Contacts of the helix formed by residues 111 - 116 (chain H) in PDB entry 2POZ
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 111 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H VAL* 1.3 94.7 - - + +
112H VAL* 1.3 67.1 + - - +
113H TYR* 3.4 44.9 - - + +
114H GLU* 2.9 28.0 + - + +
115H LEU 3.6 2.3 + - - -
320H GLN* 3.9 4.0 - - - +
361H PRO 4.7 0.2 - - - +
362H ASN* 3.5 17.0 - - - +
363H GLY 3.5 18.2 - - - +
365H GLY 3.4 8.5 - - - +
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H TRP* 3.5 44.2 - - + +
110H VAL 3.6 0.8 + - - -
111H PRO* 1.3 70.5 - - - +
113H TYR* 1.3 58.8 + - - +
115H LEU* 2.8 30.2 + - + +
116H PHE* 3.1 45.1 + - + -
287H LEU* 4.4 6.1 - - + -
320H GLN* 3.1 13.1 + - + +
365H GLY* 3.0 29.0 + - - +
366H LEU* 4.1 11.2 - - + +
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Residues in contact with TYR 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PRO* 3.4 26.7 - - + +
112H VAL* 1.3 78.7 - - - +
114H GLU* 1.3 82.8 + - + +
116H PHE* 3.3 14.2 + - - -
117H GLY 3.4 1.0 + - - -
118H GLY* 2.8 24.2 + - - +
119H LYS* 3.5 41.7 + - + +
320H GLN* 3.2 49.6 + - - +
323H ALA* 4.0 19.3 - - + -
324H ASN* 3.6 12.3 + - + -
360H MSE 4.7 4.0 - - + -
361H PRO* 2.9 30.5 + - + -
362H ASN* 3.6 8.8 + - - -
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Residues in contact with GLU 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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66C SER* 3.7 17.6 + - - -
104C LYS* 3.0 49.4 + - - +
108C LEU* 5.6 3.1 - - + -
110H VAL* 4.0 18.2 - - + -
111H PRO* 2.9 31.6 + - + +
113H TYR* 1.3 96.6 - - + +
115H LEU* 1.3 65.0 + - - +
117H GLY 3.1 7.4 + - - -
118H GLY* 3.7 11.1 - - - +
119H LYS* 4.2 10.0 + - - +
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Residues in contact with LEU 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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101C TRP* 3.5 18.7 - - - -
104C LYS* 5.2 0.7 - - - -
108C LEU* 4.0 2.5 - - + -
115C LEU* 3.7 38.9 - - + +
288C MSE 4.8 1.4 - - - +
101H TRP* 3.9 28.7 - - + +
104H LYS* 3.9 18.8 - - + -
105H GLY* 4.0 17.7 - - - +
108H LEU* 3.4 29.8 - - + -
110H VAL* 3.8 15.9 - - + -
111H PRO 4.0 6.3 - - - +
112H VAL* 2.8 16.7 + - - +
114H GLU* 1.3 79.3 - - - +
116H PHE* 1.3 59.0 + - - +
117H GLY 3.1 4.4 + - - -
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Residues in contact with PHE 116 (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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69C GLU* 3.9 2.8 - - - +
101C TRP* 4.0 4.0 - - - -
288C MSE 3.9 7.5 - - - +
101H TRP* 3.7 35.7 - + - -
112H VAL* 3.1 32.2 + - + +
113H TYR* 3.7 8.5 - - - +
114H GLU 3.2 0.4 - - - -
115H LEU* 1.3 79.2 - - - +
117H GLY* 1.3 53.3 + - - +
287H LEU* 3.9 29.6 - - + -
288H MSE 3.8 36.8 - - + -
291H LYS* 3.4 39.9 + - + +
320H GLN 5.5 1.1 - - - -
321H LEU* 5.3 10.1 - - + -
324H ASN* 3.2 31.8 + - + +
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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