Contacts of the helix formed by residues 81 - 97 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 1.3 72.3 - - - +
82A ALA* 1.3 57.1 + - - +
84A LEU* 3.3 9.4 + - - +
85A ASN* 3.0 56.3 + - - +
123A GLN* 5.6 3.6 - - - +
118D GLU* 4.8 1.8 + - - +
121D ALA* 4.8 11.9 - - + +
122D ILE* 3.6 30.1 - - + +
155D SER* 4.6 17.4 + - - +
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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
----------------------------------------------------------
80A SER* 3.3 8.8 + - - +
81A ASP* 1.3 78.5 + - - +
83A LEU* 1.3 58.1 + - + +
85A ASN* 3.4 9.9 + - - +
86A LYS* 3.1 27.4 + - - +
101C ASP* 4.6 3.3 - - - +
151D GLN* 5.8 1.3 - - + +
193D GLN* 3.6 35.7 - - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 5.1 2.9 - - - +
76A SER* 4.1 27.1 + - - +
77A VAL 5.4 0.7 - - - -
78A PRO* 3.4 26.5 - - + +
79A LEU* 4.4 10.0 - - + +
80A SER* 3.2 22.3 + - - +
82A ALA* 1.3 77.6 - - + +
84A LEU* 1.4 60.0 + - - +
86A LYS* 3.4 31.8 + - + +
87A LEU* 3.0 28.2 + - - +
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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
----------------------------------------------------------
79A LEU* 4.1 23.5 - - + +
80A SER 2.9 17.0 + - - +
81A ASP* 3.6 10.3 - - - +
83A LEU* 1.4 73.7 - - - +
85A ASN* 1.3 60.2 + - - +
87A LEU* 3.3 4.9 + - + +
88A ILE* 3.0 47.8 + - + +
119A LEU* 3.7 32.5 - - + +
122A ILE* 3.9 14.8 - - + -
123A GLN* 4.1 19.5 - - + +
122D ILE* 3.7 31.2 - - + -
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Residues in contact with ASN 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 ASP* 3.0 42.9 + - - +
82A ALA* 3.7 8.2 - - - +
83A LEU 3.4 0.2 - - - -
84A LEU* 1.3 75.8 - - - +
86A LYS* 1.3 57.1 + - - +
88A ILE* 3.5 4.0 + - - +
89A GLY 3.0 24.3 + - - -
123A GLN* 2.7 35.0 + - - +
101C ASP* 3.6 22.2 - - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.7 32.5 - - + +
75A ASN 5.5 2.0 + - - -
76A SER* 4.4 4.4 + - - -
82A ALA 3.1 14.3 + - - +
83A LEU* 3.6 34.8 - - + +
84A LEU 3.3 0.2 - - - -
85A ASN* 1.3 75.9 - - - +
87A LEU* 1.4 60.9 + - - +
89A GLY* 3.3 2.4 + - - -
90A ARG* 3.1 23.6 + - + +
99C PRO* 6.3 0.4 - - + -
101C ASP* 3.6 28.6 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.2 2.9 - - + +
72A LEU* 3.9 26.7 - - + -
73A GLU* 3.6 55.6 - - + +
76A SER* 4.9 5.6 - - - +
79A LEU* 5.1 10.8 - - + -
83A LEU 3.0 17.2 + - - +
84A LEU* 3.6 8.3 - - + +
86A LYS* 1.4 73.4 - - - +
88A ILE* 1.3 64.3 + - + +
90A ARG* 3.2 4.7 + - - +
91A TYR* 3.1 46.3 + - + -
119A LEU* 3.9 22.7 - - + -
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Residues in contact with ILE 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 LEU* 3.0 28.8 + - + +
85A ASN* 3.9 5.2 - - - +
86A LYS 3.4 0.2 - - - -
87A LEU* 1.3 73.5 - - - +
89A GLY* 1.3 57.5 + - - +
91A TYR* 3.3 9.2 + - - +
92A SER* 3.0 24.7 + - - -
116A PHE* 3.6 23.7 - - + +
119A LEU* 3.6 44.4 - - + +
120A LYS* 3.8 20.4 - - + +
123A GLN* 3.5 36.8 - - + +
138C ASN* 5.5 4.0 - - - +
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Residues in contact with GLY 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 ASN 3.0 14.5 + - - -
86A LYS 3.7 4.0 - - - -
88A ILE* 1.3 76.9 - - - +
90A ARG* 1.3 59.0 + - - +
92A SER* 2.7 22.9 + - - -
93A GLN* 3.1 7.1 + - - +
100C PRO* 3.5 36.4 - - - +
101C ASP* 4.7 2.7 - - - -
138C ASN* 4.9 1.3 - - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.6 17.6 - - + -
68A LEU* 3.8 30.6 - - + +
69A LEU* 3.7 20.9 - - + +
72A LEU* 3.7 27.6 - - + +
86A LYS* 3.1 11.8 + - - +
87A LEU 3.2 7.8 + - - +
89A GLY* 1.3 75.0 - - - +
