Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 1JQI
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 CYS 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.3 11.6 - - + +
33A ALA* 4.3 16.6 - - + -
36A LEU* 4.3 19.1 - - + -
81A ILE 3.0 11.8 + - - +
82A SER* 3.4 4.7 + - - -
84A GLY* 1.3 80.5 - - - +
86A ALA* 1.3 65.3 + - - +
87A SER* 3.2 15.2 + - - -
88A THR* 3.3 34.3 + - - +
89A GLY 3.1 17.0 + - - -
211A ALA* 5.1 1.3 - - - -
356A ARG* 4.9 4.3 - - - +
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Residues in contact with ALA 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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82A SER* 3.4 14.1 + - - +
85A CYS* 1.3 73.1 - - - +
87A SER* 1.3 62.1 + - - +
89A GLY* 3.3 1.0 + - - -
90A VAL* 3.2 8.5 + - - +
209A ILE* 4.1 2.9 - - + -
254A GLN* 2.8 29.6 + - - +
258A ILE* 3.7 32.3 - - + -
356A ARG* 5.5 1.8 - - - +
360A ASP* 3.5 30.1 + - + +
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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
----------------------------------------------------------
85A CYS* 3.2 8.5 - - - -
86A ALA* 1.3 75.9 - - - +
88A THR* 1.3 66.5 + - - +
90A VAL* 3.1 13.2 + - - +
91A ILE* 3.0 27.0 + - - +
209A ILE* 3.1 34.1 - - - -
210A ARG 3.7 0.2 + - - -
211A ALA* 3.3 31.2 + - - +
212A SER* 4.0 8.7 - - - -
360A ASP* 5.1 0.9 + - - -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.0 17.5 - - + +
36A LEU* 4.6 0.5 - - - +
43A PRO* 3.7 22.9 - - + +
46A GLN* 5.2 1.3 - - + -
47A VAL* 5.0 4.7 - - + -
50A MET* 3.3 34.1 - - + -
81A ILE* 4.0 9.2 - - + -
85A CYS* 3.3 27.0 + - - +
87A SER* 1.3 77.6 - - - +
89A GLY* 1.3 62.9 + - - +
91A ILE* 3.4 12.5 + - - +
92A MET* 3.1 22.5 + - - +
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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
----------------------------------------------------------
78A LEU* 3.1 19.9 - - - +
81A ILE* 4.1 8.3 - - - +
82A SER* 3.6 22.2 - - - -
85A CYS 3.1 11.1 + - - -
86A ALA 3.3 3.8 + - - -
87A SER 3.0 1.0 - - - -
88A THR* 1.3 79.0 - - - +
90A VAL* 1.3 55.3 + - - +
92A MET* 3.4 1.8 + - - +
93A SER* 2.9 22.1 + - - -
254A GLN* 4.7 2.9 - - - -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 3.2 6.4 + - - +
87A SER* 3.1 20.8 + - - +
89A GLY* 1.3 71.6 - - - +
91A ILE* 1.3 66.6 + - - +
92A MET 3.1 1.6 - - - -
93A SER* 4.0 5.2 - - - -
94A VAL* 2.8 50.1 + - + +
163A THR* 4.5 7.4 - - + -
209A ILE* 4.6 7.6 - - + -
212A SER* 4.2 21.1 - - - +
251A ILE* 4.3 12.1 - - + -
254A GLN* 3.6 16.5 - - - +
367A TYR* 3.5 28.5 - - + +
400A CAA 4.3 3.8 - - + -
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Residues in contact with ILE 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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42A PHE* 3.5 41.3 - - + -
43A PRO* 4.0 22.9 - - + -
47A VAL* 4.5 13.9 - - + -
56A LEU* 5.2 2.2 - - + +
87A SER* 3.0 18.8 + - - +
88A THR* 3.6 7.9 - - - +
89A GLY 3.3 0.2 - - - -
90A VAL* 1.3 78.3 - - - +
92A MET* 1.3 61.3 + - - +
95A ASN* 3.5 19.4 + - - +
125A ILE* 4.2 8.4 - - + +
164A ASN* 3.7 33.8 + - - +
212A SER* 4.2 20.2 - - - +
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Residues in contact with MET 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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50A MET* 3.3 31.0 - - + -
