Contacts of the helix formed by residues 111 - 116 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 1.3 96.1 - - + +
112A VAL* 1.3 67.2 + - - +
113A TYR* 3.4 46.7 - - + +
114A GLU* 3.0 25.7 + - + +
115A LEU* 3.7 2.9 + - - +
320A GLN* 3.8 3.1 - - - +
361A PRO 4.7 0.2 - - - +
362A ASN* 3.5 16.6 - - - +
363A GLY 3.4 18.6 - - - +
364A PRO* 4.7 0.4 - - + -
365A GLY 3.5 8.7 - - - +
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Residues in contact with VAL 112 (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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101A TRP* 3.5 45.8 - - + +
111A PRO* 1.3 72.1 - - - +
113A TYR* 1.3 64.5 + - - +
115A LEU* 3.0 22.2 + - + +
116A PHE* 3.1 42.8 + - + -
287A LEU* 4.2 7.0 - - + -
320A GLN* 2.9 17.9 + - + +
365A GLY* 3.0 26.9 + - - +
366A LEU* 4.1 8.7 - - + -
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Residues in contact with TYR 113 (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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111A PRO* 3.4 25.8 - - + +
112A VAL* 1.3 77.8 - - - +
114A GLU* 1.3 84.4 + - + +
116A PHE* 3.4 13.8 + - - -
117A GLY 3.5 1.2 + - - -
118A GLY* 2.8 25.1 + - - +
119A LYS* 3.7 31.1 + - + -
320A GLN* 2.9 49.9 + - - +
323A ALA* 3.7 21.3 - - + -
324A ASN* 3.6 11.3 + - + -
360A MSE 4.6 5.6 - - + +
361A PRO* 3.0 29.3 + - + -
362A ASN* 3.2 16.8 + - - -
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Residues in contact with GLU 114 (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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110A VAL* 4.0 18.8 - - + -
111A PRO* 3.0 30.4 + - + +
113A TYR* 1.3 94.5 - - + +
115A LEU* 1.3 65.8 + - - +
117A GLY 3.2 7.3 + - - -
118A GLY* 3.3 10.1 + - - +
119A LYS* 4.1 9.4 + - - +
66E SER* 3.8 15.4 + - - -
104E LYS* 3.0 49.1 + - - +
108E LEU* 5.6 3.4 - - + -
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Residues in contact with LEU 115 (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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101A TRP* 3.9 27.4 - - + +
104A LYS* 3.9 19.1 - - + -
105A GLY* 4.0 18.4 - - - +
108A LEU* 3.5 28.0 - - + -
110A VAL* 4.1 15.9 - - + -
111A PRO 4.1 6.7 - - - +
112A VAL* 3.0 15.3 + - - +
114A GLU* 1.3 76.6 - - - +
116A PHE* 1.3 58.4 + - + +
117A GLY 3.1 5.2 + - - -
101E TRP* 3.5 18.5 - - - -
104E LYS* 5.1 0.9 - - - -
108E LEU* 4.1 3.1 - - + -
115E LEU* 3.7 40.5 - - + +
288E MSE 4.8 1.4 - - - +
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Residues in contact with PHE 116 (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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101A TRP* 3.8 35.2 - + - -
112A VAL* 3.1 30.9 + - + +
113A TYR* 3.6 9.6 - - - +
114A GLU 3.2 0.4 - - - -
115A LEU* 1.3 79.6 - - - +
117A GLY* 1.3 55.3 + - - +
287A LEU* 4.0 28.3 - - + -
288A MSE 3.8 37.2 - - + -
291A LYS* 3.4 37.4 + - + +
320A GLN 5.0 4.5 - - - -
321A LEU* 5.1 7.9 - - + -
324A ASN* 3.1 33.0 + - + +
69E GLU* 3.8 3.6 - - - +
101E TRP* 4.0 3.6 - - - -
288E MSE 3.8 7.8 - - - +
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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