Contacts of the helix formed by residues 94 - 106 (chain A) in PDB entry 2N06
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 ASP 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A SER* 3.6 14.7 + - - +
92A VAL 3.3 3.1 - - - -
93A LYS* 1.3 83.7 - - + +
95A PRO* 1.4 65.1 - - - +
96A SER* 4.1 5.7 + - - -
97A PRO* 3.3 39.9 - - + +
98A LEU* 3.5 11.8 - - - +
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Residues in contact with PRO 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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92A VAL 5.0 2.7 - - - +
93A LYS 3.4 12.3 - - - +
94A ASP* 1.4 86.6 - - - +
96A SER* 1.3 60.5 + - - +
98A LEU* 3.6 13.9 - - + +
99A TYR* 2.9 32.1 + - - +
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Residues in contact with SER 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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94A ASP* 3.4 5.5 + - - -
95A PRO* 1.3 82.8 - - - +
97A PRO* 1.4 68.8 - - - +
99A TYR* 3.4 6.2 + - - +
100A ASP* 3.3 17.7 + - - +
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Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER 5.7 0.9 - - - +
94A ASP* 3.3 40.8 - - + +
96A SER* 1.4 93.7 - - - +
98A LEU* 1.3 58.8 + - - +
100A ASP* 3.3 10.5 + - + +
101A MET* 3.1 28.6 + - + +
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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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90A PHE* 3.7 17.9 - - + -
91A SER 5.0 0.2 - - - +
92A VAL* 4.5 14.6 - - + +
94A ASP 3.5 14.6 - - - +
95A PRO* 3.4 15.0 + - + +
96A SER 3.3 0.4 - - - -
97A PRO* 1.3 77.2 - - + +
99A TYR* 1.3 59.4 + - - +
101A MET* 3.3 28.1 + - + +
102A LEU* 2.9 45.1 + - + +
200A 44Z 3.6 48.7 - - + -
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Residues in contact with TYR 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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95A PRO 2.9 20.4 + - - +
96A SER* 3.7 7.0 - - - +
98A LEU* 1.3 72.1 - - - +
100A ASP* 1.3 59.4 + - - +
102A LEU* 3.4 14.6 + - + +
103A ARG* 2.9 45.1 + - + +
108A THR* 5.0 7.1 - - + +
110A ALA* 3.5 29.5 - - + +
111A THR* 5.5 4.7 - - + -
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Residues in contact with ASP 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 SER 3.3 9.5 + - - +
97A PRO* 3.3 14.2 + - + +
99A TYR* 1.3 81.7 - - - +
101A MET* 1.3 63.7 + - - +
103A ARG* 3.6 9.5 + - - +
104A LYS* 3.5 30.3 + - - +
111A THR* 5.4 8.3 - - - +
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Residues in contact with MET 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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85A LEU* 5.8 9.0 - - + -
87A ARG 5.4 1.1 - - - +
88A GLN* 3.5 45.3 - - + +
89A SER 5.1 1.8 - - - +
90A PHE* 3.5 41.7 - - + -
97A PRO* 3.1 16.7 + - + +
98A LEU* 3.5 28.3 - - + +
100A ASP* 1.3 74.2 + - + +
102A LEU* 1.3 65.3 + - + +
104A LYS* 3.0 17.0 + - - +
105A ASN* 3.1 18.8 + - - +
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Residues in contact with LEU 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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33A LEU* 6.5 0.9 - - + -
49A VAL* 4.2 22.7 - - + -
52A VAL* 6.1 4.3 - - + -
98A LEU* 2.9 40.1 + - + +
99A TYR* 3.6 16.6 - - + +
101A MET* 1.3 72.7 - - + +
103A ARG* 1.3 56.7 + - - +
105A ASN* 2.9 11.3 + - + +
106A LEU* 2.8 40.6 + - + +
200A 44Z 3.7 46.4 - - + +
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Residues in contact with ARG 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 TYR* 2.9 29.7 + - + +
100A ASP* 3.7 10.5 - - - +
101A MET 3.3 0.2 - - - -
102A LEU* 1.3 73.4 - - - +
104A LYS* 1.3 75.6 + - - +
106A LEU 3.9 12.6 - - - +
107A VAL* 4.9 3.0 - - - +
108A THR* 3.4 32.0 + - + +
109A LEU* 3.0 21.9 + - - +
110A ALA* 2.9 25.1 + - + -
111A THR* 2.9 34.8 + - + +
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Residues in contact with LYS 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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30A LYS* 2.9 36.2 + - - +
85A LEU* 4.2 23.0 - - + +
100A ASP* 3.5 23.8 + - - +
101A MET* 3.0 10.9 + - - +
103A ARG* 1.3 97.0 - - - +
105A ASN* 1.3 59.0 + - - +
106A LEU 3.8 1.6 - - - -
107A VAL* 5.4 0.8 - - - +
111A THR* 5.8 0.8 + - - -
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Residues in contact with ASN 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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30A LYS* 2.9 32.9 + - - +
33A LEU* 3.6 23.6 - - + +
81A LEU* 3.5 19.2 + - + +
84A LEU* 3.3 31.7 - - - +
85A LEU* 3.7 16.3 - - - +
88A GLN* 2.8 29.9 + - - +
101A MET 3.1 14.6 + - - +
102A LEU* 2.9 9.1 + - + +
104A LYS* 1.3 77.1 + - - +
106A LEU* 1.3 58.8 + - - +
107A VAL 4.0 0.2 - - - -
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Residues in contact with LEU 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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27A VAL* 4.4 10.1 - - + -
28A ARG 4.6 0.4 - - - +
29A PRO* 4.2 19.7 - - + -
33A LEU* 4.5 5.4 - - + -
47A PHE 3.9 13.0 - - - +
48A THR* 3.8 5.6 - - - -
49A VAL* 3.6 47.6 - - + +
52A VAL* 4.0 12.8 - - + -
102A LEU* 2.8 26.9 + - + +
103A ARG* 3.9 6.2 - - - +
104A LYS 5.0 0.2 - - - -
105A ASN* 1.3 71.5 - - - +
107A VAL* 1.3 78.7 + - - +
108A THR* 3.3 12.8 + - - +
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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