Contacts of the helix formed by residues 96 - 105 (chain A) in PDB entry 2NP2
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 GLY 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PHE 2.9 25.5 + - - -
61A GLY* 3.4 2.7 - - - -
94A ARG 4.6 0.2 - - - -
95A PRO* 1.3 74.8 - - - +
97A LYS* 1.3 67.9 + - - -
98A ASP 3.4 1.8 - - - -
99A LEU* 3.1 4.7 + - - +
100A LYS* 2.7 26.5 + - - +
211D T 3.4 19.7 - - - -
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Residues in contact with LYS 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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59A SER* 5.5 0.2 - - - -
96A GLY* 1.3 69.6 - - - +
98A ASP* 1.3 66.5 + - - +
100A LYS* 3.1 5.8 + - - -
101A GLU* 2.8 61.7 + - + +
210D A 3.2 45.1 + - + +
211D T 2.8 26.5 + - + +
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Residues in contact with ASP 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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59A SER* 3.2 27.0 + - - +
96A GLY 3.4 0.6 - - - -
97A LYS* 1.3 79.1 - - - +
99A LEU* 1.3 57.9 + - - +
101A GLU* 3.8 4.6 - - - +
102A ARG* 2.9 60.3 + - - +
46B LYS* 3.2 30.8 + - - +
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Residues in contact with LEU 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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59A SER 4.0 1.6 + - - -
60A PHE* 3.1 43.7 - - + +
93A PHE* 3.6 25.8 - - + -
95A PRO* 4.5 2.9 - - + -
96A GLY 3.1 3.8 + - - +
98A ASP* 1.3 78.0 + - - +
100A LYS* 1.3 63.4 + - - +
102A ARG* 3.2 5.5 + - + -
103A VAL* 3.1 38.1 + - + +
46B LYS* 3.7 30.3 - - + +
49B LEU* 3.9 23.6 - - + -
50B CYS* 5.8 0.2 - - - -
91B ALA* 3.8 16.8 - - + -
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Residues in contact with LYS 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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95A PRO* 4.3 22.0 - - + +
96A GLY 2.7 24.3 + - - +
97A LYS* 3.7 5.4 - - - +
99A LEU* 1.3 73.7 - - - +
101A GLU* 1.3 60.7 + - + +
103A VAL* 4.2 3.6 - - - +
104A TRP* 3.2 53.8 + - + +
89B HIS 5.0 0.7 - - - +
90B VAL* 5.9 8.7 - - + -
91B ALA* 5.8 2.7 - - - +
224C A 3.7 25.2 + - - -
225C T 6.1 0.4 - - - +
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Residues in contact with GLU 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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97A LYS* 2.8 56.5 + - + +
98A ASP* 3.9 3.9 + - - +
100A LYS* 1.3 79.9 - - + +
102A ARG* 1.3 65.8 + - + +
103A VAL 3.2 2.4 + - - -
104A TRP* 3.8 14.4 + - - +
105A GLY 4.7 2.3 + - - -
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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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98A ASP* 2.9 53.8 + - - +
99A LEU* 3.2 4.7 + - + +
101A GLU* 1.3 79.1 - - + +
103A VAL* 1.3 60.5 + - + +
105A GLY 4.9 4.1 - - - +
106A ILE* 4.2 8.8 - - - +
43B GLU* 5.0 1.6 + - - +
46B LYS* 3.5 26.1 - - - +
47B SER* 3.6 20.2 - - - +
50B CYS* 3.0 42.5 - - - +
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Residues in contact with VAL 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 LEU* 3.1 25.7 + - + +
100A LYS* 4.4 2.5 - - - +
102A ARG* 1.3 82.2 - - - +
104A TRP* 1.3 68.2 + - - +
105A GLY 3.5 1.1 - - - -
106A ILE* 3.2 35.0 - - + +
49B LEU* 4.3 20.0 - - + -
50B CYS* 4.4 3.6 - - - +
65B VAL* 4.1 15.5 - - + -
89B HIS* 3.4 26.7 - - + +
90B VAL* 3.9 17.3 - - - +
91B ALA* 4.0 5.4 - - + +
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Residues in contact with TRP 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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100A LYS* 3.2 46.0 + - + +
101A GLU* 4.0 10.3 - - - +
102A ARG 3.6 0.6 - - - -
103A VAL* 1.3 78.0 - - - +
105A GLY* 1.3 64.4 + - - +
106A ILE 3.2 5.0 + - - -
85B VAL* 4.6 10.8 - - + -
86B LEU* 4.6 12.7 + - + +
88B HIS* 3.2 57.8 - + + +
89B HIS* 3.2 30.3 + - - +
90B VAL* 6.5 1.1 - - + -
224C A 4.2 15.3 - - - -
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Residues in contact with GLY 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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101A GLU 4.7 3.0 + - - -
102A ARG 4.9 3.1 + - - +
103A VAL 3.5 0.4 - - - -
104A TRP* 1.3 83.4 - - - +
106A ILE* 1.3 64.4 + - - +
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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