Contacts of the helix formed by residues 148 - 156 (chain A) in PDB entry 5UHF
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.9 28.5 - - + +
147A VAL* 1.3 97.2 - - - +
149A ALA* 1.3 64.5 + - - +
150A VAL* 3.4 19.5 - - + -
151A GLN* 3.7 32.2 + - - +
164A VAL 5.0 0.2 - - - +
165A ASP* 3.2 9.6 - - - +
878C LYS* 5.8 3.6 - - + -
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Residues in contact with ALA 149 (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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81A LYS* 5.7 0.2 - - - +
148A PRO* 1.3 68.7 - - - +
150A VAL* 1.3 59.2 - - + +
151A GLN 2.7 18.4 + - - -
152A ASN* 3.1 12.6 + - - +
153A ARG* 6.3 0.2 - - - +
163A PRO* 3.3 25.1 - - + +
164A VAL* 3.3 21.1 - - - +
165A ASP* 2.5 37.8 + - - +
876C LYS* 6.2 2.0 - - - +
878C LYS* 5.8 0.7 - - - +
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Residues in contact with VAL 150 (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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148A PRO* 4.1 18.2 - - + -
149A ALA* 1.3 77.4 - - + +
151A GLN* 1.3 69.4 + - + +
152A ASN 3.4 0.8 + - - -
153A ARG* 3.6 42.3 + - - +
154A ALA* 4.6 3.1 + - - +
876C LYS 6.0 1.6 - - - +
878C LYS* 6.4 2.0 - - + -
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Residues in contact with GLN 151 (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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147A VAL* 3.6 22.2 - - + +
148A PRO* 3.7 33.2 - - + +
149A ALA 2.7 7.1 + - - -
150A VAL* 1.3 83.7 - - + +
152A ASN* 1.3 62.4 + - - +
153A ARG 3.4 0.5 + - - -
154A ALA* 3.9 9.9 + - - +
155A SER* 4.2 7.4 + - - -
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Residues in contact with ASN 152 (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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52A THR* 5.1 10.0 + - - +
53A SER* 4.1 21.9 + - - -
141A GLU* 5.5 3.8 + - - -
149A ALA 3.1 4.8 + - - +
151A GLN* 1.3 77.4 - - - +
153A ARG* 1.3 63.9 + - - +
154A ALA 3.4 0.9 + - - -
155A SER* 3.5 18.8 + - - -
157A ALA* 3.7 23.5 - - - +
161A ARG* 5.1 6.2 - - - +
163A PRO* 3.7 26.4 - - + +
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLU* 5.9 0.8 + - - -
149A ALA* 6.3 0.4 - - - +
150A VAL* 3.6 39.5 + - - +
151A GLN 3.2 0.8 - - - -
152A ASN* 1.3 81.8 - - - +
154A ALA* 1.3 63.1 + - + +
155A SER 3.3 1.7 + - - -
156A GLY* 3.8 1.4 + - - -
157A ALA* 3.8 20.7 + - - +
163A PRO* 3.9 23.7 - - + +
795C GLU* 3.4 32.3 - - + +
845C GLY* 5.6 4.8 + - - -
846C LYS* 3.8 33.0 - - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL 5.4 2.7 - - - +
151A GLN 3.9 7.5 + - - +
152A ASN 3.4 0.6 - - - -
153A ARG* 1.3 78.1 - - + +
155A SER* 1.3 62.7 + - - +
156A GLY* 3.1 3.6 + - - -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLN 4.2 8.6 + - - -
152A ASN* 3.7 17.0 + - - -
153A ARG 3.3 1.2 - - - -
154A ALA* 1.3 78.4 - - - +
156A GLY* 1.3 57.3 + - - +
157A ALA* 4.5 3.6 - - - -
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Residues in contact with GLY 156 (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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153A ARG 3.8 1.9 + - - -
154A ALA 3.1 5.2 - - - -
155A SER* 1.3 78.9 - - - +
157A ALA* 1.3 67.2 + - - +
158A GLU* 3.3 4.0 + - - -
161A ARG* 5.3 0.3 + - - -
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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