Contacts of the helix formed by residues 182 - 191 (chain B) in PDB entry 1LWU
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.8 6.5 - - + -
122A GLN* 3.4 25.6 - - + +
123A LEU* 3.7 28.3 - - + -
126A LEU* 3.9 8.7 - - + -
177B ARG 2.8 21.2 + - - +
178B ILE* 4.0 3.4 - - - +
180B SER 2.7 4.4 + - - -
181B THR* 1.3 72.4 - - - +
183B ALA* 1.3 51.3 + - - +
184B GLY 2.7 7.7 + - - -
185B SER* 2.9 0.9 + - - -
186B LEU* 2.6 50.7 + - + +
102C HIS* 3.0 33.4 - - + +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE 3.4 13.4 + - - +
179B GLU* 3.7 15.5 - - - +
180B SER 3.6 0.4 + - - -
182B VAL* 1.3 78.6 - - - +
184B GLY* 1.3 56.1 + - - +
186B LEU* 3.8 6.2 - - - +
187B ARG* 3.2 27.3 + - - +
102C HIS* 3.5 24.7 - - - +
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Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 5.1 3.5 - - - +
179B GLU 4.5 0.6 + - - -
180B SER* 2.8 18.4 + - - -
182B VAL 2.7 3.4 + - - -
183B ALA* 1.3 77.9 - - - +
185B SER* 1.3 64.4 + - - -
187B ARG* 3.3 2.3 + - - +
188B SER* 3.1 26.7 + - - -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 4.2 12.6 - - - -
181A ILE* 3.5 24.6 - - - +
183A ASN* 5.6 1.4 + - - +
184A LEU* 2.8 36.1 - - - +
180B SER 4.0 1.8 + - - -
181B THR 3.1 10.0 + - - -
182B VAL 2.9 5.4 + - - -
184B GLY* 1.3 76.4 - - - +
186B LEU* 1.3 66.6 + - - +
187B ARG 3.2 0.2 + - - -
188B SER* 3.5 1.3 + - - -
189B MET* 3.0 35.3 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.8 16.4 - - + -
182B VAL* 2.6 37.1 + - + +
183B ALA* 3.8 8.7 - - - -
185B SER* 1.3 74.4 - - - +
187B ARG* 1.3 64.8 + - - +
189B MET* 3.5 4.6 - - - +
190B LYS* 3.4 16.5 + - + +
102C HIS* 4.3 7.4 - - + +
105C GLN* 3.2 53.6 - - + +
106C ILE* 3.4 30.7 - - + -
109C LEU* 3.7 11.5 - - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ALA 3.2 18.5 + - - +
184B GLY* 4.0 2.2 - - - +
185B SER 3.2 0.8 - - - -
186B LEU* 1.3 77.0 + - - +
188B SER* 1.3 55.4 + - - +
189B MET 2.7 16.3 + - - -
190B LYS* 3.1 58.1 + - - +
191B SER* 3.5 9.2 + - - -
105C GLN* 3.8 22.2 + - - +
108C GLU* 5.1 2.0 + - - -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 5.0 1.1 - - - +
177A ALA* 5.6 10.3 - - - -
178A ALA* 3.9 20.0 + - - +
181A ILE* 6.0 4.0 - - - -
184B GLY 3.1 13.7 + - - -
185B SER* 3.8 2.7 - - - -
187B ARG* 1.3 76.6 - - - +
189B MET* 1.3 57.5 + - - +
191B SER* 4.2 10.8 - - - -
192B VAL* 4.0 10.9 + - - +
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.6 46.0 - - - +
129A LEU* 4.1 15.3 - - - +
130A GLN* 3.7 26.7 - - + +
133A ILE* 3.9 16.3 - - + +
178A ALA* 4.0 19.1 - - + +
181A ILE* 6.2 0.9 - - + -
184A LEU* 4.2 7.2 - - + -
185B SER* 3.0 26.2 + - - +
186B LEU 3.5 4.5 - - - +
187B ARG 2.7 6.3 + - - -
188B SER* 1.3 77.3 - - - +
190B LYS* 1.3 56.7 + - - +
191B SER 2.8 10.4 + - - -
192B VAL* 3.1 3.9 + - - +
193B LEU* 3.0 28.6 + - - +
109C LEU* 3.7 9.6 - - + -
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU* 3.4 7.4 + - + +
187B ARG* 3.1 50.3 + - - +
189B MET* 1.3 77.4 - - - +
191B SER* 1.3 57.1 + - - +
193B LEU* 4.6 3.4 - - - -
194B GLU* 2.9 43.4 + - - +
108C GLU* 3.7 28.4 + - - +
109C LEU* 3.3 26.1 - - + +
112C MET* 3.9 16.6 - - - +
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 5.3 10.4 - - - +
187B ARG 3.5 10.6 + - - -
188B SER* 4.4 10.5 - - - -
189B MET 2.8 0.4 - - - -
190B LYS* 1.3 78.8 - - - +
192B VAL* 1.3 54.9 + - - +
194B GLU* 2.9 8.5 + - - +
195B HIS* 2.5 39.3 + - - +
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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