Contacts of the helix formed by residues 168 - 176 (chain A) in PDB entry 1L6N
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A TRP* 4.4 7.4 - - + -
158A VAL* 3.8 28.0 - - + +
161A GLU* 6.0 0.2 - - + -
162A LYS* 2.6 35.0 - - + +
163A ALA* 2.8 27.6 - - - +
164A PHE* 4.2 0.2 - - - -
165A SER* 3.0 24.0 + - - +
166A PRO 3.2 0.2 - - - -
167A GLU* 1.3 79.6 - - - +
169A ILE* 1.3 64.6 + - + +
170A PRO* 3.1 2.0 - - - -
171A MET* 3.5 2.8 - - - +
172A PHE* 2.7 37.2 + - + +
270A LEU* 6.5 0.2 - - + -
274A VAL* 4.5 0.7 - - + -
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Residues in contact with ILE 169 (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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165A SER 3.2 17.5 - - - +
166A PRO* 4.3 5.4 - - + +
168A VAL* 1.3 78.7 - - + +
170A PRO* 1.4 67.0 - - + +
172A PHE* 3.6 5.3 + - - +
173A SER* 3.2 25.5 + - - -
267A ILE* 3.8 24.9 - - + +
270A LEU* 2.9 55.4 - - + +
271A ASN* 3.6 21.1 - - - +
274A VAL* 3.8 11.0 - - + -
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Residues in contact with PRO 170 (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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166A PRO 2.8 26.7 - - - +
167A GLU* 3.9 9.9 - - + +
168A VAL 3.1 6.1 - - - +
169A ILE* 1.4 94.5 - - + +
171A MET* 1.3 59.8 + - - +
172A PHE 3.2 0.4 - - - -
173A SER* 2.9 22.9 + - - +
174A ALA* 2.9 17.5 + - - +
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Residues in contact with MET 171 (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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155A TRP* 4.6 2.2 - - - -
158A VAL* 3.2 47.8 - - + -
161A GLU* 6.1 2.0 - - - +
167A GLU 3.5 20.2 - - - +
168A VAL 3.5 4.7 - - - +
170A PRO* 1.3 82.2 - - - +
172A PHE* 1.3 60.4 + - - +
174A ALA* 3.4 9.9 + - + +
175A LEU* 3.2 31.3 + - + +
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Residues in contact with PHE 172 (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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155A TRP* 3.3 32.3 - + + -
168A VAL 2.7 20.3 + - - +
169A ILE* 3.7 6.3 - - - +
171A MET* 1.3 70.4 - - - +
173A SER* 1.3 59.7 - - - +
174A ALA 3.0 1.6 - - - -
175A LEU 3.1 3.1 + - - -
176A SER* 2.7 57.5 + - - -
184A LEU* 4.2 2.7 - - + -
187A MET* 3.1 40.4 - - + +
188A LEU* 3.3 21.5 - - + -
263A LYS 4.8 0.2 - - - -
266A ILE* 3.3 43.1 - - + -
267A ILE* 4.4 9.4 - - + -
270A LEU* 3.8 16.6 - - + -
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Residues in contact with SER 173 (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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169A ILE 3.2 7.6 + - - -
170A PRO* 2.9 20.3 + - - +
172A PHE* 1.3 82.2 - - - +
174A ALA* 1.3 53.6 + - - +
176A SER* 3.1 10.3 - - - -
177A GLU* 2.5 35.5 + - - +
263A LYS* 4.6 7.1 - - - +
267A ILE* 3.4 27.4 - - - -
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Residues in contact with ALA 174 (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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170A PRO 2.9 16.5 + - - +
171A MET* 3.4 12.1 - - + +
173A SER* 1.3 75.8 - - - +
175A LEU* 1.3 59.2 + - - +
176A SER 3.0 4.0 - - - -
177A GLU* 2.7 35.4 + - - +
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Residues in contact with LEU 175 (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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147A ILE* 4.9 10.2 - - - +
151A THR* 2.7 48.9 - - + +
154A ALA* 4.3 9.6 - - + -
155A TRP* 4.1 27.8 - - + +
158A VAL* 4.3 13.2 - - + -
171A MET* 3.2 17.1 + - + +
172A PHE 3.1 2.0 + - - -
174A ALA* 1.3 78.8 - - + +
176A SER* 1.3 58.2 + - - +
177A GLU* 3.5 1.3 - - - +
183A ASP* 4.9 2.6 - - - +
187A MET* 3.5 20.5 - - + +
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Residues in contact with SER 176 (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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172A PHE* 2.7 29.9 + - - -
173A SER* 3.1 3.6 - - - -
175A LEU* 1.3 80.5 - - - +
177A GLU* 1.3 65.8 + - - +
178A GLY 2.9 4.2 + - - -
179A ALA* 3.0 20.9 + - - +
183A ASP* 4.9 2.2 - - - -
184A LEU* 3.2 29.8 - - - +
187A MET* 4.2 6.7 - - - -
263A LYS* 3.2 18.0 - - - +
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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