Contacts of the strand formed by residues 181 - 186 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99J LYS* 5.3 6.7 - - - +
101J LEU* 5.5 0.9 - - - -
138K TYR* 5.5 0.4 - - - -
175K ILE* 4.6 2.9 - - - -
176K ASN* 2.9 28.0 + - - +
179K THR* 3.2 32.0 + - - +
180K MET* 1.3 79.4 - - - +
182K CYS* 1.3 61.4 + - - +
183K ILE* 3.0 16.0 + - + +
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Residues in contact with CYS 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J LEU* 4.0 27.5 - - + +
102J ASN* 5.5 4.7 - - - +
104J VAL* 6.0 0.2 - - - -
173K ARG* 3.5 37.9 - - - +
174K ILE 3.3 11.4 - - - +
175K ILE* 4.2 4.9 - - + +
181K GLN* 1.3 69.1 - - - +
183K ILE* 1.3 60.5 + - - +
184K LYS* 3.1 29.1 - - - -
185K HIS* 4.8 3.1 - - - -
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Residues in contact with ILE 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K ASP* 6.2 1.8 - - + +
162K LEU* 3.6 31.4 - - + -
174K ILE* 3.1 19.8 + - + +
176K ASN* 3.9 19.3 - - + +
179K THR* 4.2 8.5 - - + +
181K GLN* 3.0 24.3 + - + +
182K CYS* 1.3 73.0 - - - +
184K LYS* 1.3 79.0 + - + +
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Residues in contact with LYS 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K ILE* 2.9 42.1 + - + -
182K CYS* 3.1 13.9 - - - -
183K ILE* 1.3 103.9 - - + +
185K HIS* 1.3 62.7 + - - +
186K TYR* 3.2 28.3 - - + +
220K ILE* 2.5 34.5 + - + +
221K GLN* 3.9 11.5 + - - +
223K ASP* 3.4 15.8 + - - +
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Residues in contact with HIS 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J VAL* 3.6 40.2 - - + +
105J ALA 5.5 1.2 + - - -
171K ILE* 4.8 2.5 - - + -
172K ILE 3.1 11.0 - - - +
173K ARG* 4.6 8.5 - - + -
182K CYS* 4.8 3.5 - - - -
184K LYS* 1.3 74.9 - - - +
186K TYR* 1.3 78.0 + - - +
187K VAL* 4.0 22.9 - - + +
223K ASP* 5.2 1.0 - - - +
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Residues in contact with TYR 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K GLY 4.1 2.1 - - - +
171K ILE* 3.8 3.3 - - - -
172K ILE* 2.7 57.7 + - + +
174K ILE* 4.5 4.0 - - + -
184K LYS* 3.2 20.1 - - + +
185K HIS* 1.3 87.8 - - - +
187K VAL* 1.3 61.8 + - - +
188K GLY 3.6 3.6 + - - -
206K LEU* 5.3 0.2 - - + -
218K TRP* 4.0 39.7 - + + -
219K ASN 5.0 0.7 - - - -
220K ILE* 3.2 45.8 + - + -
223K ASP* 2.7 51.6 + - + -
572L LEU* 5.8 2.0 - - + -
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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