Contacts of the helix formed by residues 171 - 178 (chain F) in PDB entry 4XLR
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 VAL 171 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F VAL* 4.4 10.8 - - + -
148F ALA* 4.0 19.7 - - + -
157F GLN* 3.2 27.8 - - - +
165F LYS* 3.6 18.4 - - - +
166F PRO 3.4 13.5 - - - +
167F ASP* 3.1 20.1 + - - +
169F LYS 3.3 0.2 - - - -
170F THR* 1.3 78.9 - - - +
172F GLU* 1.3 68.3 + - - +
173F GLU 3.4 1.1 - - - -
174F VAL* 3.0 9.8 + - - +
175F ASP* 3.0 37.3 + - - +
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Residues in contact with GLU 172 (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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167F ASP 3.2 4.8 + - - +
168F PRO* 3.1 28.6 + - + +
171F VAL* 1.3 77.8 - - - +
173F GLU* 1.3 76.9 + - - +
175F ASP* 3.0 24.6 + - - +
176F GLY* 3.3 7.6 + - - -
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Residues in contact with GLU 173 (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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168F PRO 4.8 0.2 + - - -
169F LYS* 3.3 26.4 + - - +
170F THR* 5.0 2.2 - - - -
171F VAL 4.9 0.2 - - - +
172F GLU* 1.3 86.7 + - - +
174F VAL* 1.3 61.0 + - + +
176F GLY* 2.9 4.7 + - - +
177F LYS* 2.6 53.0 + - + +
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Residues in contact with VAL 174 (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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137F LEU* 3.7 22.7 - - + -
141F LEU* 4.2 14.1 - - + -
142F ILE* 3.9 16.6 - - + -
145F VAL* 4.1 18.6 - - + -
170F THR 3.3 24.7 - - - +
171F VAL 3.0 7.5 + - - +
173F GLU* 1.3 81.6 - - + +
175F ASP* 1.3 63.0 + - - +
177F LYS* 3.0 31.8 + - - +
178F LEU* 3.5 16.4 + - + +
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Residues in contact with ASP 175 (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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145F VAL* 3.3 18.4 - - - +
148F ALA* 4.5 3.8 - - - +
149F LYS* 3.3 40.3 + - - +
171F VAL* 3.0 37.0 + - - +
172F GLU* 3.0 15.7 + - - +
174F VAL* 1.3 75.7 - - - +
176F GLY* 1.3 56.3 + - - +
178F LEU* 4.8 1.0 + - - +
179F LYS* 3.5 27.1 + - - +
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Residues in contact with GLY 176 (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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172F GLU* 3.3 9.0 + - - -
173F GLU* 2.9 8.8 + - - -
175F ASP* 1.3 75.8 - - - +
177F LYS* 1.3 63.7 + - - +
178F LEU 3.4 0.7 - - - -
179F LYS* 3.7 20.3 + - - +
180F SER* 4.3 6.8 + - - -
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Residues in contact with LYS 177 (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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135F THR* 3.8 28.9 - - + +
137F LEU* 3.6 23.2 - - - +
141F LEU* 5.7 0.2 - - - +
173F GLU* 2.6 28.3 + - + +
174F VAL* 3.0 37.8 + - - +
176F GLY* 1.3 74.7 - - - +
178F LEU* 1.3 59.4 + - + +
179F LYS 3.4 0.2 - - - -
180F SER* 3.0 19.1 + - - -
181F LEU* 3.2 8.8 - - - +
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Residues in contact with LEU 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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131F LEU* 3.8 30.1 - - + +
134F ALA* 5.3 0.4 - - + -
135F THR* 3.6 15.7 - - - +
137F LEU* 3.6 42.2 - - + -
142F ILE* 4.4 7.9 - - + -
174F VAL* 3.5 22.5 + - + +
175F ASP 5.7 0.7 - - - +
176F GLY 3.4 0.2 - - - -
177F LYS* 1.3 77.7 - - + +
179F LYS* 1.3 59.9 + - - +
180F SER 3.1 6.6 + - - -
181F LEU* 3.4 28.5 + - + +
185F LEU* 5.6 1.4 - - - +
186F LYS* 3.7 11.6 - - - +
189F LEU* 4.7 16.3 - - + +
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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