Contacts of the helix formed by residues 96 - 101 (chain A) in PDB entry 2QPW
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 ASN 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.9 15.0 - - + +
56A GLY 5.6 0.4 - - - -
57A PRO* 2.9 26.3 + - - +
58A PHE* 4.4 2.6 - - - -
59A VAL* 3.7 23.7 + - + +
95A GLY* 1.3 74.7 - - - +
97A TRP* 1.3 69.6 + - + +
98A LEU* 3.1 30.5 + - - +
99A ARG* 3.1 22.3 + - - +
100A TYR* 4.0 4.5 - - - -
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Residues in contact with TRP 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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21A VAL* 3.8 15.9 + - + +
24A GLY* 3.9 20.4 + - - -
25A LEU* 3.7 28.7 - - + -
26A PRO* 3.5 24.2 - - + +
29A VAL* 4.0 15.9 - - + -
31A LEU* 4.5 5.8 - - + -
43A VAL* 3.8 31.6 - - + +
55A PHE* 3.7 48.9 - + + -
56A GLY 5.1 1.1 - - - +
96A ASN* 1.3 83.4 - - + +
98A LEU* 1.3 82.9 + - + +
100A TYR* 3.0 22.8 + - - +
101A VAL* 4.0 13.8 + - + -
123A TYR* 6.3 0.2 - + - -
135A LEU* 4.4 4.3 - - + -
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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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55A PHE* 3.9 8.7 - - + +
56A GLY* 3.8 34.3 - - - +
57A PRO 4.4 0.2 - - - +
58A PHE* 3.9 29.6 - - + +
96A ASN* 3.1 21.8 + - - +
97A TRP* 1.3 115.0 - - + +
99A ARG* 1.3 62.9 + - - +
101A VAL* 3.1 22.4 + - - +
123A TYR* 3.7 40.4 + - + +
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Residues in contact with ARG 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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12A GLU* 3.1 26.8 + - - -
40A ARG* 3.6 10.7 + - - -
58A PHE* 4.1 13.6 - - - -
72A VAL 5.7 0.2 - - - +
73A TYR* 3.6 50.9 + - + -
89A ALA* 2.8 39.4 + - + +
90A THR* 2.9 21.2 + - - +
92A PRO* 3.8 29.4 - - - +
95A GLY* 5.7 0.7 - - - -
96A ASN* 3.1 19.1 + - - +
98A LEU* 1.3 77.2 - - - +
100A TYR* 1.3 84.0 + - + +
101A VAL 3.5 4.5 + - - +
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Residues in contact with TYR 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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12A GLU* 3.7 17.8 + - - -
16A GLU 4.7 0.5 + - - -
17A VAL* 3.8 22.4 - - + +
18A PRO* 3.5 13.5 - - - +
21A VAL* 4.0 22.0 - - + -
31A LEU* 4.1 12.3 - - + -
40A ARG* 3.3 12.7 + - - +
41A ILE* 3.7 27.4 - - + +
42A GLY* 3.3 20.1 - - - -
43A VAL* 3.5 11.4 - - + -
92A PRO* 3.4 24.4 - - + +
96A ASN 4.0 7.9 - - - -
97A TRP* 3.0 19.1 + - - +
99A ARG* 1.3 108.0 + - - +
101A VAL* 1.3 63.6 + - - +
102A ASN 3.2 3.6 + - - -
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Residues in contact with VAL 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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40A ARG* 4.1 1.4 + - - -
43A VAL* 3.5 25.1 - - + +
97A TRP* 4.2 16.8 - - + -
98A LEU* 3.1 17.9 + - - +
99A ARG 4.0 6.4 - - - +
100A TYR* 1.3 73.8 - - - +
102A ASN* 1.3 73.1 + - - +
103A TRP* 4.0 5.9 + - - -
112A LEU* 3.7 24.7 - - + -
123A TYR* 3.9 17.5 + - + -
135A LEU* 3.7 15.9 - - + +
137A VAL* 3.9 20.0 - - + +
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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