Contacts of the helix formed by residues 111 - 116 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 1.3 96.1 - - + +
112B VAL* 1.3 64.9 + - - +
113B TYR* 3.1 45.1 - - + +
114B GLU* 3.0 27.8 + - + +
115B LEU* 3.7 1.4 + - - +
320B GLN* 3.8 5.2 - - - +
362B ASN* 3.8 14.8 - - - +
363B GLY 3.4 19.5 - - - +
364B PRO* 4.8 0.2 - - + -
365B GLY 3.4 8.1 - - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.6 36.6 - - + +
105B GLY* 5.0 0.9 - - - -
111B PRO* 1.3 71.0 - - - +
113B TYR* 1.3 63.9 + - - +
115B LEU* 2.9 21.6 + - + +
116B PHE* 3.1 43.1 + - + -
287B LEU* 4.4 6.5 - - + -
320B GLN* 3.0 13.7 + - + +
365B GLY* 2.9 32.7 + - - +
366B LEU* 4.0 16.2 - - + -
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PRO* 3.5 26.5 - - + +
112B VAL* 1.3 77.2 - - - +
114B GLU* 1.3 79.8 + - - +
116B PHE* 3.4 13.7 + - - -
117B GLY 3.4 1.7 + - - -
118B GLY* 2.8 24.6 + - - +
119B LYS* 3.8 44.4 + - + -
319B LEU 4.9 0.2 - - - -
320B GLN* 3.1 49.6 + - - +
323B ALA* 3.9 20.9 - - + -
324B ASN* 3.7 12.8 + - + -
360B MSE 4.6 6.5 + - + +
361B PRO* 3.1 29.4 + - + -
362B ASN* 4.2 5.5 - - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 4.0 18.8 - - + -
111B PRO* 3.0 31.1 + - + +
113B TYR* 1.3 94.8 - - + +
115B LEU* 1.3 64.2 + - - +
117B GLY 3.3 4.3 + - - -
118B GLY* 3.5 12.0 - - - +
119B LYS* 4.3 8.5 + - - +
66F SER* 3.9 15.5 + - - -
67F ARG* 6.0 0.5 - - - +
104F LYS* 2.9 53.7 + - - +
108F LEU* 5.6 2.5 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.9 21.8 - - + +
104B LYS* 3.9 26.9 - - + -
105B GLY* 4.1 18.2 - - - +
108B LEU* 3.4 27.6 - - + -
110B VAL* 3.7 16.4 - - + -
111B PRO 4.0 6.5 - - - +
112B VAL* 2.9 14.2 + - - +
114B GLU* 1.3 78.1 - - - +
116B PHE* 1.3 58.4 + - - +
117B GLY 3.2 3.7 + - - -
288B MSE 6.0 0.2 - - - +
101F TRP* 3.6 18.4 - - - -
104F LYS* 5.0 0.9 - - - -
108F LEU* 3.9 4.0 - - + -
115F LEU* 3.7 39.8 - - + +
288F MSE 4.9 1.7 - - - +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.6 37.7 - + - -
112B VAL* 3.1 29.8 + - + +
113B TYR* 3.8 7.6 - - - +
114B GLU 3.2 0.6 - - - -
115B LEU* 1.3 79.6 - - - +
117B GLY* 1.3 55.3 + - - +
287B LEU* 3.9 30.7 - - + -
288B MSE 3.8 33.4 - - + -
291B LYS* 3.4 39.6 + - + +
320B GLN 5.3 4.0 - - - -
321B LEU* 4.9 8.7 - - + -
324B ASN* 3.1 32.0 + - + +
69F GLU* 3.8 3.6 - - - +
101F TRP* 4.0 4.0 - - - -
288F MSE 3.9 8.1 - - - +
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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