Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 4IP9
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 GLY 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY 3.5 5.3 + - - -
71A HIS* 1.3 74.3 + - - +
73A ALA* 1.3 66.1 + - - -
74A GLU 3.5 2.7 - - - -
75A ASP* 3.3 19.4 + - - +
76A SER* 3.1 24.1 + - - -
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Residues in contact with ALA 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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67A ARG* 6.5 0.7 - - - -
71A HIS 3.7 2.1 + - - -
72A GLY* 1.3 69.1 - - - -
74A GLU* 1.4 61.1 + - - +
76A SER* 3.2 18.1 + - - -
77A LEU* 3.4 18.6 + - + +
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Residues in contact with GLU 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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72A GLY 3.5 0.2 - - - -
73A ALA* 1.4 77.0 - - - +
75A ASP* 1.4 67.8 + - - +
77A LEU* 3.3 40.3 + - - +
78A ALA* 3.5 11.6 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 3.5 24.9 + - + +
72A GLY* 3.3 22.8 + - - +
74A GLU* 1.4 81.0 - - - +
76A SER* 1.4 59.6 + - - +
78A ALA* 3.7 7.1 + - - +
79A ASP* 3.2 27.0 + - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 4.7 16.1 + - - +
67A ARG* 5.1 12.7 - - - +
71A HIS* 3.2 27.3 + - - +
72A GLY 3.1 10.6 + - - -
73A ALA* 3.2 11.8 + - - -
75A ASP* 1.4 74.6 - - - +
77A LEU* 1.3 59.0 + - - +
79A ASP* 3.2 8.1 + - - +
80A GLN* 2.9 44.3 + - - +
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Residues in contact with LEU 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 ALA* 3.6 14.8 - - + +
74A GLU* 3.3 32.9 + - - +
76A SER* 1.3 76.6 - - - +
78A ALA* 1.4 57.3 + - - +
80A GLN* 3.3 23.3 + - + +
81A ALA* 3.1 27.9 + - - +
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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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34A LYS* 4.0 30.2 - - + +
74A GLU 3.5 7.8 + - - +
75A ASP* 3.8 10.8 - - - +
76A SER 3.3 0.4 - - - -
77A LEU* 1.4 73.8 - - - +
79A ASP* 1.3 67.3 + - - +
81A ALA* 3.5 6.4 + - - +
82A ALA* 3.2 24.1 + - - +
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Residues in contact with ASP 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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33A ASP* 4.6 10.1 - - - +
34A LYS* 4.7 3.6 - - - +
37A HIS* 3.6 34.1 + - + -
62A ARG* 4.1 10.9 + - - +
63A GLU* 6.1 2.0 - - + -
66A GLN* 3.8 11.1 + - - +
71A HIS* 3.1 26.9 + - - -
75A ASP 3.2 14.2 - - - +
76A SER* 3.2 9.5 + - - +
78A ALA* 1.3 79.5 - - - +
80A GLN* 1.3 56.1 + - + +
82A ALA* 3.5 4.6 + - - +
83A ASN* 3.0 35.3 + - - +
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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
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63A GLU* 3.3 43.4 + - + +
67A ARG* 4.5 3.0 - - - +
76A SER* 2.9 37.1 + - - +
77A LEU* 3.4 26.6 - - + +
79A ASP* 1.3 73.9 - - + +
81A ALA* 1.3 62.7 + - - +
83A ASN* 3.6 7.6 + - - +
84A GLU* 3.0 35.4 + - - +
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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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34A LYS* 6.1 1.8 - - - +
77A LEU 3.1 15.5 + - - +
78A ALA* 3.9 6.5 - - - +
79A ASP 3.5 0.2 - - - -
80A GLN* 1.3 72.4 - - - +
82A ALA* 1.4 63.7 + - - +
84A GLU* 3.5 6.7 + - - +
85A TRP* 3.1 24.0 + - - +
95A PHE* 4.7 5.5 - - + -
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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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34A LYS* 3.9 39.9 - - + +
37A HIS* 4.3 5.4 - - + -
38A ALA* 3.0 23.7 - - + +
78A ALA 3.2 15.9 + - - +
79A ASP 3.6 6.1 - - - +
80A GLN 3.4 0.2 - - - -
81A ALA* 1.4 76.9 - - - +
83A ASN* 1.4 62.6 + - - +
85A TRP* 3.5 2.8 + - - +
86A GLY 3.5 8.8 + - - -
95A PHE* 4.1 14.3 - - + -
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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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21A TYR* 4.3 0.2 + - - -
37A HIS* 3.0 21.3 + - - +
41A ASN* 2.8 35.5 - - - +
59A SER* 3.5 12.1 - - - +
62A ARG* 2.8 34.8 + - - +
63A GLU* 5.6 1.6 - - - +
79A ASP 3.0 18.2 + - - +
80A GLN* 3.8 9.5 - - - +
81A ALA 3.4 0.2 - - - -
82A ALA* 1.4 77.9 - - - +
84A GLU* 1.4 61.9 + - - +
87A ARG* 3.1 40.4 + - - +
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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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80A GLN* 3.0 28.1 + - - +
81A ALA* 3.8 6.5 - - - +
82A ALA 3.4 0.2 - - - -
83A ASN* 1.4 74.7 - - - +
85A TRP* 1.4 64.9 + - - +
87A ARG* 3.5 27.7 + - + +
88A SER* 3.0 28.3 + - - -
90A LYS* 5.1 1.3 - - - -
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Residues in contact with TRP 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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38A ALA* 5.2 0.4 - - + -
81A ALA 3.1 13.7 + - - +
82A ALA 3.6 9.2 - - - +
83A ASN 3.4 0.4 - - - -
84A GLU* 1.4 74.1 - - - +
86A GLY* 1.3 63.5 + - - +
88A SER* 2.7 21.8 + - - -
90A LYS* 3.3 63.7 + - + +
91A ASP* 2.8 29.3 + - + -
92A PRO* 4.6 2.2 - - + -
94A HIS* 3.2 45.7 - + + +
95A PHE* 3.5 30.1 - + + -
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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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38A ALA* 3.6 23.3 - - - +
42A TYR* 3.4 25.8 - - - +
45A ALA* 4.6 0.3 - - - +
82A ALA 3.5 7.5 + - - -
83A ASN 3.9 1.8 - - - -
84A GLU 3.4 0.2 - - - -
85A TRP* 1.3 81.2 - - - +
87A ARG* 1.3 52.5 + - - +
89A GLY* 2.8 27.2 + - - -
90A LYS 4.1 6.3 - - - -
92A PRO* 5.7 0.4 - - - -
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Residues in contact with ARG 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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41A ASN* 2.9 40.9 + - - +
45A ALA* 3.3 18.6 - - + +
52A VAL* 3.7 41.2 - - + +
55A ALA* 4.4 6.3 - - + -
56A GLU* 3.7 36.9 + - - +
59A SER* 3.3 24.7 + - - -
60A ASP* 5.6 2.2 + - - -
83A ASN* 3.1 29.5 + - - +
84A GLU* 3.9 27.0 + - + +
86A GLY* 1.3 72.6 - - - +
88A SER* 1.3 56.5 + - - +
89A GLY 3.1 4.0 + - - -
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Residues in contact with SER 88 (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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84A GLU 3.0 13.1 + - - -
85A TRP 2.7 16.3 + - - -
86A GLY 3.1 0.2 + - - -
87A ARG* 1.3 73.4 - - - +
89A GLY* 1.3 58.1 + - - +
90A LYS* 2.6 38.8 + - - +
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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