Contacts of the helix formed by residues 72 - 88 (chain D) in PDB entry 4IP8
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D GLY 3.4 4.9 + - - -
71D HIS* 1.3 75.8 + - - +
73D ALA* 1.3 65.3 + - - -
74D GLU 3.2 3.4 - - - -
75D ASP* 3.0 26.2 + - - +
76D SER* 3.1 14.3 + - - -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 4.5 17.5 - - - +
71D HIS 3.7 2.3 + - - -
72D GLY* 1.3 70.1 - - - -
74D GLU* 1.3 63.8 + - + +
76D SER* 3.5 9.2 + - - -
77D LEU* 3.3 25.5 + - - +
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLY 3.2 1.0 - - - -
73D ALA* 1.3 74.5 - - + +
75D ASP* 1.3 68.2 + - - +
77D LEU* 3.2 25.0 + - - +
78D ALA* 3.2 19.8 + - - +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LYS* 5.3 0.7 - - - +
71D HIS* 3.4 28.8 + - + +
72D GLY* 3.0 21.0 + - - +
74D GLU* 1.3 79.9 - - - +
76D SER* 1.3 62.5 + - - +
78D ALA* 3.2 9.8 + - - +
79D ASP* 3.0 24.6 + - - +
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Residues in contact with SER 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU* 3.2 30.4 + - - +
66D GLN* 5.9 0.2 - - - -
67D ARG* 4.8 11.9 - - - +
71D HIS* 3.3 26.0 + - - +
72D GLY 3.1 10.8 + - - -
73D ALA* 3.7 10.7 - - - -
75D ASP* 1.3 76.6 - - - +
77D LEU* 1.3 58.1 + - - +
79D ASP* 2.9 9.4 + - - +
80D GLN* 2.8 26.6 + - - -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA 3.3 12.7 + - - +
74D GLU* 3.2 29.8 + - - +
75D ASP 3.2 0.6 - - - -
76D SER* 1.3 77.7 - - - +
78D ALA* 1.3 62.8 + - - +
80D GLN* 3.2 28.6 + - + +
81D ALA* 3.1 21.7 + - - +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LYS* 4.4 18.0 - - + +
74D GLU 3.2 8.3 + - - +
75D ASP* 3.2 13.5 + - - +
77D LEU* 1.3 78.9 - - - +
79D ASP* 1.3 62.3 + - - +
81D ALA* 3.4 9.6 - - - +
82D ALA* 3.3 18.9 + - - +
95D PHE* 5.5 1.7 - - - -
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASP* 4.9 1.3 - - - +
34D LYS* 3.3 29.8 + - - +
37D HIS* 3.5 30.3 + - + +
62D ARG* 4.1 11.0 - - - +
63D GLU* 4.9 0.9 - - - +
66D GLN* 3.9 5.8 + - - +
71D HIS* 2.8 34.3 + - - -
75D ASP 3.0 11.1 + - - +
76D SER* 2.9 10.4 + - - +
78D ALA* 1.3 75.1 - - - +
80D GLN* 1.3 59.8 + - - +
82D ALA* 3.0 6.9 + - - +
83D ASN* 2.8 32.3 + - - +
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Residues in contact with GLN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLU* 2.9 43.4 + - - +
76D SER* 2.8 12.3 + - - +
77D LEU* 3.2 31.0 + - + +
79D ASP* 1.3 73.9 - - - +
81D ALA* 1.3 58.3 + - - +
83D ASN* 3.0 10.7 + - - +
84D GLU* 2.8 53.3 + - + +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU 3.1 9.7 + - - +
78D ALA* 3.4 14.1 - - - +
80D GLN* 1.3 78.7 - - - +
82D ALA* 1.3 57.1 + - - +
84D GLU* 4.0 7.5 - - - +
85D TRP* 2.9 30.8 + - - +
95D PHE* 4.7 4.7 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LYS* 3.7 38.6 - - + +
37D HIS* 4.0 6.3 - - + -
38D ALA* 3.5 12.3 - - - +
78D ALA 3.3 9.0 + - - +
79D ASP* 3.0 10.2 + - - +
81D ALA* 1.3 77.5 - - - +
83D ASN* 1.3 67.0 + - - +
85D TRP* 3.3 2.3 + - - +
86D GLY 3.1 16.3 + - - -
95D PHE* 3.9 18.3 - - + -
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 3.5 9.3 - - - +
41D ASN* 3.0 28.1 + - - +
59D SER* 3.5 13.1 - - - -
62D ARG* 2.4 46.8 + - - +
63D GLU* 4.6 6.5 + - - -
79D ASP 2.8 15.6 + - - -
80D GLN* 3.3 16.7 - - - +
82D ALA* 1.3 77.4 - - - +
84D GLU* 1.3 58.8 + - + +
87D ARG* 2.9 41.5 + - - +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLN* 2.8 41.5 + - - +
81D ALA* 4.3 5.7 - - - +
83D ASN* 1.3 72.7 - - + +
85D TRP* 1.3 60.1 + - - +
87D ARG* 3.9 25.8 + - - +
88D SER* 2.9 32.9 + - - -
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Residues in contact with TRP 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 4.8 0.4 - - + -
81D ALA 2.9 22.6 + - - +
82D ALA 3.4 4.7 - - - +
83D ASN 3.3 0.2 - - - -
84D GLU* 1.3 77.2 - - - +
86D GLY* 1.3 60.2 + - - +
88D SER* 2.7 21.5 + - - -
90D LYS* 3.1 70.7 + - + +
91D ASP* 3.1 23.7 + - + -
92D PRO* 4.7 1.3 - - + -
94D HIS* 3.7 41.5 - + + +
95D PHE* 3.6 27.1 - + + -
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Residues in contact with GLY 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 3.5 22.9 - - - -
42D TYR* 3.3 21.5 - - - +
45D ALA* 4.6 0.2 - - - +
82D ALA 3.1 8.2 + - - -
83D ASN 3.8 1.3 - - - -
85D TRP* 1.3 79.1 - - - +
87D ARG* 1.3 58.0 + - - +
88D SER 3.1 1.6 - - - -
89D GLY* 2.7 25.1 + - - -
90D LYS 3.9 11.4 - - - -
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Residues in contact with ARG 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 2.8 39.7 + - + +
45D ALA* 3.5 19.9 - - + +
52D VAL* 4.1 24.9 - - + +
55D ALA* 3.9 7.3 + - + +
56D GLU* 3.4 40.9 + - - +
59D SER* 3.1 25.1 + - - -
60D ASP* 5.4 2.0 + - - -
83D ASN* 2.9 28.4 + - - +
84D GLU* 3.9 24.8 + - - +
86D GLY* 1.3 75.0 - - - +
88D SER* 1.3 61.7 + - - +
89D GLY* 3.0 1.4 + - - -
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Residues in contact with SER 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D GLU 2.9 14.9 + - - -
85D TRP* 2.7 20.1 + - - -
87D ARG* 1.3 76.6 - - - +
89D GLY* 1.3 58.0 + - - +
90D LYS* 3.1 27.3 + - - +
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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