91A TYR* 1.4 62.5 - - - +
93A GLN* 2.8 42.0 + - - +
94A ALA* 3.1 17.5 + - - +
1200A PG4 4.1 4.8 - - - -
96C GLU* 3.1 36.3 + - - -
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Residues in contact with TYR 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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66A LEU* 4.7 2.3 - - + +
69A LEU* 3.7 41.3 - - + +
70A LEU* 4.3 7.3 - - - +
73A GLU* 2.6 30.1 + - - +
87A LEU* 3.1 40.7 + - + -
88A ILE* 3.3 8.9 + - - +
90A ARG* 1.4 71.4 - - - +
92A SER* 1.4 65.1 + - - +
94A ALA* 3.2 5.7 + - - +
95A ILE* 3.0 26.0 + - - +
112A ILE* 3.6 30.5 - - + -
115A ARG* 3.5 27.2 - - + +
116A PHE* 3.6 20.6 - - + -
119A LEU* 3.7 16.8 - - + -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE 3.0 13.1 + - - -
89A GLY 2.7 18.5 + - - -
91A TYR* 1.4 74.4 - - - +
93A GLN* 1.4 57.0 + - - +
95A ILE* 3.3 3.1 + - - +
96A GLU* 2.9 34.1 + - - +
116A PHE* 4.0 7.1 - - - -
100C PRO* 3.4 7.8 - - - +
113C GLN* 5.5 0.2 + - - -
134C MET* 3.8 24.4 - - - +
138C ASN* 3.1 35.3 + - - -
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Residues in contact with GLN 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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65A TRP* 4.1 4.1 - - + -
89A GLY 3.1 7.6 + - - +
90A ARG* 2.8 53.0 + - - +
92A SER* 1.4 78.5 + - - +
94A ALA* 1.4 62.7 + - - +
96A GLU* 3.4 9.9 + - - +
97A ALA* 3.2 23.6 + - - +
95C ILE* 2.9 34.9 + - + +
96C GLU* 3.4 24.0 + - - +
98C LEU 3.5 17.6 + - - -
99C PRO* 4.0 6.2 - - - +
100C PRO* 3.8 19.1 - - + +
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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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65A TRP* 3.5 39.8 - - + -
69A LEU* 3.8 20.2 - - + -
90A ARG 3.1 7.1 + - - +
91A TYR 3.2 8.7 + - - +
93A GLN* 1.4 75.7 - - - +
95A ILE* 1.4 56.5 + - - +
97A ALA* 3.0 16.3 + - - -
98A LEU* 3.1 24.1 + - + +
112A ILE* 4.1 9.2 - - + -
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Residues in contact with ILE 95 (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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91A TYR 3.0 16.6 + - - +
92A SER 3.7 6.5 - - - +
94A ALA* 1.4 74.3 - - - +
96A GLU* 1.4 61.1 + - - +
97A ALA 3.3 0.5 + - - -
98A LEU* 3.5 20.6 + - - +
109A PHE* 5.5 1.1 - - + -
112A ILE* 4.0 20.2 - - + +
113A GLN* 3.9 26.2 - - - +
116A PHE* 3.7 38.1 - - + -
134A MET* 4.3 10.1 - - + -
130C ASP* 4.2 16.5 - - + +
131C TYR* 3.9 8.7 - - - -
134C MET* 3.6 31.0 - - + -
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Residues in contact with GLU 96 (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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92A SER* 2.9 23.7 + - - +
93A GLN 3.6 6.3 - - - +
94A ALA 3.3 0.2 - - - -
95A ILE* 1.4 76.3 - - - +
97A ALA* 1.4 59.0 + - + +
98A LEU 3.5 0.2 - - - -
92C SER* 5.1 1.4 + - - -
95C ILE* 3.8 32.6 - - + +
113C GLN* 3.6 29.3 + - - +
116C PHE* 3.6 27.6 - - + -
120C LYS* 5.2 0.7 - - - -
131C TYR* 3.3 44.4 + - - +
134C MET* 3.4 25.9 - - + +
138C ASN* 5.4 0.2 - - - +
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Residues in contact with ALA 97 (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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-1A PRO 5.1 1.7 - - - +
65A TRP* 3.9 24.2 - - + +
93A GLN 3.2 15.2 + - - +
94A ALA 3.0 5.6 + - - +
96A GLU* 1.4 77.2 - - - +
98A LEU* 1.3 63.5 + - - +
99A PRO* 3.6 10.2 - - - +
92C SER* 6.0 3.6 - - - -
96C GLU* 5.7 0.7 - - - +
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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