Contacts of the helix formed by residues 188 - 192 (chain A) in PDB entry 1LC7
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 PHE 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN* 3.9 13.2 - - + -
153A CYS* 5.9 2.0 - - - -
155A PRO* 3.7 27.3 + - + +
157A ASN* 4.0 13.2 - - + -
185A ASP 5.3 0.2 + - - -
186A GLU 3.1 0.4 - - - -
187A ALA* 1.3 82.2 - - + +
189A ILE* 1.3 65.1 + - - +
190A ASP* 3.1 6.9 + - - -
191A PHE* 3.2 26.9 + + - +
192A ILE* 4.0 3.1 - - - +
216A LYS* 3.6 35.0 - - + -
297A ALA* 3.9 9.4 - - + +
298A ASN* 3.3 26.5 - - - -
299A TYR* 3.6 27.8 - + - -
990A TPO 3.2 28.3 - - - -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 3.6 18.4 - - - +
155A PRO* 3.9 4.4 - - - +
162A LEU* 4.1 13.9 - - + -
186A GLU* 3.1 28.3 + - + +
188A PHE* 1.3 76.1 - - - +
190A ASP* 1.3 65.7 + - - +
191A PHE 3.3 0.7 + - - -
192A ILE* 3.3 23.3 + - + +
195A GLU* 3.6 45.1 - - + +
196A THR 5.4 0.4 - - - +
197A GLY* 4.4 14.4 - - - -
212A ARG* 3.5 37.7 - - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU 4.8 0.2 - - - -
187A ALA 3.1 25.3 - - - +
188A PHE* 3.5 3.8 - - - -
189A ILE* 1.3 75.7 + - - +
191A PHE* 1.3 52.2 + - - +
192A ILE 4.3 0.2 - - - +
195A GLU 5.7 0.7 - - - -
212A ARG* 3.3 26.4 + - - +
213A SER 4.0 12.7 - - - +
217A PHE* 3.3 46.6 - - + +
218A TYR* 5.7 2.1 - - - -
270A TRP* 2.7 35.2 + - - -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.2 8.7 - - + -
187A ALA 5.2 0.2 - - - -
188A PHE* 3.2 30.8 + + - +
190A ASP* 1.3 79.1 - - - +
192A ILE* 1.3 59.9 + - - +
193A PRO 3.3 6.6 - - - -
216A LYS* 3.7 13.5 - - + -
217A PHE* 3.6 45.5 - + + -
269A THR* 3.8 22.9 - - + -
270A TRP* 3.4 10.8 - - - +
272A TRP* 4.2 10.8 - + - -
273A LEU* 3.2 24.8 - - + +
297A ALA* 3.8 13.7 - - + -
298A ASN* 3.5 45.8 - - + -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PRO* 4.0 27.4 - - + -
162A LEU* 3.7 19.7 - - + -
188A PHE 4.0 9.2 - - - +
189A ILE* 3.3 14.6 + - + +
190A ASP 3.3 0.8 - - - -
191A PHE* 1.3 75.6 - - - +
193A PRO* 1.3 71.2 - - + +
194A HIS 3.2 3.0 + - - +
195A GLU* 3.3 28.2 + - + +
270A TRP* 3.9 5.3 + - - -
296A ARG* 3.5 67.1 - - + +
297A ALA* 4.4 1.6 - - + -
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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