Contacts of the strand formed by residues 182 - 189 (chain H) in PDB entry 1LNU
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 182 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ASP* 4.4 1.3 - - - -
148H ASP* 3.1 7.8 + - - -
149H PHE* 2.4 66.6 + - + +
150H TYR* 3.7 20.9 - + - -
151H PRO 4.0 1.1 - - - -
152H ALA* 3.4 43.3 - - + -
174H LEU* 4.5 14.6 - - + +
175H ILE 3.8 5.2 - - - +
176H ARG* 2.9 76.1 - - + -
177H ASN* 3.9 1.8 - - - -
181H THR* 1.3 77.5 - - - +
183H GLN* 1.3 59.7 + - - +
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Residues in contact with GLN 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G PHE* 3.6 11.9 - - - -
94G PRO 3.1 24.9 + - - +
95G LYS 3.2 11.5 + - - +
96G SER* 5.6 0.2 - - - -
146H VAL 3.2 13.0 - - - +
147H THR* 3.9 16.3 - - + +
148H ASP 4.3 0.4 - - - +
149H PHE* 3.2 2.0 - - - -
174H LEU 2.6 22.5 - - - +
175H ILE* 3.0 24.3 + - + +
177H ASN* 2.9 29.7 + - - +
182H PHE* 1.3 77.9 - - - +
184H VAL* 1.3 58.0 + - - +
185H LEU* 3.4 24.5 - - - +
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Residues in contact with VAL 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H VAL* 2.9 46.4 + - + +
149H PHE* 3.6 14.1 - - + -
154H ILE* 4.8 7.4 - - + -
156H VAL* 4.2 17.3 - - + -
171H SER* 4.8 5.4 - - - -
172H THR* 3.1 32.3 - - - +
173H GLN 3.2 14.4 - - - +
174H LEU* 4.3 3.8 - - - +
183H GLN* 1.3 75.7 - - - +
185H LEU* 1.3 67.4 + - - +
186H VAL* 4.0 4.3 + - + +
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Residues in contact with LEU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H VAL* 4.9 6.1 - - + -
144H CYS 4.1 3.4 - - - -
145H SER* 4.7 20.4 - - - +
146H VAL 5.0 0.7 - - - +
147H THR* 5.3 2.2 - - + -
170H SER 3.9 0.9 - - - +
171H SER* 3.1 3.5 - - - -
172H THR* 2.8 54.1 + - + +
175H ILE* 6.3 1.1 - - + -
183H GLN* 3.4 26.9 - - + +
184H VAL* 1.3 79.9 - - - +
186H VAL* 1.3 63.3 + - - +
187H MET* 4.4 12.3 - - + -
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H VAL* 3.7 0.7 - - - +
144H CYS* 3.0 39.7 + - + +
146H VAL* 5.2 0.2 - - + -
156H VAL* 3.7 43.5 - - + +
157H ARG* 6.0 0.4 - - - -
158H TRP* 3.3 31.6 + - + +
169H VAL* 5.7 2.5 - - + -
170H SER 3.4 5.6 - - - +
171H SER* 3.5 21.8 - - - -
184H VAL* 4.4 7.9 - - + +
185H LEU* 1.3 80.9 - - - +
187H MET* 1.3 65.0 + - - +
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Residues in contact with MET 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ARG* 5.5 6.1 - - - +
141H THR* 4.0 11.7 - - + -
142H LEU 3.7 4.0 - - - -
143H VAL* 3.6 28.9 - - + -
158H TRP* 3.7 5.2 + - - -
168H GLY 4.5 0.9 - - - -
169H VAL* 3.7 3.8 - - - -
170H SER* 2.6 57.0 + - - +
171H SER 5.3 0.2 - - - -
172H THR* 4.3 21.1 - - + +
185H LEU* 4.4 7.2 - - + +
186H VAL* 1.3 84.8 - - - +
188H LEU* 1.3 63.1 + - - +
189H GLU* 4.3 4.0 - - - +
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Residues in contact with LEU 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H THR* 3.6 2.6 - - - +
142H LEU* 3.0 37.3 + - + +
158H TRP* 3.4 41.7 - - + +
159H PHE 5.7 1.1 - - - +
160H ARG* 6.2 0.2 - - - +
165H GLU* 4.7 11.4 - - + -
167H VAL 4.4 9.6 - - - +
168H GLY 3.6 7.9 - - - +
169H VAL* 4.7 7.4 - - + -
187H MET* 1.3 77.0 - - - +
189H GLU* 1.3 81.0 + - - +
190H MET* 3.3 18.3 + - + +
198H TYR* 4.0 28.0 - - + -
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Residues in contact with GLU 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ARG* 2.9 42.9 + - - +
138H HIS* 4.3 15.3 + - + +
140H ASN* 4.2 4.0 + - - +
141H THR* 3.1 18.4 + - - +
167H VAL 4.9 1.0 - - - +
168H GLY* 2.9 30.1 + - - +
187H MET* 5.3 2.6 - - - +
188H LEU* 1.3 82.6 + - - +
190H MET* 1.3 58.9 + - - +
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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