Contacts of the strand formed by residues 180 - 185 (chain T) in PDB entry 5K0Y
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 180 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145T ASN* 3.2 28.5 + - + +
171T ASN* 3.5 21.1 - - - +
172T GLN 3.6 5.4 - - - -
179T GLU* 1.4 83.4 + - + +
181T LEU* 1.3 62.0 + - - +
182T VAL* 3.7 17.3 - - - +
183T ASN* 4.5 4.0 - - + -
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Residues in contact with LEU 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160T CYS* 5.2 5.4 - - - -
172T GLN* 3.1 46.6 + - + +
173T TYR 4.7 0.2 - - - +
174T SER* 3.7 26.2 - - - +
179T GLU 4.6 0.9 - - - +
180T VAL* 1.3 75.6 - - - +
182T VAL* 1.4 68.3 + - + +
218T THR 6.1 0.4 - - - +
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Residues in contact with VAL 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T ASN* 3.9 0.2 - - - -
172T GLN* 3.1 52.6 + - + +
180T VAL* 3.7 8.3 - - - +
181T LEU* 1.4 82.5 - - + +
183T ASN* 1.4 78.0 + - - +
218T THR 5.1 4.7 - - - +
219T THR 4.7 12.6 - - - +
220T LEU* 3.7 14.5 - - + +
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Residues in contact with ASN 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146T ASP* 4.0 6.2 + - - +
169T GLU* 3.1 33.7 + - - +
170T LEU 3.0 23.9 - - - +
171T ASN* 3.2 27.6 + - - +
180T VAL* 4.5 4.5 - - + -
182T VAL* 1.4 85.9 - - - +
184T VAL* 1.4 76.3 + - - +
185T LYS* 4.6 1.2 - - - +
220T LEU* 3.8 4.5 - - - -
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Residues in contact with VAL 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T GLU* 3.6 4.3 - - - -
170T LEU* 3.2 33.7 + - + +
183T ASN* 1.4 81.8 + - - +
185T LYS* 1.4 65.4 + - - +
186T GLU* 3.7 29.1 + - + -
215T PHE* 3.8 23.8 - - + -
220T LEU* 3.8 24.0 - - + +
222T HIS* 6.2 1.6 - - - +
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Residues in contact with LYS 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167T SER* 4.1 17.8 - - - -
168T GLY 4.5 1.6 - - - +
169T GLU* 4.0 27.9 - - + +
183T ASN* 5.3 1.3 - - - +
184T VAL* 1.4 76.8 - - - +
186T GLU* 1.4 59.2 + - - +
187T HIS 3.4 22.4 - - - +
188T SER* 4.9 5.8 - - - +
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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