Contacts of the helix formed by residues 110 - 115 (chain H) in PDB entry 6AHU
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 PHE 110 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H SER* 3.6 29.8 - - - -
21H TYR* 3.7 6.3 - - - -
108H SER* 3.0 22.1 + - - +
109H PRO* 1.3 101.6 - - + +
111H LEU* 1.3 60.3 + - - +
112H LEU 4.2 5.6 - - - +
113H ALA* 3.3 11.6 + - + +
114H LEU* 3.1 11.3 + - - +
13L HIS* 5.8 4.5 - - + -
15L LEU* 3.6 31.0 - - + -
238L LEU* 5.2 5.2 - - + -
241L PHE* 3.5 49.4 - + + +
242L ASP* 4.6 18.6 - - + -
354L ALA* 5.6 3.8 - - + -
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TYR* 3.6 52.2 - - + +
64H LEU* 4.4 12.1 - - + -
74H ILE* 3.7 32.1 - - + -
110H PHE* 1.3 70.0 - - - +
112H LEU* 1.3 56.3 + - - +
113H ALA 3.3 0.2 - - - -
114H LEU* 3.6 10.0 - - + +
115H SER* 2.5 39.5 + - - +
241L PHE 5.6 1.2 + - - -
242L ASP* 4.9 6.9 + - - +
245L GLY* 3.5 19.5 - - - +
246L ALA* 3.8 29.4 - - + +
249L SER* 5.1 2.2 - - - +
251L VAL* 5.2 2.5 - - + -
264L TYR* 5.3 1.3 - - + -
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H PHE* 3.2 1.9 - - + +
111H LEU* 1.3 79.5 - - - +
113H ALA* 1.3 57.3 + - - +
115H SER* 4.4 1.1 - - - -
41L ARG* 3.4 19.4 + - - +
241L PHE* 3.8 26.9 + - + +
244L LEU* 4.1 14.8 - - + -
245L GLY* 3.5 17.2 - - - +
248L PHE* 3.6 35.7 - - + -
313L SER* 4.0 22.2 - - - +
315L GLN* 3.0 19.4 - - - +
338L LEU* 3.7 32.8 - - + +
340L ASN* 4.5 0.7 - - - +
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Residues in contact with ALA 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H SER* 3.5 22.3 + - - +
109H PRO* 5.9 0.4 - - + -
110H PHE* 3.3 14.8 + - + +
111H LEU 3.3 0.4 - - - -
112H LEU* 1.3 76.2 - - - +
114H LEU* 1.3 59.4 + - - +
117H ASN 4.8 0.7 - - - +
118H SER* 4.4 10.0 + - - -
241L PHE* 6.0 1.3 - - + -
315L GLN* 2.6 31.3 + - - +
336L GLU* 4.2 18.3 - - + +
338L LEU* 4.2 12.5 - - + +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TYR* 3.7 42.0 - - + +
22H MET* 3.8 4.5 - - - +
23H LYS* 3.8 23.6 - - + +
74H ILE* 4.2 24.5 - - + -
106H GLN* 2.4 55.4 + - + +
108H SER* 3.3 20.4 - - - +
110H PHE 3.1 9.7 + - - +
111H LEU* 3.9 9.9 - - + +
112H LEU 3.3 0.6 - - - -
113H ALA* 1.3 78.1 - - - +
115H SER* 1.3 62.7 + - - +
116H GLY 3.4 2.3 + - - -
118H SER* 5.6 0.2 - - - -
249L SER* 5.7 0.9 - - - +
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Residues in contact with SER 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H GLN* 5.1 0.7 + - - -
111H LEU 2.5 21.6 + - - -
112H LEU* 4.0 1.0 + - - -
113H ALA 3.5 1.0 - - - -
114H LEU* 1.3 81.7 - - - +
116H GLY* 1.3 65.9 + - - +
41L ARG* 3.4 26.5 - - - -
245L GLY 3.6 5.4 + - - -
248L PHE* 4.6 4.4 - - - +
249L SER* 3.5 28.7 + - - -
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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