Contacts of the helix formed by residues 143 - 151 (chain H) in PDB entry 6GYS
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 THR 143 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H TRP* 5.6 0.2 - - - -
126H GLU* 4.9 10.1 + - + +
127H LEU 3.8 14.9 + - - -
128H ARG* 3.5 26.0 - - - +
129H LEU* 5.2 0.4 - - - -
142H TYR* 1.3 76.4 - - - +
144H PHE* 1.3 60.6 + - - +
145H LYS* 3.6 18.6 + - + +
146H GLU* 2.9 42.9 + - + +
147H TYR* 2.6 35.7 + - - +
190H LYS* 5.4 3.5 + - - -
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Residues in contact with PHE 144 (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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120H TRP* 3.6 35.4 - + + -
129H LEU* 4.6 10.1 - - + +
142H TYR 4.0 0.4 + - - -
143H THR* 1.3 76.5 + - - +
145H LYS* 1.3 61.9 + - + +
147H TYR* 4.2 9.9 - + - +
148H LYS* 2.8 63.2 + - + +
165H VAL* 4.0 23.3 - - + -
190H LYS* 5.5 10.5 - - + +
191H ASP* 5.6 3.6 - - - -
192H LEU* 3.7 20.4 - - + -
195H THR* 3.6 27.8 - - + -
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Residues in contact with LYS 145 (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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143H THR* 3.6 13.8 + - + +
144H PHE* 1.3 79.5 - - + +
146H GLU* 1.3 57.6 + - + +
148H LYS* 3.7 3.8 - - - +
149H LYS* 2.8 32.8 + - - +
190H LYS* 3.9 25.1 - - - +
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Residues in contact with GLU 146 (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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95H ARG* 5.0 0.3 + - - -
96H TYR* 4.9 8.0 + - - -
128H ARG* 3.2 20.5 + - - -
141H TRP 3.9 0.2 - - - +
142H TYR* 3.3 13.7 - - + +
143H THR* 2.9 35.4 + - + +
145H LYS* 1.3 79.7 - - + +
147H TYR* 1.3 62.2 + - - +
149H LYS* 3.3 11.5 + - - +
150H TRP* 3.3 55.7 + - + -
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Residues in contact with TYR 147 (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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104H PHE* 4.1 27.9 + + + -
108H HIS* 3.6 29.1 - - - +
118H LEU* 4.5 18.3 - - + +
129H LEU* 4.6 16.8 - - + -
142H TYR* 4.5 20.2 - + + +
143H THR 2.6 20.1 + - - +
144H PHE* 4.1 11.2 - + - +
146H GLU* 1.3 71.7 - - - +
148H LYS* 1.3 64.8 + - - +
149H LYS 3.4 0.2 + - - -
150H TRP* 5.1 0.7 - - - +
151H VAL* 3.2 40.1 - - + +
152H ILE* 3.3 30.3 + - + +
165H VAL* 3.7 24.0 - - + -
167H ASN* 5.6 0.2 + - - -
168H ILE* 5.8 0.4 - - + -
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Residues in contact with LYS 148 (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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144H PHE* 2.8 52.7 + - + +
145H LYS* 3.9 4.0 - - - +
147H TYR* 1.3 78.1 - - - +
149H LYS* 1.3 60.6 + - - +
152H ILE* 3.7 14.8 - - + +
153H ASP* 2.7 50.7 + - - +
163H LEU* 3.2 30.1 + - + +
165H VAL* 4.2 8.7 - - + +
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Residues in contact with LYS 149 (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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145H LYS 2.8 19.2 + - - +
146H GLU* 3.5 9.4 - - - +
147H TYR 3.2 0.8 - - - -
148H LYS* 1.3 80.6 - - - +
150H TRP* 1.3 88.7 + - + +
153H ASP* 3.4 20.5 - - - +
154H SER 4.5 0.2 + - - -
12I HIS* 6.2 1.8 - - - -
13I PRO* 6.3 2.0 - - - -
26I ARG* 5.6 2.3 + - - -
176K PHE* 6.1 1.6 - - - +
177K THR* 4.7 19.6 + - - +
180K GLU* 4.1 27.7 + - - +
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Residues in contact with TRP 150 (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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96H TYR* 4.4 9.9 - + - -
101H LEU* 3.4 30.2 - - + +
105H LYS* 4.6 2.9 - - - -
142H TYR* 3.8 33.0 - + - -
146H GLU* 3.3 50.6 + - + -
149H LYS* 1.3 104.5 - - + +
151H VAL* 1.3 93.6 + - + +
154H SER* 3.2 22.0 - - - -
11I LYS* 4.8 9.9 - - - +
12I HIS* 6.6 0.2 - - + -
26I ARG* 5.1 1.1 + - - +
175K ASP 5.0 8.5 - - - +
176K PHE* 3.8 34.5 - + + -
180K GLU* 5.3 9.2 - - + -
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Residues in contact with VAL 151 (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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101H LEU* 3.6 28.7 - - + +
104H PHE* 3.7 20.9 - - + +
105H LYS* 3.7 16.7 - - + +
108H HIS* 6.4 0.4 - - + -
142H TYR* 5.6 0.9 - - + -
147H TYR* 3.2 42.2 - - + +
150H TRP* 1.3 99.7 - - + +
152H ILE* 1.3 69.6 + - + +
154H SER* 3.7 7.4 + - - -
155H VAL* 3.5 16.5 - - - +
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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