Contacts of the helix formed by residues 123 - 126 (chain H) in PDB entry 1UW9
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 ASN 123 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H GLU* 4.5 10.9 + - + +
119H SER 5.1 2.0 + - - -
122H GLY* 1.3 81.9 - - - +
124H VAL* 1.3 67.3 + - - +
125H PHE 3.2 2.9 - - - -
126H GLY* 3.1 12.9 + - - -
127H PHE* 3.7 7.4 - - + -
177R LYS* 3.8 3.4 - - - +
204R GLU* 3.1 20.6 + - - -
294R HIS* 3.3 20.8 - - - -
296R ALA* 4.5 0.3 - - - -
298R HIS* 6.0 1.1 - - - -
299R ALA* 5.2 1.7 - - - +
335R LEU* 3.4 24.7 - - + +
1476R CAP 2.9 50.8 + - - +
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H PHE* 4.6 0.4 - - + -
56H ALA 4.4 0.2 - - - +
57H VAL* 3.4 44.2 - - + +
60H GLU* 3.8 29.6 - - + +
61H SER* 4.0 3.8 - - - +
119H SER 5.6 0.2 - - - +
120H ILE 3.7 23.6 - - - +
121H VAL* 4.7 1.8 - - - -
122H GLY 3.9 0.2 - - - -
123H ASN* 1.3 77.8 - - - +
125H PHE* 1.3 75.7 + - + +
126H GLY 3.1 1.1 + - - -
127H PHE* 3.4 18.0 + - + +
130H LEU* 3.5 19.1 - - - +
133H LEU* 3.7 14.8 - - + -
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Residues in contact with PHE 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H PHE* 4.1 7.2 - + - -
121H VAL* 3.5 43.7 - - + +
123H ASN 3.1 1.6 + - - -
124H VAL* 1.3 87.5 - - + +
126H GLY* 1.3 56.9 + - - +
127H PHE 3.5 0.2 - - - -
130H LEU* 3.9 6.0 - - - +
133H LEU* 3.1 53.8 - - + -
134H ARG 4.0 0.2 - - - -
135H LEU* 4.0 9.9 - - + -
307H HIS* 3.9 12.4 - + + -
308H GLY 3.2 21.8 - - - -
309H ILE* 4.6 0.2 - - + -
299R ALA* 3.5 25.8 - - + +
300R VAL* 3.7 20.6 - - + +
303R ARG* 2.9 27.1 + - - +
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Residues in contact with GLY 126 (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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123H ASN 3.1 8.7 + - - -
124H VAL 3.1 1.2 - - - -
125H PHE* 1.3 78.3 - - - +
127H PHE* 1.3 59.8 + - - +
298R HIS* 5.7 2.9 - - - -
299R ALA* 3.3 17.6 - - - +
303R ARG* 3.4 11.7 - - - -
335R LEU* 3.5 11.5 - - - +
336R GLU* 2.9 33.2 + - - +
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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