Contacts of the strand formed by residues 181 - 186 (chain E) in PDB entry 5LS6
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 GLN 181 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LYS* 4.1 21.1 - - - +
101D LEU* 5.7 1.3 - - - -
138E TYR* 4.4 2.3 - - - -
175E ILE* 4.5 4.5 - - - -
176E ASN* 3.2 24.2 + - - +
179E THR* 3.3 23.9 + - - +
180E MET* 1.3 85.8 - - + +
182E CYS* 1.3 61.9 + - - +
183E ILE* 3.0 18.2 + - + +
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Residues in contact with CYS 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 4.2 12.4 - - + +
102D ASN* 5.4 5.8 - - - +
104D VAL* 5.5 0.7 - - - -
173E ARG* 3.0 47.1 - - - +
174E ILE 3.5 6.3 - - - -
175E ILE* 3.9 14.2 - - + +
181E GLN* 1.3 69.6 - - - +
183E ILE* 1.3 62.1 + - - +
184E LYS 4.1 18.8 - - - -
185E HIS* 4.8 5.8 - - - -
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Residues in contact with ILE 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E LEU* 3.8 28.9 - - + -
174E ILE* 3.0 26.1 + - + +
176E ASN* 4.3 9.9 - - + +
179E THR* 4.0 17.0 - - + +
181E GLN* 3.0 19.4 + - + +
182E CYS* 1.3 73.5 - - - +
184E LYS* 1.3 78.5 + - + +
185E HIS* 5.6 1.0 + - - -
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Residues in contact with LYS 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ARG* 3.6 1.4 - - - -
174E ILE* 2.8 50.6 + - + +
182E CYS* 3.5 4.3 - - - -
183E ILE* 1.3 105.0 - - + +
185E HIS* 1.3 60.9 + - - +
186E TYR* 3.4 24.5 - - + +
220E ILE* 2.9 25.0 + - + +
221E GLN* 4.0 8.5 + - - +
223E ASP* 3.4 25.0 + - - +
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Residues in contact with HIS 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 3.6 35.9 - - + +
105D ALA 5.6 0.8 + - - -
171E ILE* 4.8 5.8 - - + -
172E ILE 3.3 7.9 - - - +
173E ARG* 4.9 1.8 - - + -
182E CYS* 4.8 9.5 - - - -
183E ILE 5.6 0.4 + - - -
184E LYS* 1.3 75.2 - - - +
186E TYR* 1.3 75.9 + - - +
187E VAL* 4.0 24.2 - - + +
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Residues in contact with TYR 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLY 4.5 0.9 - - - +
171E ILE* 4.0 3.1 - - - -
172E ILE* 3.0 58.1 + - + +
174E ILE* 4.3 13.7 - - + -
184E LYS* 3.4 16.9 - - + +
185E HIS* 1.3 91.6 - - - +
187E VAL* 1.3 59.7 + - - +
188E GLY 3.5 6.7 + - - -
206E LEU* 5.1 1.1 - - + -
218E TRP* 3.8 39.3 - + + -
220E ILE* 3.1 58.1 + - + +
223E ASP* 3.6 34.6 + - + -
572F LEU* 6.4 0.2 - - - -
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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