Contacts of the helix formed by residues 81 - 97 (chain D) in PDB entry 4B94
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 81 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU 5.1 1.2 + - - -
121A ALA* 4.6 12.3 - - + +
122A ILE* 3.6 30.2 - - + +
125A PRO* 6.1 0.2 - - - +
155A SER* 4.6 17.6 + - - +
80D SER* 1.3 72.9 - - - +
82D ALA* 1.3 57.3 + - - +
84D LEU* 3.3 10.6 + - - +
85D ASN* 3.0 54.2 + - - +
123D GLN* 5.9 2.1 - - - +
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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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151A GLN* 5.7 0.4 - - - +
193A GLN* 3.5 39.3 - - + +
101B ASP* 4.6 2.9 - - - +
80D SER* 3.3 7.9 + - - +
81D ASP* 1.3 78.9 + - - +
83D LEU* 1.3 57.7 + - + +
85D ASN* 3.4 10.3 + - - +
86D LYS* 3.1 27.0 + - - +
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Residues in contact with LEU 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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75D ASN 5.6 1.1 - - - +
76D SER* 3.9 32.6 + - - +
77D VAL 5.7 0.2 - - - -
78D PRO 3.5 25.1 - - - +
79D LEU* 4.3 4.8 - - + +
80D SER* 3.2 22.6 + - - +
82D ALA* 1.3 76.1 - - + +
84D LEU* 1.4 60.6 + - - +
86D LYS* 3.4 30.6 + - + +
87D LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.7 29.6 - - + -
79D LEU* 4.0 24.6 - - + +
80D SER 2.9 18.3 + - - +
81D ASP* 3.6 11.4 - - - +
83D LEU* 1.4 72.9 - - - +
85D ASN* 1.3 59.9 + - - +
87D LEU* 3.3 6.4 + - + +
88D ILE* 2.9 46.4 + - + +
119D LEU* 3.7 32.3 - - + +
122D ILE* 3.9 15.9 - - + -
123D GLN* 4.2 19.5 - - + -
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Residues in contact with ASN 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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101B ASP* 3.6 11.7 - - + +
1198B GOL 2.6 30.3 + - - +
81D ASP* 3.0 45.6 + - - +
82D ALA* 3.7 8.0 - - - +
83D LEU 3.4 0.2 - - - -
84D LEU* 1.3 76.3 - - - +
86D LYS* 1.3 61.0 + - - +
88D ILE* 3.4 1.7 + - - +
89D GLY 3.0 13.2 + - - -
123D GLN* 2.7 33.8 + - - +
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Residues in contact with LYS 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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99B PRO* 6.2 1.3 - - + -
101B ASP* 3.7 27.4 - - - +
102B LYS* 6.4 0.2 - - - +
72D LEU* 3.7 32.5 - - + +
76D SER* 4.1 4.6 + - - -
82D ALA 3.1 17.2 + - - +
83D LEU* 3.6 31.3 - - + +
85D ASN* 1.3 74.3 - - - +
87D LEU* 1.4 57.1 + - - +
89D GLY* 3.3 2.8 + - - -
90D ARG* 3.1 28.3 + - + +
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Residues in contact with LEU 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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79A LEU* 6.4 0.7 - - + -
69D LEU* 4.1 3.4 - - + +
72D LEU* 3.9 31.0 - - + -
73D GLU* 3.7 51.1 - - + +
76D SER* 5.2 3.8 - - - +
79D LEU* 4.8 15.5 - - + -
83D LEU 3.0 17.7 + - - +
84D LEU* 3.3 6.3 + - + +
86D LYS* 1.4 72.8 - - - +
88D ILE* 1.3 63.7 + - - +
90D ARG* 3.1 4.5 + - - +
91D TYR* 3.0 46.3 + - + -
119D LEU* 4.0 19.7 - - + -
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Residues in contact with ILE 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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138B ASN* 5.7 0.2 - - - +
1198B GOL 3.9 20.6 - - - +
84D LEU* 2.9 31.4 + - + +
85D ASN 3.8 4.0 - - - +
87D LEU* 1.3 72.9 - - - +
89D GLY* 1.3 56.8 + - - +
91D TYR* 3.3 10.6 + - - +
92D SER* 3.0 24.3 + - - -
116D PHE* 3.6 22.4 - - + -
119D LEU* 3.7 43.7 - - + +
120D LYS* 3.9 14.8 - - + +
123D GLN* 3.5 33.0 - - + +
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Residues in contact with GLY 89 (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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100B PRO* 3.6 27.4 - - - +
101B ASP* 4.8 1.6 - - - -
1198B GOL 3.8 9.6 - - - -
85D ASN 3.0 14.5 + - - -
86D LYS 3.6 4.5 - - - -
88D ILE* 1.3 76.7 - - - +
90D ARG* 1.3 59.1 + - - +
92D SER* 2.7 22.4 + - - -
93D GLN* 3.1 11.7 + - - +
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Residues in contact with ARG 90 (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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96B GLU* 3.0 37.3 + - - -
