Contacts of the helix formed by residues 169 - 178 (chain A) in PDB entry 1LL9
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 SER 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLY 4.2 0.4 + - - -
168A LEU* 1.3 76.9 - - - +
170A PHE* 1.3 66.5 + - - +
171A GLU* 3.7 5.6 + - - +
172A GLN* 3.0 36.9 + - - +
173A ALA* 2.9 20.8 + - - +
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Residues in contact with PHE 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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70A THR* 3.5 24.9 - - + -
73A LEU* 3.6 19.5 - - + -
159A GLY* 3.6 30.7 - - - -
160A ALA* 5.5 0.9 - - - -
163A VAL* 4.1 15.8 - - + +
168A LEU 3.8 0.6 + - - -
169A SER* 1.3 73.4 - - - +
171A GLU* 1.3 59.5 + - - +
173A ALA* 3.3 2.1 + - - +
174A MET* 2.9 52.4 + - + +
189A ILE* 3.9 14.6 - - + -
218A ALA* 3.6 29.8 - - + -
219A GLU* 3.6 36.3 - - + +
223A VAL* 6.2 0.2 - - + -
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Residues in contact with GLU 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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169A SER* 3.3 5.4 + - - +
170A PHE* 1.3 79.6 - - - +
172A GLN* 1.3 62.9 - - - +
174A MET* 3.4 0.9 + - - +
175A GLN* 3.0 39.2 + - + +
188A TRP* 5.6 0.2 - - - +
189A ILE* 3.4 32.1 + - + +
190A ASN* 3.0 49.4 + - - +
218A ALA* 5.8 0.6 - - + +
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Residues in contact with GLN 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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167A GLY 4.7 1.2 - - - +
168A LEU* 3.3 27.8 - - + +
169A SER* 3.0 39.1 + - - +
171A GLU* 1.3 78.4 - - - +
173A ALA* 1.3 60.6 + - - +
175A GLN* 3.9 3.3 - - - +
176A THR* 3.0 36.1 + - + +
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Residues in contact with ALA 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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73A LEU* 4.0 9.6 - - + -
163A VAL* 3.8 24.2 - - + -
166A SER* 4.6 1.8 - - - +
168A LEU* 4.0 19.4 - - + +
169A SER 2.9 16.1 + - - +
170A PHE 3.7 3.4 - - - +
172A GLN* 1.3 76.7 - - - +
174A MET* 1.3 58.0 + - - +
176A THR* 3.8 5.2 - - - -
177A ARG* 2.8 44.0 + - - +
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Residues in contact with MET 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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69A PHE* 3.6 44.4 - - + +
70A THR* 3.8 1.1 - - - +
73A LEU* 3.7 12.7 - - + +
170A PHE* 2.9 47.9 + - + +
171A GLU 3.7 4.0 - - - +
173A ALA* 1.3 76.7 - - - +
175A GLN* 1.3 57.1 + - - +
178A VAL* 2.9 51.9 + - - +
179A PHE* 3.0 38.4 + - + -
189A ILE* 4.2 12.8 - - + -
223A VAL* 5.5 3.1 - - + -
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Residues in contact with GLN 175 (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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171A GLU* 3.0 34.8 + - + +
172A GLN* 3.9 4.3 - - - +
174A MET* 1.3 77.5 - - - +
176A THR* 1.3 59.5 + - + +
179A PHE* 3.4 35.7 - - + +
180A GLN* 2.9 55.2 + - - +
184A LEU 5.2 1.4 + - - -
187A THR 3.5 11.8 + - - +
188A TRP* 4.0 19.2 - - - -
189A ILE 5.0 1.7 + - - -
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Residues in contact with THR 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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80A ARG* 5.7 0.2 + - - -
168A LEU* 4.1 11.1 - - + +
172A GLN* 3.0 24.0 + - + +
173A ALA* 3.5 6.1 + - - -
175A GLN* 1.3 78.2 - - + +
177A ARG* 1.3 69.6 + - - +
178A VAL 3.6 0.2 - - - -
180A GLN* 3.8 24.6 - - - +
181A PRO* 3.4 17.7 - - - +
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Residues in contact with ARG 177 (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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73A LEU* 4.1 15.3 - - + +
76A ASP* 3.5 21.8 + - - +
77A ALA* 4.7 5.9 - - - +
80A ARG* 3.2 44.2 + - - +
82A GLU* 2.6 41.6 + - - -
163A VAL* 6.0 2.4 - - - +
166A SER* 3.2 25.1 + - - +
168A LEU* 4.2 13.3 - - - +
173A ALA* 2.8 28.9 + - - +
176A THR* 1.3 81.5 - - - +
178A VAL* 1.3 62.8 + - + +
181A PRO* 3.6 12.8 - - - +
248A LEU* 3.6 18.0 - - - +
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Residues in contact with VAL 178 (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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69A PHE* 4.2 8.3 - - + +
72A VAL* 4.7 0.9 - - + -
73A LEU* 3.9 29.8 - - + +
76A ASP* 5.5 0.9 - - + -
174A MET* 2.9 29.9 + - - +
176A THR 3.6 0.2 - - - -
177A ARG* 1.3 84.6 - - + +
179A PHE* 1.3 79.4 + - + +
180A GLN 3.5 0.9 - - - -
181A PRO* 3.4 1.3 - - - +
182A LEU* 3.2 32.6 + - + +
184A LEU* 4.9 0.2 - - + -
233A TRP* 4.0 29.6 - - + -
248A LEU* 4.3 14.4 - - + -
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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