Contacts of the helix formed by residues 20 - 23 (chain T) in PDB entry 3H1I
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 PRO 20 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434N TYR* 4.3 9.6 - - + -
435N ASN* 3.7 15.7 - - - +
438N ARG* 5.5 3.8 - - + -
225Q HIS* 3.2 44.0 + - + +
226Q LYS* 4.8 0.9 - - + +
228Q SER* 3.6 11.5 + - - +
229Q VAL* 3.2 29.6 - - + -
15R ARG* 3.4 8.1 + - - -
19T SER* 1.3 89.7 - - - +
21T PHE* 1.3 59.8 + - + +
22T GLU 3.2 0.9 - - - -
23T GLN* 3.1 26.3 - - + +
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Residues in contact with PHE 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419N CYS* 3.4 32.8 - - - -
438N ARG* 3.7 24.9 - - + -
225Q HIS* 3.8 16.2 - + - -
226Q LYS* 5.8 5.8 - - - -
15R ARG* 3.7 7.5 - - - +
32R ARG* 2.8 45.1 + - + +
33R LYS* 3.3 41.5 - - + -
36R SER* 3.7 21.3 - - - -
37R TYR* 3.3 32.5 - + - -
19T SER* 3.0 4.3 + - - -
20T PRO* 1.3 82.9 - - + +
22T GLU* 1.3 56.6 + - - +
23T GLN 3.5 0.2 - - - -
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Residues in contact with GLU 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N PHE 4.0 6.9 - - - +
237N THR* 3.9 20.1 + - + +
238N GLY 3.7 32.0 + - - +
419N CYS* 4.3 13.0 - - - +
14R ARG* 3.6 9.4 + - - +
15R ARG* 3.1 23.6 + - - +
18R VAL* 3.8 21.3 - - + +
25R SER* 4.3 2.5 + - - -
32R ARG* 2.3 38.3 + - - +
18T LEU* 4.5 13.6 - - + +
19T SER* 3.1 15.1 + - - +
21T PHE* 1.3 78.4 - - - +
23T GLN* 1.3 60.3 + - - +
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Residues in contact with GLN 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225Q HIS* 5.5 0.2 + - - -
228Q SER* 3.4 33.0 + - - +
229Q VAL* 3.5 1.7 + - - -
231Q LYS* 5.7 0.2 - - - +
232Q SER* 2.6 42.0 + - - +
13R TYR* 3.7 19.8 - - + +
14R ARG* 4.9 0.4 - - - -
15R ARG* 2.6 32.6 + - - -
18T LEU* 3.1 28.9 + - + +
19T SER 3.4 12.8 - - - +
20T PRO* 3.1 16.5 + - + +
22T GLU* 1.3 81.7 - - - +
24T ARG* 1.3 67.2 + - - +
25T ALA 3.8 0.2 + - - -
27T PRO* 5.8 0.8 - - - +
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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