Contacts of the helix formed by residues 88 - 106 (chain A) in PDB entry 1INR
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 LYS 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.3 55.7 + - + +
82A ASN* 5.1 0.8 - - - +
85A PRO* 3.1 32.9 + - + +
86A ASP 3.3 1.0 - - - -
87A ILE* 1.3 76.1 - - - +
89A ALA* 1.3 56.3 + - - +
91A VAL* 4.1 1.9 - - - +
92A ASN* 2.9 35.4 + - + +
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Residues in contact with ALA 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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86A ASP 4.8 3.1 + - - +
87A ILE 3.1 1.0 + - - -
88A LYS* 1.3 77.5 - - - +
90A HIS* 1.3 71.9 + - + +
92A ASN* 3.9 5.9 + - - +
93A SER* 3.1 29.5 + - - -
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Residues in contact with HIS 90 (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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29A ALA* 4.7 2.4 - - - +
32A ARG* 3.4 39.9 - - + +
33A VAL* 3.5 24.2 - - + +
36A PHE* 3.4 33.3 - + - -
86A ASP 4.8 2.5 + - - -
87A ILE* 3.1 9.7 + - + +
89A ALA* 1.3 85.6 - - + +
91A VAL* 1.3 61.9 + - - +
93A SER* 3.4 6.8 + - - +
94A LEU* 2.9 28.4 + - - +
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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
----------------------------------------------------------
33A VAL* 4.4 11.7 - - + -
37A PHE* 5.6 0.9 - - + -
77A MET* 3.6 45.3 - - + +
80A ALA* 4.8 8.1 - - + -
81A GLU* 4.5 7.9 - - + -
87A ILE* 3.2 46.8 + - + +
88A LYS* 4.1 4.0 - - - +
90A HIS* 1.3 75.4 - - - +
92A ASN* 1.4 60.1 + - - +
94A LEU* 3.3 8.9 + - + +
95A GLY* 3.0 25.6 + - - -
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 2.9 20.6 + - + +
89A ALA* 3.9 5.6 + - - +
91A VAL* 1.4 75.4 - - - +
93A SER* 1.3 69.3 + - - +
95A GLY* 3.6 1.6 + - - +
96A GLU* 3.0 44.9 + - - +
99A LYS* 5.6 0.5 + - - -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.4 7.6 - - - -
89A ALA 3.1 18.3 + - - -
90A HIS* 3.7 7.6 - - - -
91A VAL 3.4 0.2 - - - -
92A ASN* 1.3 83.1 + - - +
94A LEU* 1.3 57.0 + - - +
96A GLU* 3.6 5.2 + - - +
97A ASN* 2.6 40.2 + - - +
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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
----------------------------------------------------------
26A LEU* 3.7 24.4 - - + +
29A ALA* 4.0 8.7 - - + +
30A PHE* 3.7 48.7 - - + +
33A VAL* 4.3 14.1 - - + -
77A MET* 4.2 23.8 - - + -
90A HIS 2.9 20.9 + - - +
91A VAL* 3.3 8.2 + - + +
93A SER* 1.3 74.0 - - - +
95A GLY* 1.3 59.3 + - - +
97A ASN* 3.5 3.1 + - - +
98A LEU* 3.1 22.9 + - + +
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Residues in contact with GLY 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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73A LEU* 3.5 19.2 - - - +
77A MET* 3.7 21.6 - - - -
91A VAL 3.0 12.7 + - - -
92A ASN* 4.0 2.0 - - - -
93A SER 3.4 0.2 - - - -
94A LEU* 1.3 73.1 - - - +
96A GLU* 1.3 56.3 + - - +
98A LEU* 3.2 2.5 + - - -
99A LYS* 2.9 31.9 + - - +
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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 ASN* 3.0 44.3 + - - +
93A SER* 3.9 6.3 - - - +
95A GLY* 1.3 72.5 - - - +
97A ASN* 1.3 57.7 + - - +
99A LYS* 3.3 30.5 + - - +
100A THR* 3.0 32.0 + - - -
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Residues in contact with ASN 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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25A ASP* 3.2 35.3 + - + +
26A LEU* 3.8 25.5 - - + +
29A ALA* 4.0 11.9 - - - +
93A SER* 2.6 33.5 + - - +
94A LEU* 3.8 2.0 - - - +
96A GLU* 1.3 73.9 - - - +
98A LEU* 1.3 60.0 + - - +
100A THR* 3.8 10.1 - - - +
101A LEU* 3.0 26.3 + - - +