55A LEU* 3.5 23.6 - - + +
56A LEU* 4.1 13.7 - - + -
58A MET* 3.9 20.0 - - - -
74A TYR* 4.4 4.3 - - + -
77A ALA* 4.3 4.7 - - + +
78A LEU* 3.7 38.1 - - + +
81A ILE* 4.1 10.8 - - + -
88A THR 3.1 16.2 + - - +
89A GLY 3.5 3.6 - - - +
91A ILE* 1.3 77.9 - - - +
93A SER* 1.3 63.5 + - - +
95A ASN* 3.5 2.1 + - - +
96A ASN* 2.9 42.2 + - - +
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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
----------------------------------------------------------
74A TYR* 3.1 21.8 + - - -
78A LEU* 3.8 11.7 - - - -
89A GLY 2.9 16.6 + - - -
90A VAL* 3.1 13.2 + - - -
92A MET* 1.3 76.2 - - - +
94A VAL* 1.3 60.7 + - - +
97A SER* 2.9 33.4 + - - -
98A LEU* 5.0 0.6 - - - +
247A GLY 4.4 3.6 + - - -
250A GLY* 3.6 19.4 - - - -
251A ILE* 4.2 7.9 + - - +
254A GLN* 6.0 0.9 - - - -
368A GLU* 4.8 3.3 + - - -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 2.8 26.9 + - + +
91A ILE 4.0 0.2 - - - +
93A SER* 1.3 76.6 - - - +
95A ASN* 1.3 63.6 + - - +
98A LEU* 3.0 25.4 + - + -
99A TYR 3.0 21.3 + - - -
126A GLY 3.9 9.9 - - - +
127A CYS* 4.0 14.6 - - - -
128A PHE* 4.5 2.2 - - + +
163A THR* 4.1 15.7 - - + +
164A ASN* 3.7 21.5 - - - +
368A GLU* 5.2 0.7 - - - +
399A FAD 5.6 0.7 - - - +
400A CAA 3.5 31.4 - - + -
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Residues in contact with ASN 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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56A LEU* 2.9 36.8 + - + +
91A ILE 3.5 14.1 + - - +
92A MET* 4.0 4.7 - - - +
94A VAL* 1.3 80.3 - - - +
96A ASN* 1.3 57.6 + - - +
99A TYR* 3.9 12.0 - - - -
100A LEU* 3.1 39.4 + - - +
119A PHE* 3.3 21.8 + - - +
124A LYS 4.8 0.8 + - - -
125A ILE* 3.4 21.2 - - + +
126A GLY 2.9 29.9 + - - +
164A ASN* 4.7 0.2 - - - +
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Residues in contact with ASN 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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55A LEU 2.9 24.6 + - - -
56A LEU* 3.3 11.6 + - - +
57A ALA* 3.3 5.0 + - - -
58A MET* 2.9 30.0 + - - +
59A ASP* 4.3 6.9 + - + +
71A TYR* 4.6 3.8 + - + +
74A TYR* 3.4 31.0 - - + +
92A MET* 2.9 30.6 + - - +
95A ASN* 1.3 77.2 - - - +
97A SER* 1.3 59.0 + - - +
100A LEU* 3.7 6.7 - - - +
101A GLY* 3.1 24.8 + - - -
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Residues in contact with SER 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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71A TYR* 2.8 25.2 + - - -
74A TYR* 2.7 26.4 + - - -
93A SER* 2.9 16.8 + - - -
96A ASN* 1.3 73.0 - - - +
98A LEU* 1.3 61.5 + - - +
101A GLY* 3.4 19.5 - - - +
102A PRO* 3.6 3.6 - - - +
243A THR* 3.7 8.3 - - - +
246A MET* 3.7 9.1 + - - +
247A GLY* 3.5 28.5 - - - -
250A GLY* 4.8 0.2 - - - -
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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
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93A SER 3.9 1.8 + - - +
94A VAL* 3.0 21.4 + - + +
97A SER* 1.3 82.3 - - - +
99A TYR* 1.3 60.6 + - - +
102A PRO* 3.1 19.5 - - - +
128A PHE* 3.4 49.6 - - + +
172A VAL* 4.4 1.6 - - - +
243A THR* 4.0 14.1 - - + +
244A LEU* 5.0 3.8 - - + -
247A GLY* 3.8 24.9 - - - -
368A GLU* 3.6 14.6 - - - +
400A CAA 3.5 40.4 - - + -
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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