1196B GOL 3.8 28.4 + - - -
65D TRP* 3.7 21.1 - - + -
68D LEU* 3.8 27.2 - - + +
69D LEU* 3.7 18.4 - - + +
72D LEU* 3.7 30.7 - - + +
86D LYS* 3.1 11.1 + - - +
87D LEU 3.1 8.7 + - - +
89D GLY* 1.3 73.4 - - - +
91D TYR* 1.4 62.7 + - - +
93D GLN* 2.9 33.3 + - - +
94D ALA* 3.1 17.5 + - - +
1200D PG4 4.4 3.6 + - - -
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Residues in contact with TYR 91 (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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66D LEU* 4.7 2.1 - - + +
69D LEU* 3.7 41.8 - - + +
70D LEU* 4.3 6.1 - - - +
73D GLU* 2.4 30.0 + - - -
87D LEU* 3.0 38.9 + - + -
88D ILE* 3.3 5.4 + - - +
90D ARG* 1.4 71.3 - - - +
92D SER* 1.3 65.8 + - - +
94D ALA* 3.2 5.7 + - - +
95D ILE* 3.0 25.3 + - - +
112D ILE* 3.6 28.0 - - + -
115D ARG* 3.4 30.6 - - + +
116D PHE* 3.5 24.9 - + + -
119D LEU* 3.7 21.5 - - + -
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Residues in contact with SER 92 (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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100B PRO* 3.4 8.1 - - - +
134B MET* 3.7 24.8 - - - +
138B ASN* 3.2 34.7 + - - -
88D ILE 3.0 12.9 + - - -
89D GLY 2.7 18.6 + - - -
91D TYR* 1.3 75.8 - - - +
93D GLN* 1.3 56.2 + - - +
95D ILE* 3.3 2.8 + - - +
96D GLU* 2.9 33.7 + - - +
116D PHE* 4.0 6.9 - - - -
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Residues in contact with GLN 93 (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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95B ILE* 2.9 33.7 + - + +
96B GLU* 3.4 10.4 + - - +
98B LEU 3.5 12.1 + - - -
99B PRO* 4.9 0.5 - - - +
100B PRO* 3.9 18.2 - - + +
1196B GOL 2.8 27.0 + - - -
65D TRP* 4.1 3.5 - - - -
89D GLY 3.1 6.9 + - - +
90D ARG* 2.9 53.5 + - - +
92D SER* 1.3 78.9 + - - +
94D ALA* 1.4 63.2 + - - +
96D GLU* 3.4 10.3 + - - +
97D ALA* 3.2 22.3 + - - +
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Residues in contact with ALA 94 (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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65D TRP* 3.5 40.7 - - + -
69D LEU* 3.8 20.2 - - + -
90D ARG 3.1 8.3 + - - +
91D TYR 3.4 9.4 - - - +
93D GLN* 1.4 74.8 - - - +
95D ILE* 1.3 57.4 + - - +
97D ALA* 3.0 16.5 + - - +
98D LEU* 3.1 23.3 + - + +
112D ILE* 4.2 9.0 - - + -
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Residues in contact with ILE 95 (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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130B ASP* 3.8 28.6 - - + +
131B TYR* 3.8 8.0 - - - -
134B MET* 3.6 30.1 - - + -
91D TYR 3.0 15.6 + - - +
92D SER 3.3 6.3 + - - +
94D ALA* 1.3 73.5 - - - +
96D GLU* 1.3 61.3 + - - +
97D ALA 3.3 0.5 + - - -
98D LEU* 3.4 20.3 + - - +
109D PHE* 5.5 4.0 - - + -
112D ILE* 3.9 18.2 - - + -
113D GLN* 4.4 12.3 - - + -
116D PHE* 3.7 39.5 - - + -
134D MET* 4.2 11.0 - - + -
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Residues in contact with GLU 96 (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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92B SER* 5.2 1.0 + - - -
95B ILE* 3.8 32.0 - - + +
113B GLN* 3.4 30.4 + - - +
116B PHE* 3.6 27.1 - - + -
120B LYS* 5.5 0.2 - - - -
131B TYR* 3.3 53.7 + - - +
134B MET* 3.4 17.9 - - + +
92D SER* 2.9 27.1 + - - +
93D GLN 3.6 6.3 - - - +
94D ALA 3.3 0.2 - - - -
95D ILE* 1.3 75.7 - - - +
97D ALA* 1.4 58.4 + - + +
98D LEU 3.5 0.2 - - - -
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Residues in contact with ALA 97 (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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92B SER* 6.1 2.5 - - - -
96B GLU* 5.9 0.4 - - - +
-2D GLY 5.1 9.9 + - - +
-1D PRO 4.9 2.6 - - - +
65D TRP* 3.9 24.5 - - + +
93D GLN 3.2 15.2 + - - +
94D ALA 3.0 6.2 + - - +
96D GLU* 1.4 77.3 - - - +
98D LEU* 1.3 64.4 + - - +
99D PRO* 3.6 11.0 - - - +
1200D PG4 5.4 3.8 - - - +
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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
------------------------------------------------------------
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