Contacts of the strand formed by residues 144 - 148 (chain f) 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 THR 144 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60b ARG* 4.2 1.3 + - - +
122f LEU* 3.6 13.6 - - + +
124f VAL* 3.8 22.9 - - + -
134f LEU* 4.2 18.6 - - + +
137f ALA* 3.8 22.7 - - - +
142f LEU 4.0 1.9 + - - -
143f PRO* 1.4 77.0 + - - +
145f ILE* 1.4 76.2 + - - +
146f ALA* 4.7 3.4 - - + -
156f TYR 3.9 15.8 + - - +
157f VAL* 3.8 2.3 - - - -
158f ASP* 3.0 34.3 + - - +
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Residues in contact with ILE 145 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34b MET* 3.7 23.8 - - + -
61f ALA* 3.9 30.5 - - + -
64f ALA* 5.2 0.9 - - + -
65f ILE* 6.3 0.2 - - + -
121f LEU* 3.9 22.7 - - + -
122f LEU 2.9 16.1 + - - +
123f VAL* 4.6 15.5 - - + -
124f VAL 3.2 19.5 + - - -
144f THR* 1.4 80.2 - - - +
146f ALA* 1.4 67.1 + - - +
158f ASP 3.4 17.0 - - - +
159f ILE* 3.9 30.1 - - + +
161f ILE* 4.3 12.3 - - + -
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Residues in contact with ALA 146 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123f VAL* 5.6 0.2 - - - -
124f VAL* 3.5 28.7 - - + -
127f PRO* 4.3 9.2 - - + -
144f THR* 4.7 2.5 - - + -
145f ILE* 1.4 84.0 - - - +
147f LEU* 1.4 66.7 + - - +
148f CYS* 3.4 16.6 + - - -
157f VAL* 3.9 16.6 - - + +
159f ILE 3.5 4.9 + - - -
160f ALA* 3.5 3.6 - - - -
161f ILE* 3.4 20.2 + - - -
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Residues in contact with LEU 147 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58f LEU* 6.3 0.2 - - + -
123f VAL* 4.5 14.4 - - + -
124f VAL 3.2 17.5 + - - +
125f THR* 3.6 32.8 - - + +
126f ASP* 3.8 0.2 - - - -
127f PRO* 3.8 13.5 - - - +
146f ALA* 1.4 70.6 - - - +
148f CYS* 1.4 56.5 + - - +
161f ILE* 3.9 29.4 - - + +
163f CYS* 5.4 0.4 - - + -
165f ASN* 3.3 35.8 + - + +
171f VAL* 5.1 8.3 - - - +
174f MET* 3.9 35.0 - - + -
175f TRP* 5.5 5.8 - - + +
178f LEU* 5.2 6.5 - - + -
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Residues in contact with CYS 148 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34f MET* 3.4 13.2 - - + +
127f PRO* 4.0 15.5 - - - -
146f ALA* 3.4 28.4 + - - -
147f LEU* 1.4 75.2 - - - +
149f ASN* 1.4 66.2 + - - +
152f SER* 3.9 7.0 - - - -
153f PRO 4.2 1.3 - - - -
154f LEU* 4.0 22.2 - - + -
157f VAL* 4.1 7.0 - - - -
160f ALA* 4.0 18.8 - - + -
161f ILE 3.1 20.3 + - - +
162f PRO* 3.5 1.9 - - - +
163f CYS 3.4 6.9 - - - +
165f ASN* 3.3 4.5 + - - -
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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