Contacts of the helix formed by residues 78 - 83 (chain A) in PDB entry 2P18
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 HIS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A HIS* 3.2 10.1 + + - +
77A LYS* 1.3 91.3 - - + +
79A TRP* 1.3 57.0 + - - +
80A ASP* 3.1 16.4 - - - +
81A HIS* 2.8 25.0 + - + -
82A SER 3.0 7.8 + - - -
139A HIS* 3.0 18.8 + + - -
140A THR* 3.4 20.0 - - + +
175A PHE* 3.4 27.6 - + - +
176A GLU* 4.9 2.8 + - - -
302A ZN 2.1 35.7 - - - -
1022A ACY 3.3 4.9 + - - -
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Residues in contact with TRP 79 (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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43A ASN* 3.8 4.3 - - - +
44A ALA* 4.8 13.8 - - + +
77A LYS 3.4 3.0 + - - -
78A HIS* 1.3 73.1 - - - +
80A ASP* 1.3 58.0 + - - +
81A HIS 3.0 1.4 + - - -
82A SER* 3.9 7.9 - - - -
83A GLY* 2.8 57.5 + - - -
87A LYS* 6.4 1.6 - - - -
112A PRO* 3.9 27.8 - - + -
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Residues in contact with ASP 80 (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 LEU* 3.7 17.3 - - + -
24A ASN* 2.9 26.8 + - - +
41A ASP* 4.3 1.7 - - - +
43A ASN* 3.1 30.9 + - - -
78A HIS* 3.4 14.4 - - - +
79A TRP* 1.3 72.0 + - - +
81A HIS* 1.3 64.8 + - - +
210A HIS* 3.0 7.1 - - - -
301A ZN 2.3 32.3 - - - -
1022A ACY 3.3 6.3 - - - +
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Residues in contact with HIS 81 (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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24A ASN* 3.8 11.0 - - - -
25A PHE 5.2 0.8 + - - -
41A ASP* 2.8 58.0 + - + +
42A VAL 3.2 13.9 + - - +
74A SER* 4.0 6.8 + - - -
75A THR* 4.8 0.2 - - - -
76A HIS* 3.2 35.1 - + + +
78A HIS* 2.8 8.1 + - + +
80A ASP* 1.3 91.2 + - - +
82A SER* 1.3 56.8 + - - +
85A ASN* 4.4 0.2 - - - +
163A GLY 4.8 0.4 - - - -
164A ASP* 3.1 21.4 + - - -
209A GLY* 3.8 13.7 - - - -
301A ZN 2.1 33.6 - - - -
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Residues in contact with SER 82 (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 VAL 3.2 3.6 - - - -
74A SER* 4.4 0.4 - - - -
76A HIS 4.2 4.3 - - - -
77A LYS 2.8 26.6 + - - -
78A HIS 3.0 4.6 + - - -
79A TRP* 3.9 4.7 - - - -
81A HIS* 1.3 77.6 - - - +
83A GLY* 1.3 59.7 + - - +
84A GLY 2.9 12.0 + - - -
85A ASN* 3.1 36.0 + - - +
86A ALA 4.9 0.2 + - - -
111A ILE* 4.0 7.4 - - - -
112A PRO* 3.6 28.8 - - - +
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Residues in contact with GLY 83 (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 VAL 3.4 1.4 + - - -
43A ASN* 3.8 7.8 - - - +
44A ALA* 3.9 8.4 + - - +
79A TRP* 2.8 61.5 + - - -
82A SER* 1.3 75.8 + - - +
84A GLY* 1.3 55.5 + - - +
86A ALA 5.6 0.4 - - - -
87A LYS* 4.9 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