Contacts of the strand formed by residues 238 - 242 (chain C) in PDB entry 2PKS
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 PRO 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B TRP* 4.1 20.6 - - + +
51B GLN* 3.0 32.3 - - - +
66B ALA 4.1 6.5 - - - +
67B SER* 4.2 7.8 - - - -
154B VAL* 5.7 0.2 - - + -
173B ARG 3.4 10.6 - - - +
174B VAL* 3.7 11.6 - - - +
175B THR* 3.9 9.9 + - - +
237C GLY* 1.4 82.4 - - - +
239C PHE* 1.3 57.8 + - - +
240C VAL* 3.8 20.8 + - + +
251C GLN* 3.6 24.9 - - - +
255C VAL* 4.5 2.9 - - - -
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Residues in contact with PHE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 3.3 36.1 - - - -
173B ARG 3.4 4.7 - - - -
174B VAL* 3.2 28.9 - - + -
195C LEU* 4.3 5.2 - - + -
197C ILE* 4.0 13.0 - - + -
216C PHE* 3.6 30.3 - + - -
218C ALA* 4.0 20.2 - - + -
237C GLY 3.8 0.8 + - - -
238C PRO* 1.3 71.9 - - - +
240C VAL* 1.3 58.0 + - - +
241C MET* 3.9 18.4 - - + -
251C GLN* 3.4 2.9 - - - -
252C MET* 2.9 28.5 + - + -
253C GLY 2.8 23.8 + - - +
255C VAL* 4.7 0.8 - - - +
270C TYR* 3.7 27.4 - + + -
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 5.0 0.2 - - - +
48B SER* 6.0 0.4 - - - +
50B TRP* 3.8 23.1 - - + +
154B VAL* 3.9 15.5 - - + -
172B GLY* 3.5 0.7 - - - -
173B ARG* 2.8 53.2 + - + +
175B THR* 6.1 1.8 - - + +
238C PRO* 3.8 26.2 - - + +
239C PHE* 1.3 73.9 - - - +
241C MET* 1.3 67.9 + - - +
249C TRP* 3.5 29.8 - - + -
250C TYR 2.9 11.9 - - - +
251C GLN* 4.3 1.8 - - - -
252C MET 5.0 0.2 - - - -
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.1 1.8 - - - -
32A TYR* 3.8 22.0 - - + +
165B LEU* 3.4 42.2 - - + +
170B TYR* 3.9 6.1 - - + -
171B LYS 2.9 27.6 - - - +
172B GLY* 3.9 9.6 - - - -
197C ILE* 4.0 16.6 - - + -
239C PHE* 3.9 4.5 - - + -
240C VAL* 1.3 79.9 - - - +
242C LYS* 1.3 60.2 + - - +
243C SER 3.7 1.0 + - - -
249C TRP* 3.5 6.4 - - - -
250C TYR* 2.7 40.6 + - - +
252C MET* 3.6 28.3 - - + -
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Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.7 27.3 + - - +
20A LEU 5.4 1.6 + - - -
21A GLU* 5.6 0.8 - - - +
25A GLU* 2.7 29.7 + - + +
28A LEU* 4.6 6.4 - - + +
29A LEU* 4.1 20.9 - - + +
32A TYR* 2.9 26.2 + - - +
165B LEU* 4.6 0.9 - - - -
241C MET* 1.3 72.0 - - - +
243C SER* 1.3 69.5 + - - +
244C PRO 3.5 2.4 - - - -
247C ASN* 3.4 42.7 - - - +
248C ARG 3.6 4.3 - - - +
249C TRP* 3.7 38.2 - - + +
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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