Contacts of the helix formed by residues 177 - 184 (chain F) in PDB entry 3V5I
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 ALA 177 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114F ALA* 4.2 13.5 - - + -
115F LEU 3.7 23.1 - - - +
116F PRO* 3.7 15.9 + - + +
118F ALA 3.6 13.6 + - - +
120F VAL* 5.7 1.6 - - - -
176F THR* 1.3 72.4 - - - +
178F GLU* 1.3 63.0 + - + +
180F ALA* 3.2 9.6 + - - +
181F LYS* 3.1 19.4 + - - +
186F ILE* 3.4 9.1 - - - +
189F VAL* 4.1 16.4 - - + -
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Residues in contact with GLU 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F THR* 3.3 7.8 + - - +
177F ALA* 1.3 77.8 - - + +
179F GLU* 1.3 64.2 + - + +
181F LYS* 3.2 22.2 + - - +
182F GLU* 3.0 23.7 + - - +
189F VAL* 3.8 26.9 - - + +
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Residues in contact with GLU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E LYS* 4.1 13.8 + - - -
174F PHE 3.9 5.9 - - - +
175F LEU* 3.3 20.6 - - + +
176F THR* 2.8 49.8 + - - +
178F GLU* 1.3 76.8 - - + +
180F ALA* 1.3 53.9 + - - +
182F GLU* 3.3 8.8 + - - +
183F TYR* 2.8 35.4 + - - +
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Residues in contact with ALA 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F VAL* 4.0 29.4 - - + -
175F LEU* 4.3 4.0 - - + +
176F THR 2.8 13.0 + - - +
177F ALA* 3.4 10.3 - - - +
179F GLU* 1.3 74.7 - - - +
181F LYS* 1.3 57.1 + - - +
183F TYR* 3.3 6.6 + - - +
184F GLY 3.1 7.1 + - - -
185F LEU* 2.9 39.5 + - + -
186F ILE* 3.7 14.8 - - + -
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Residues in contact with LYS 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F ALA 3.1 11.3 + - - +
178F GLU* 3.2 20.8 + - - +
180F ALA* 1.3 72.7 - - - +
182F GLU* 1.3 66.6 + - - +
184F GLY* 3.1 14.2 + - - -
186F ILE* 3.4 24.6 - - + +
187F ASP* 3.5 28.9 - - - +
188F GLU* 3.8 16.7 + - - +
189F VAL* 4.2 17.0 - - + +
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Residues in contact with GLU 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F GLN* 4.0 5.9 + - - -
178F GLU 3.0 12.8 + - - +
179F GLU* 3.4 13.7 - - - +
181F LYS* 1.3 77.0 - - - +
183F TYR* 1.3 61.1 + - - +
184F GLY* 3.5 0.5 + - - -
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Residues in contact with TYR 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ILE* 4.2 18.6 - - + +
154F LEU* 5.8 0.7 - - + -
158F THR* 3.6 10.8 - - + +
160F GLN* 2.8 43.1 + - + +
164F LYS* 3.7 20.1 - - - +
165F ILE* 3.8 28.5 - - + +
168F ASP* 2.8 41.5 + - + +
173F ASN* 5.3 2.7 - - - -
175F LEU* 4.6 12.3 - - + -
179F GLU 2.8 16.2 + - - +
180F ALA* 3.5 9.6 - - - +
181F LYS 3.1 0.4 - - - -
182F GLU* 1.3 77.2 - - - +
184F GLY* 1.3 58.1 + - - +
185F LEU* 4.1 23.8 - - + -
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Residues in contact with GLY 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ARG* 3.4 16.3 + - - -
157F ARG 3.4 2.1 - - - +
158F THR* 3.4 31.4 - - - +
180F ALA 3.1 0.2 + - - -
181F LYS 3.1 15.0 + - - -
182F GLU 3.2 0.8 + - - -
183F TYR* 1.3 78.6 - - - +
185F LEU* 1.3 61.9 + - - +
186F ILE 3.3 6.1 - - - -
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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