0 - - - -
97A ALA* 4.2 10.9 - - + +
98A HIS* 3.2 28.2 + - - +
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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