Contacts of the helix formed by residues 16 - 21 (chain F) in PDB entry 6H25
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 16 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 5.0 2.5 - - + -
66C PHE* 4.7 0.2 - - - -
71E LEU* 5.8 2.7 - - + -
72E GLU* 5.5 1.1 - - - +
14F SER 4.5 2.5 - - - +
15F GLN* 1.3 90.4 - - + +
17F PRO* 1.3 73.0 - - + +
18F GLN* 3.3 7.1 + - + +
19F LEU* 3.9 31.5 + - + +
20F TYR* 3.4 18.2 - - - -
108F ARG* 5.2 2.7 - - + +
109F ARG* 4.7 26.9 - - + +
110F ARG 5.8 0.2 - - - +
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Residues in contact with PRO 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP* 5.8 2.9 - - - +
63C LYS* 6.3 0.4 - - - +
64C ALA* 3.7 23.3 - - + +
65C GLU* 4.9 0.7 - - - -
66C PHE* 3.6 30.6 - - + -
133C TRP* 5.4 7.6 - - + -
166C PRO* 5.8 4.3 - - + -
177C ALA* 4.9 6.3 - - + +
179C VAL* 5.3 9.1 - - + +
15F GLN 4.3 1.6 - - - +
16F PRO* 1.3 86.9 - - + +
18F GLN* 1.3 61.3 + - + +
19F LEU 3.2 0.2 - - - -
20F TYR* 3.2 6.1 + - + +
21F ALA* 2.9 26.9 + - - +
108F ARG 5.7 3.4 - - - +
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Residues in contact with GLN 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C VAL* 5.9 1.8 - - - -
72E GLU* 5.3 1.4 - - - +
16F PRO* 3.3 5.4 - - + -
17F PRO* 1.3 82.2 - - + +
19F LEU* 1.3 76.8 + - + +
21F ALA* 3.3 25.6 + - + +
108F ARG* 3.9 41.3 - - + +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 3.8 44.2 - - + +
72E GLU* 3.4 38.1 - - + +
16F PRO* 3.9 30.6 + - + +
17F PRO 3.2 0.4 - - - -
18F GLN* 1.3 92.4 - - - +
20F TYR* 1.3 65.6 + - + +
21F ALA 3.5 4.3 + - - +
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Residues in contact with TYR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 4.3 22.0 - + + -
131C LEU* 6.5 0.7 - - + -
174C THR* 6.5 0.2 - - + -
175C ALA* 4.3 33.8 - - + +
176C LEU* 4.8 1.0 - - - -
177C ALA* 4.2 15.9 + - + -
71E LEU* 5.1 13.2 - - + +
15F GLN* 3.6 31.0 - - + +
16F PRO 3.4 15.7 - - - -
17F PRO 3.2 7.0 + - - +
19F LEU* 1.3 81.2 - - + +
21F ALA* 1.3 64.2 + - - +
22F ALA* 3.4 5.5 + - - +
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ALA* 3.9 10.8 - - + +
179C VAL* 4.1 23.8 - - + +
17F PRO 2.9 13.0 + - - +
18F GLN* 3.4 25.8 - - + +
19F LEU 3.2 4.9 - - - +
20F TYR* 1.3 78.0 - - - +
22F ALA* 1.3 60.7 + - - +
23F ASP* 3.6 11.1 + - + +
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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