104A ARG* 5.3 1.2 + - - -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.6 16.8 - - + +
69A ILE* 3.7 36.7 - - + +
72A TYR* 4.5 7.4 - - + -
73A LEU* 3.7 28.7 - - + -
77A MET* 4.2 15.7 - - + -
94A LEU* 3.1 14.5 + - + +
95A GLY* 3.2 8.0 + - - +
97A ASN* 1.3 75.7 - - - +
99A LYS* 1.3 63.4 + - - +
101A LEU* 4.2 21.1 - - + -
102A ARG* 3.0 21.5 + - - +
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Residues in contact with LYS 99 (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 LEU* 3.8 30.3 - - + -
92A ASN* 5.6 0.4 + - - -
95A GLY* 2.9 23.4 + - - +
96A GLU* 3.3 37.0 + - - +
98A LEU* 1.3 73.7 - - - +
100A THR* 1.3 51.9 + - - +
102A ARG* 3.0 13.0 + - - +
103A LEU* 2.7 47.6 + - + +
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Residues in contact with THR 100 (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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96A GLU 3.0 17.0 + - - -
97A ASN* 3.8 10.1 - - - +
98A LEU 3.3 0.2 - - - -
99A LYS* 1.3 77.1 - - - +
101A LEU* 1.3 60.3 + - - +
103A LEU* 3.1 11.7 + - - +
104A ARG* 2.9 56.6 + - - +
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Residues in contact with LEU 101 (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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22A MET* 4.3 19.5 - - + +
23A LEU* 3.8 32.5 - - + -
26A LEU* 4.0 17.7 - - + -
69A ILE* 5.6 2.5 - - + -
97A ASN 3.0 19.5 + - - +
98A LEU* 3.6 16.6 - - + +
100A THR* 1.3 74.5 - - - +
102A ARG* 1.3 64.5 + - - +
104A ARG* 3.1 28.7 + - - +
105A LEU* 3.1 42.6 + - + +
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Residues in contact with ARG 102 (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 SER* 4.2 12.1 + - - -
69A ILE* 3.7 40.8 - - + +
70A GLN* 4.4 12.1 - - - +
73A LEU* 3.5 23.0 - - - +
98A LEU 3.0 13.6 + - - +
99A LYS* 3.0 14.5 + - - +
101A LEU* 1.3 79.0 - - - +
103A LEU* 1.3 65.5 + - + +
105A LEU* 3.5 8.8 + - - +
106A ARG* 3.4 32.0 + - - +
112A LEU* 4.2 6.7 - - + -
115A GLU* 3.4 39.6 + - - -
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Residues in contact with LEU 103 (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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99A LYS* 2.7 37.7 + - + +
100A THR* 3.1 12.1 + - - +
102A ARG* 1.3 73.6 - - + +
104A ARG* 1.3 62.6 + - + +
106A ARG* 3.1 52.9 + - - +
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Residues in contact with ARG 104 (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 ASN 4.7 1.2 + - - -
22A MET* 2.7 70.1 + - + +
25A ASP* 5.8 4.8 + - - +
97A ASN 5.3 1.0 + - - -
100A THR* 2.9 46.9 + - - +
101A LEU* 3.1 18.6 + - - +
103A LEU* 1.3 75.3 - - + +
105A LEU* 1.3 61.3 + - + +
106A ARG 3.2 1.2 + - - -
107A ARG* 3.4 20.3 - - - +
111A PHE* 4.9 2.3 - - - -
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Residues in contact with LEU 105 (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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22A MET* 4.1 10.8 - - + -
65A LEU* 4.1 26.0 - - + -
69A ILE* 4.8 8.7 - - + -
101A LEU* 3.1 46.2 + - + +
102A ARG* 3.9 4.0 - - - +
103A LEU 3.4 0.2 - - - -
104A ARG* 1.3 75.4 - - - +
106A ARG* 1.3 58.7 + - - +
107A ARG 2.8 9.1 + - - -
111A PHE* 3.1 42.2 + - + +
112A LEU* 3.0 36.6 + - + -
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Residues in contact with ARG 106 (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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102A ARG* 3.4 31.6 + - - +
103A LEU* 3.1 45.1 + - + +
104A ARG 3.1 3.1 - - - -
105A LEU* 1.3 72.4 - - - +
107A ARG* 1.3 58.1 + - - +
112A LEU* 4.1 15.9 - - + +
115A GLU* 2.9 50.3 + - - +
116A ASN* 4.1 26.0 - - - +
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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