Contacts of the helix formed by residues 86 - 98 (chain A) in PDB entry 1NNQ
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 GLU 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PHE* 2.8 37.6 + - + +
84A VAL 3.5 0.2 - - - -
85A GLU* 1.3 90.3 - - + +
87A MET* 1.3 66.4 + - - +
88A TYR 3.8 0.7 - - - -
89A PRO* 3.7 3.1 - - - +
90A VAL* 3.4 33.0 + - - +
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Residues in contact with MET 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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82A PHE* 3.0 48.7 + - + -
83A GLU* 3.7 24.9 + - + +
86A GLU* 1.3 77.8 - - - +
88A TYR* 1.3 67.6 + - - +
90A VAL* 3.2 7.0 + - - +
91A TYR* 2.9 70.7 + - + +
14B GLU* 5.1 14.4 - - + +
15B ALA* 4.7 12.1 - - - -
18B GLY* 5.3 8.1 - - - -
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Residues in contact with TYR 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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83A GLU* 3.0 43.3 + - + +
87A MET* 1.3 78.8 - - - +
89A PRO* 1.3 61.2 - - + +
91A TYR* 4.4 6.7 - + - -
92A ASN* 2.8 34.1 + - - +
107A THR* 3.9 28.7 - - + +
110A ALA* 3.5 14.1 - - + -
111A LEU* 3.9 19.5 - - + -
114A GLU* 3.5 18.6 - - + -
15B ALA* 3.8 16.9 + - + +
19B GLU* 2.4 35.1 + - - +
59B HIS* 2.8 33.3 + + - -
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Residues in contact with PRO 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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83A GLU 3.5 4.9 - - - +
84A VAL 3.0 28.5 - - - +
85A GLU 4.1 10.1 - - - +
86A GLU 3.7 9.2 - - - +
87A MET 3.7 2.9 - - - -
88A TYR* 1.3 87.8 - - + +
90A VAL* 1.3 58.0 + - + +
92A ASN* 3.7 4.9 - - + +
93A LYS* 3.0 30.3 + - - +
111A LEU* 4.1 15.2 - - + -
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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 GLU* 3.4 23.5 + - - +
87A MET* 3.2 4.5 + - - +
89A PRO* 1.3 77.4 - - + +
91A TYR* 1.3 71.2 + - + +
93A LYS* 3.4 6.3 + - - +
94A ALA* 3.0 27.9 + - + +
11B PHE* 5.2 7.9 - - + -
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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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87A MET* 2.9 51.0 + - + +
88A TYR* 4.1 8.3 - + - +
90A VAL* 1.3 79.3 - - + +
92A ASN* 1.3 59.9 + - - +
94A ALA* 3.3 1.6 + - - +
95A ALA* 2.9 30.1 + - - +
107A THR* 4.1 16.4 - - + +
8B THR* 5.6 0.9 - - - +
11B PHE* 3.2 73.7 - + + +
12B LEU* 6.0 0.4 - - + -
14B GLU* 3.4 25.1 - - - +
15B ALA* 4.1 15.5 - - + -
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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
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88A TYR 2.8 20.7 + - - +
89A PRO* 3.7 5.9 - - + +
91A TYR* 1.3 77.0 - - - +
93A LYS* 1.3 59.6 + - - +
95A ALA* 3.4 4.7 + - - +
96A GLU* 3.0 34.0 + - - +
104A VAL* 3.3 26.3 + - - +
107A THR* 3.1 30.5 + - - +
108A HIS* 3.9 16.2 - - - +
111A LEU* 5.3 8.1 - - + -
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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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89A PRO 3.0 19.1 + - - +
90A VAL* 3.4 6.3 + - - +
92A ASN* 1.3 77.2 + - - +
94A ALA* 1.3 59.8 + - - +
96A GLU* 3.4 18.3 + - - +
97A PHE* 2.8 32.0 + - + +
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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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90A VAL* 3.0 18.1 + - + +
91A TYR 3.8 3.1 - - - +
93A LYS* 1.3 73.3 - - - +
95A ALA* 1.3 56.1 + - - +
97A PHE* 3.2 10.0 + - + +
98A GLN* 2.8 44.5 + - + +
7B MET* 5.8 0.9 - - + -
8B THR* 4.0 5.4 - - - +
11B PHE* 3.7 30.3 - - + -
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Residues in contact with ALA 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 2.9 18.1 + - - +
92A ASN 3.4 5.8 - - - +
93A LYS 3.3 0.2 - - - -
94A ALA* 1.3 76.5 - - - +
96A GLU* 1.3 61.0 + - - +
98A GLN* 3.2 2.1 + - - -
99A GLY 3.1 4.0 + - - -
100A GLU* 2.9 27.6 + - - +
103A ALA* 3.8 19.3 - - + +
104A VAL* 3.7 28.9 - - + +
107A THR* 5.4 0.7 - - + -
8B THR* 3.6 15.6 + - + -
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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 24.8 + - - +
93A LYS* 3.8 17.7 - - - +
95A ALA* 1.3 75.1 - - - +
97A PHE* 1.3 65.4 + - - +
99A GLY* 3.1 14.4 + - - -
100A GLU 5.1 0.4 - - - +
104A VAL* 3.4 20.8 - - + +
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Residues in contact with PHE 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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93A LYS* 2.8 20.8 + - + +
94A ALA* 3.2 7.8 + - + +
96A GLU* 1.3 78.6 - - + +
98A GLN* 1.3 74.7 + - + +
99A GLY 3.3 0.9 + - - -
5B ARG* 5.3 1.2 + - - -
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Residues in contact with GLN 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 ALA* 2.8 20.1 + - + +
95A ALA 3.9 1.8 - - - +
96A GLU 3.1 0.6 - - - -
97A PHE* 1.3 91.7 - - + +
99A GLY* 1.3 62.5 + - - +
100A GLU* 3.2 3.0 + - + +
5B ARG* 3.3 71.7 + - + +
6B THR 5.1 0.4 - - - +
7B MET* 3.6 25.2 - - - +
8B THR* 2.7 42.8 + - - +
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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