Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 1LI5
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A MET* 3.5 8.5 - - - -
144A PHE* 2.9 69.0 + + + -
146A VAL* 5.3 1.6 - - + -
152A TYR* 4.3 12.1 - + - -
179A MET 3.8 13.2 - - - +
180A ASP* 1.3 76.6 - - - +
182A VAL* 1.3 71.2 + - - +
183A LEU* 3.6 3.5 + - + -
206A HIS* 4.0 12.1 - + + +
237A ASN* 3.3 55.6 - - + +
240A ALA* 4.2 2.2 - - + -
241A GLN* 3.6 23.1 - - - -
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Residues in contact with VAL 182 (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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141A ASP* 4.3 12.6 - - + +
142A VAL 4.2 1.3 - - - +
143A MET* 3.5 24.5 - - + -
181A PHE* 1.3 83.4 - - - +
183A LEU* 1.3 63.5 + - - +
184A TRP 3.5 6.3 - - - +
185A LYS* 3.4 39.9 - - + +
204A GLY* 3.5 21.7 - - - -
205A TRP* 4.2 11.3 + - + +
206A HIS* 5.0 3.1 + - - -
207A ILE 5.5 0.2 + - - -
241A GLN* 5.2 0.9 + - - -
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Residues in contact with LEU 183 (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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125A THR* 4.3 21.1 + - + +
128A LEU* 3.7 19.7 - - + -
134A ALA* 3.6 31.2 - - + -
142A VAL* 2.8 14.6 + - + +
143A MET 4.1 1.3 - - - +
144A PHE* 3.8 20.2 - - + +
181A PHE* 3.7 18.8 - - + -
182A VAL* 1.3 74.9 - - - +
184A TRP* 1.3 63.5 + - - +
203A PRO* 3.9 1.6 - - - +
204A GLY* 3.0 18.6 + - - -
207A ILE* 3.6 22.1 - - + +
241A GLN* 3.5 33.2 - - + +
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Residues in contact with TRP 184 (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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118A ILE* 4.0 26.0 - - + -
121A ILE* 4.3 18.8 - - + -
122A ILE* 5.6 4.0 - - + -
125A THR* 4.7 4.9 - - + -
141A ASP* 3.3 5.7 - - - +
142A VAL* 2.8 44.4 + - + -
182A VAL* 3.5 2.9 - - - -
183A LEU* 1.3 81.0 - - - +
185A LYS* 1.3 64.0 + - - +
186A MET* 5.1 5.4 - - - -
194A TRP* 3.5 18.2 - - + -
195A PRO 4.3 0.2 - - - -
196A SER* 3.1 32.2 + - - -
198A TRP* 3.8 29.4 - + + -
199A GLY 3.4 9.3 + - - -
200A ALA 4.8 0.2 + - - -
201A GLY* 3.3 34.7 - - - -
202A ARG* 3.4 24.0 - - - -
203A PRO* 3.8 15.7 - - + -
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Residues in contact with LYS 185 (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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141A ASP* 3.3 11.2 - - - +
182A VAL* 3.4 19.1 - - + +
184A TRP* 1.3 75.3 + - - +
186A MET* 1.3 66.9 + - - +
201A GLY* 3.1 3.3 - - - -
202A ARG* 2.9 51.2 + - + +
203A PRO 5.1 3.6 - - - +
204A GLY* 5.4 0.7 - - - -
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Residues in contact with MET 186 (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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139A ASN 3.4 25.8 - - - +
140A GLY* 3.4 23.1 - - - +
141A ASP* 2.7 19.2 + - - +
184A TRP* 5.1 4.7 - - - -
185A LYS* 1.3 77.0 - - - +
187A SER* 1.3 66.3 + - - +
188A LYS* 3.7 10.0 + - - +
191A GLU* 4.2 3.3 - - - +
198A TRP 3.6 24.0 - - - +
199A GLY* 4.1 9.0 - - - +
200A ALA* 3.2 23.6 - - + +
202A ARG* 5.6 0.5 + - - -
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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