Contacts of the helix formed by residues 81 - 98 (chain A) in PDB entry 1NBP
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 ARG 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS 4.3 0.2 + - - -
80A LEU* 1.3 75.3 - - - +
82A PRO* 1.3 73.0 - - + +
83A ARG* 4.5 8.5 - - + +
84A ASP* 3.0 41.9 + - - +
85A LEU* 3.6 4.9 + - - +
201A MHC 4.1 3.0 - - - -
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Residues in contact with PRO 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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67A GLU* 4.3 6.7 - - + +
70A LEU* 4.1 21.3 - - + +
71A ASN* 3.4 39.9 - - - +
73A ALA 5.8 0.4 - - - +
80A LEU 3.7 7.0 - - - +
81A ARG* 1.3 84.4 - - + +
83A ARG* 1.3 63.1 + - - +
84A ASP 3.1 0.5 + - - -
85A LEU* 3.4 1.6 + - - +
86A ILE* 3.0 31.7 + - + +
201A MHC 3.6 28.5 - - + -
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.4 26.0 + - - +
71A ASN* 4.9 2.8 - - - +
81A ARG* 3.2 7.7 - - + -
82A PRO* 1.3 79.8 - - - +
84A ASP* 1.3 75.4 + - - +
86A ILE* 4.5 0.2 - - - +
87A SER* 2.7 38.1 + - - -
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Residues in contact with ASP 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 LEU* 5.9 4.5 - - + -
81A ARG* 3.0 30.9 + - - +
83A ARG* 1.3 96.3 + - - +
85A LEU* 1.3 59.8 + - - +
87A SER* 3.4 6.2 + - - -
88A ASN* 3.1 25.3 + - - +
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Residues in contact with LEU 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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20A ASP* 3.4 40.4 - - + +
23A MET* 3.9 22.9 - - + -
24A ILE* 3.6 21.1 - - + -
80A LEU* 5.1 10.3 - - + +
81A ARG 3.6 3.4 + - - +
82A PRO 3.4 3.8 + - - +
84A ASP* 1.3 76.6 - - - +
86A ILE* 1.3 66.8 + - + +
88A ASN* 3.4 8.1 + - + +
89A ILE* 3.1 29.7 + - + +
201A MHC 3.5 32.8 - - + -
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Residues in contact with ILE 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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24A ILE* 4.0 17.0 - - + -
63A LEU* 3.8 33.0 - - + +
66A LEU* 3.7 35.2 - - + -
67A GLU* 3.8 35.7 - - + +
70A LEU* 4.0 9.9 - - + -
82A PRO 3.0 19.3 + - - +
83A ARG 4.5 0.7 - - - +
85A LEU* 1.3 75.4 - - + +
87A SER* 1.3 53.5 + - - +
89A ILE* 3.2 7.1 + - + +
90A ASN* 2.7 36.3 + - + +
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Residues in contact with SER 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 ARG* 2.7 28.4 + - - -
84A ASP* 3.5 7.2 - - - -
85A LEU 3.3 0.2 - - - -
86A ILE* 1.3 78.0 - - - +
88A ASN* 1.3 56.4 + - - +
90A ASN* 3.3 8.0 + - - +
91A VAL* 2.9 35.8 + - - +
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Residues in contact with ASN 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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16A HIS* 5.5 3.4 + - - +
20A ASP* 2.6 37.2 + - - -
84A ASP 3.1 15.0 + - - +
85A LEU* 3.5 13.5 - - + +
86A ILE 3.3 0.2 - - - -
87A SER* 1.3 75.2 - - - +
89A ILE* 1.3 61.3 + - - +
91A VAL* 3.5 7.6 + - - +
92A ILE* 3.2 34.7 + - - +
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Residues in contact with ILE 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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17A LEU* 3.6 23.3 - - + -
20A ASP* 3.5 35.0 - - + +
21A LEU* 4.6 10.1 - - + -
24A ILE* 3.7 30.3 - - + -
59A LEU* 4.8 2.9 - - + -
63A LEU* 3.7 24.0 - - + -
66A LEU* 5.3 1.8 - - + -
85A LEU* 3.1 21.3 + - + +
86A ILE* 3.5 12.1 - - + +
88A ASN* 1.3 72.5 - - - +
90A ASN* 1.3 60.8 + - - +
92A ILE* 3.3 2.6 + - - +
