Contacts of the helix formed by residues 156 - 162 (chain G) in PDB entry 1F1H
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 GLY 156 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153G ASP 2.9 15.6 + - - -
155G GLU* 1.3 73.7 - - - +
157G ALA* 1.3 60.8 + - - -
158G TRP* 3.0 22.4 - - - -
159G ASN* 2.9 22.8 + - - +
172G ARG* 3.2 11.1 - - - -
215G THR* 3.7 4.9 - - - -
216G ALA* 3.7 13.6 - - - +
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Residues in contact with ALA 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G GLU 4.0 2.0 - - - -
156G GLY* 1.3 70.5 - - - -
158G TRP* 1.3 64.5 + - + +
159G ASN 3.1 1.3 + - - -
160G SER* 3.2 24.5 + - - -
172G ARG* 4.3 6.7 - - - +
173G PRO 3.8 11.0 - - - +
174G GLY* 4.1 12.8 - - - -
175G VAL* 4.3 16.8 - - + +
215G THR* 3.1 19.3 + - + +
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Residues in contact with TRP 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.7 32.5 - - + +
145A SER* 3.7 23.3 - - - +
151G ILE* 3.7 24.1 + - + -
152G ASP* 2.9 30.7 + - - -
153G ASP 4.2 1.8 - - - -
156G GLY* 3.9 13.0 - - - -
157G ALA* 1.3 81.4 - - + +
159G ASN* 1.3 70.5 + - - +
160G SER* 3.2 2.8 + - - -
161G SER* 3.4 19.8 + - - -
162G THR* 4.2 2.8 + - - -
215G THR* 4.3 7.4 - - + -
216G ALA* 3.4 28.3 - - + -
260G MET* 3.8 24.0 - - - -
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Residues in contact with ASN 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ASP* 2.9 28.1 + - - +
153G ASP 2.8 28.5 + - - +
156G GLY 2.9 11.6 + - - +
158G TRP* 1.3 87.9 - - - +
160G SER* 1.3 50.0 + - - +
161G SER 2.9 6.5 + - - -
162G THR* 2.6 33.5 + - - +
164G TYR* 3.3 22.5 + - - +
168G ASN* 2.7 31.0 + - - -
172G ARG* 3.6 11.5 + - - +
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Residues in contact with SER 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463F GLU* 4.9 3.3 + - - -
157G ALA 3.2 17.5 + - - -
158G TRP* 3.2 2.1 - - - -
159G ASN* 1.3 77.8 - - - +
161G SER* 1.3 58.6 + - - +
162G THR 3.6 0.2 - - - -
168G ASN* 3.6 5.1 + - - -
170G GLY* 5.9 0.4 - - - -
172G ARG* 3.7 19.3 - - - +
138L ILE 3.9 1.6 - - - +
139L ARG* 3.1 9.5 - - - -
140L PHE* 2.7 68.8 + - - -
141L GLY* 4.3 4.3 - - - -
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Residues in contact with SER 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G TRP 3.4 14.7 + - - -
160G SER* 1.3 81.1 + - - +
162G THR* 1.3 62.7 + - - +
163G LYS* 3.7 3.6 + - - +
139L ARG* 3.8 14.5 + - - +
140L PHE 3.5 17.7 - - - +
141L GLY* 4.8 2.0 - - - -
148L HIS* 3.5 25.8 + - - -
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Residues in contact with THR 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G TRP 4.2 2.8 + - - -
159G ASN* 2.6 41.3 + - - +
161G SER* 1.3 79.7 + - - +
163G LYS* 1.3 75.6 + - - +
164G TYR* 3.4 22.1 - - + -
168G ASN* 2.8 24.1 + - - +
139L ARG* 3.4 7.3 - - - +
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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