Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1J0B
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 SER 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A VAL 4.4 0.2 + - - -
77A GLY* 4.0 3.8 - - - -
78A ALA 2.5 28.0 + - - -
79A VAL 3.2 2.4 + - - +
80A HIS* 1.3 72.5 - - - +
82A ASN* 1.3 59.6 + - - +
83A HIS* 3.6 0.9 - - - +
84A ALA* 2.7 43.0 + - - +
85A PHE* 3.8 8.1 + - - +
102A LEU* 4.7 0.9 - - - -
111A ASN* 3.0 21.1 + - - +
115A ASP* 5.2 0.9 - - - +
1011A 5PA 2.8 30.7 + - - -
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Residues in contact with ASN 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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50A ILE* 3.5 20.6 - - + +
53A ASN* 6.0 0.2 - - - +
54A LYS* 4.9 4.5 - - + -
80A HIS 4.2 3.7 + - - +
81A SER* 1.3 73.2 - - - +
83A HIS* 1.3 64.7 + - - +
85A PHE* 4.0 0.9 - - - +
86A VAL* 3.1 31.5 + - - +
111A ASN* 2.8 28.0 - - - +
279A ASP* 5.0 0.3 - - - +
281A VAL* 5.6 0.7 - - - +
282A TYR* 3.7 14.6 - - - -
310A GLY* 3.6 27.0 + - - +
312A SER* 4.0 1.4 - - - -
313A GLY* 4.7 1.8 - - - +
1011A 5PA 2.7 37.8 + - + +
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Residues in contact with HIS 83 (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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54A LYS* 3.8 28.5 - - + +
57A LYS* 6.3 0.7 - - + -
58A LEU* 4.9 6.3 - - + +
61A LEU* 5.1 0.2 - - + -
75A THR* 2.7 28.5 + - - -
76A VAL 3.7 11.0 - - - -
82A ASN* 1.3 79.4 - - - +
84A ALA* 1.3 53.3 + - - +
85A PHE 3.3 0.2 + - - -
86A VAL* 3.6 1.4 - - - +
87A THR* 2.3 56.5 + - + -
154A ILE* 4.2 6.3 - - + -
157A GLY* 3.3 23.9 + - - -
158A GLY* 3.0 32.3 + - - -
1011A 5PA 2.7 28.0 + + + +
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Residues in contact with ALA 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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75A THR* 4.0 9.9 - - + -
76A VAL 4.1 11.0 - - - +
81A SER* 2.7 32.1 + - - +
83A HIS* 1.3 74.0 - - - +
85A PHE* 1.3 63.1 + - - +
87A THR* 3.9 3.9 - - - -
88A GLY 3.4 8.8 + - - -
100A LEU* 3.1 27.7 - - + +
102A LEU* 3.6 24.7 - - + -
115A ASP* 5.6 0.9 - - - +
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Residues in contact with PHE 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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49A GLY* 4.2 20.2 - - - -
50A ILE* 4.3 8.7 - - + -
81A SER 3.8 16.5 + - - +
82A ASN 3.7 2.8 + - - +
83A HIS 3.3 0.6 - - - -
84A ALA* 1.3 76.9 - - - +
86A VAL* 1.3 79.8 + - + +
87A THR 2.9 1.6 + - - -
88A GLY* 3.1 11.8 + - - -
89A LEU* 3.1 30.6 + - + +
100A LEU* 4.3 0.2 - - - -
111A ASN* 3.8 21.3 - - + +
114A LEU* 3.6 42.6 - - + -
115A ASP* 3.1 35.6 + - - +
118A MET* 4.0 15.7 - - + -
120A ILE* 3.9 10.5 - - + +
277B ILE* 4.6 8.7 - - + -
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Residues in contact with VAL 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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48A LEU* 3.6 23.3 - - + +
49A GLY* 4.1 2.9 - - - -
50A ILE* 4.1 16.4 - - + +
51A GLY 4.2 7.0 - - - +
54A LYS* 4.1 11.4 - - + -
55A ILE* 3.3 27.6 - - + -
58A LEU* 3.3 18.4 - - + -
82A ASN* 3.1 18.4 + - + +
83A HIS 4.3 0.4 - - - +
85A PHE* 1.3 88.8 - - + +
87A THR* 1.3 60.2 + - - +
89A LEU* 4.1 4.8 - - - +
90A ALA* 3.0 24.7 + - - +
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Residues in contact with THR 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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58A LEU* 3.8 18.0 - - + +
62A LEU* 4.8 2.8 - - + +
73A VAL* 4.7 8.3 - - + -
75A THR* 3.8 24.0 - - + -
83A HIS* 2.3 53.9 + - + -
84A ALA 3.9 0.7 - - - -
85A PHE 2.9 0.4 + - - -
86A VAL* 1.3 70.7 - - - +