93A VAL* 2.9 36.6 + - + +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 3.9 20.6 + - - +
63A LEU* 3.8 17.7 - - + +
86A ILE* 2.7 23.6 + - + +
87A SER* 3.4 10.8 - - - +
89A ILE* 1.3 73.8 - - - +
91A VAL* 1.3 62.4 + - + +
93A VAL* 3.9 0.6 - - - -
94A LEU* 3.0 46.8 + - - +
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Residues in contact with VAL 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 SER* 2.9 23.6 + - - +
88A ASN* 3.8 7.6 - - - +
89A ILE 3.3 0.2 - - - -
90A ASN* 1.3 75.4 - - + +
92A ILE* 1.3 60.1 + - + +
94A LEU* 3.7 7.2 - - + +
95A GLU* 3.0 53.6 + - - +
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Residues in contact with ILE 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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13A GLN* 3.5 30.1 - - + +
16A HIS* 4.0 21.5 - - + -
17A LEU* 3.9 15.7 - - + +
20A ASP* 3.7 20.9 - - - +
88A ASN* 3.2 27.2 + - - +
89A ILE* 3.3 6.9 + - - +
91A VAL* 1.3 77.2 - - + +
93A VAL* 1.3 59.9 + - - +
95A GLU* 3.3 9.1 + - - +
96A LEU* 2.9 46.2 + - + +
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Residues in contact with VAL 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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17A LEU* 4.1 12.6 - - + -
56A LEU* 3.5 36.2 - - + +
59A LEU* 3.8 28.3 - - + -
60A GLU* 3.9 22.7 - - + +
63A LEU* 4.8 3.1 - - + -
89A ILE* 2.9 32.0 + - + +
90A ASN* 3.9 4.5 - - - +
92A ILE* 1.3 72.5 - - - +
94A LEU* 1.3 59.3 + - - +
96A LEU* 3.9 4.4 - - - +
97A LYS* 2.9 33.4 + - + +
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Residues in contact with LEU 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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60A GLU* 4.0 23.3 - - - +
90A ASN* 3.0 40.8 + - - +
91A VAL* 3.7 6.5 - - + +
93A VAL* 1.3 79.6 - - - +
95A GLU* 1.3 61.6 + - + +
97A LYS* 4.1 14.7 - - - +
98A GLY* 3.5 20.2 + - - +
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Residues in contact with GLU 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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13A GLN* 3.2 30.1 + - - +
91A VAL* 3.0 40.5 + - + +
92A ILE* 3.9 3.1 - - - +
94A LEU* 1.3 77.9 - - + +
96A LEU* 1.3 63.5 + - - +
98A GLY* 4.2 5.6 + - - -
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Residues in contact with LEU 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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10A THR* 3.9 29.2 - - + +
13A GLN* 3.7 32.1 - - + +
14A LEU* 3.7 28.7 - - + +
17A LEU* 4.5 4.3 - - + -
53A LEU* 3.8 29.8 - - + +
56A LEU* 3.9 19.1 - - + -
92A ILE* 2.9 38.6 + - + +
93A VAL 3.9 0.2 - - - +
95A GLU* 1.3 79.1 - - - +
97A LYS* 1.3 63.8 + - - +
98A GLY* 3.3 1.3 + - - -
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Residues in contact with LYS 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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53A LEU* 3.5 26.1 + - - +
54A LYS* 4.4 16.5 - - - +
56A LEU* 4.1 7.6 - - + -
57A GLN* 3.0 38.0 + - + +
60A GLU* 3.2 25.4 + - - +
93A VAL* 2.9 22.2 + - + +
94A LEU* 4.1 18.9 - - - +
96A LEU* 1.3 77.0 - - - +
98A GLY* 1.3 78.4 + - - +
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Residues in contact with GLY 98 (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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94A LEU* 3.5 13.8 + - - +
95A GLU 4.2 4.5 + - - -
96A LEU 3.3 4.9 - - - -
97A LYS* 1.3 104.9 + - - +
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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