88A GLY* 1.3 56.7 + - - +
90A ALA* 3.6 2.4 - - - +
91A ALA* 2.7 34.0 + - - +
100A LEU* 6.0 0.2 - - + -
154A ILE* 3.8 29.8 - - + -
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Residues in contact with GLY 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 ALA 3.4 4.4 + - - -
85A PHE 3.1 4.7 + - - -
87A THR* 1.3 76.4 - - - +
89A LEU* 1.3 55.9 + - - +
91A ALA* 2.6 4.0 + - - +
92A LYS* 2.5 43.0 + - - +
98A ALA* 3.4 25.1 - - - -
100A LEU* 4.2 10.5 - - - +
120A ILE* 4.2 4.5 - - - -
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Residues in contact with LEU 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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48A LEU* 3.5 22.9 - - + -
49A GLY* 3.8 20.0 - - - +
85A PHE* 3.1 29.9 + - + +
86A VAL* 4.1 3.1 - - - +
88A GLY* 1.3 70.8 - - - +
90A ALA* 1.3 65.6 + - - +
92A LYS* 2.7 19.0 + - - +
93A LYS* 2.7 13.4 + - - +
118A MET* 3.9 34.1 - - + -
120A ILE* 3.5 12.1 - - + +
271B GLY 3.4 34.5 - - - +
272B THR* 4.0 6.9 - - + +
275B GLY* 4.3 5.4 - - - -
276B ILE 5.1 0.2 - - - +
277B ILE* 5.4 1.1 - - + -
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Residues in contact with ALA 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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17A LEU* 4.9 0.4 - - + -
48A LEU* 3.4 31.8 - - + +
58A LEU* 4.1 11.0 - - + -
62A LEU* 3.8 17.9 - - + -
86A VAL 3.0 19.5 + - - +
87A THR 3.6 3.6 - - - +
89A LEU* 1.3 79.0 - - - +
91A ALA* 1.3 64.1 + - - +
93A LYS* 3.1 14.1 + - - +
94A LEU* 3.2 17.7 + - - +
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Residues in contact with ALA 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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62A LEU* 4.1 12.5 - - + +
73A VAL* 4.0 29.8 - - + -
87A THR 2.7 17.3 + - - +
88A GLY* 2.6 19.4 + - - +
90A ALA* 1.3 70.6 - - - +
92A LYS* 1.3 51.6 + - - +
94A LEU* 3.2 8.7 + - - +
96A LEU* 2.7 37.7 + - - +
98A ALA* 4.0 10.8 - - + -
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Residues in contact with LYS 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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88A GLY 2.5 20.3 + - - +
89A LEU* 2.7 13.7 + - - +
91A ALA* 1.3 71.4 - - - +
93A LYS* 1.3 55.0 + - - -
95A GLY* 2.9 19.2 + - - -
96A LEU 3.2 13.7 + - - +
97A ASP* 4.6 14.8 + - - +
98A ALA* 4.5 9.2 - - + +
118A MET 4.0 9.2 - - - +
119A GLY 3.6 24.2 - - - -
120A ILE* 3.9 23.6 - - + +
121A GLU 5.4 0.4 - - - +
272B THR* 3.5 30.0 - - + +
273B ARG* 5.2 1.2 - - - +
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Residues in contact with LYS 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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16A GLU 5.2 4.0 + - - -
17A LEU* 4.7 16.8 - - + +
48A LEU* 4.5 15.2 - - + +
89A LEU 2.7 15.4 + - - +
90A ALA* 3.1 11.9 + - - +
92A LYS* 1.3 69.0 - - - +
94A LEU* 1.3 70.5 + - + +
95A GLY 3.0 8.0 + - - -
28B PRO* 6.0 5.8 - - - +
29B ASN* 5.6 3.1 + - - +
272B THR 3.6 10.7 + - - +
273B ARG* 3.4 27.3 - - - +
274B GLU* 3.8 25.6 + - - +
275B GLY* 4.6 6.5 - - - +
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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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15A VAL* 3.8 26.0 - - + -
17A LEU* 4.6 7.4 - - + -
62A LEU* 3.3 46.7 - - + +
66A LEU* 4.1 28.7 - - + +
90A ALA 3.2 9.8 + - - +
91A ALA 3.2 6.7 + - - +
93A LYS* 1.3 88.8 - - + +
95A GLY* 1.3 61.9 + - - +
96A LEU* 3.1 15.2 + - + +
11R LYS* 4.8 16.8 + - + +
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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
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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