Contacts of the helix formed by residues 250 - 257 (chain A) in PDB entry 5PL7
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 SER 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY* 2.9 20.3 + - - -
126A TRP* 3.4 30.6 - - - -
249A ILE* 1.3 75.5 - - - +
251A PRO* 1.4 75.5 - - - +
252A THR* 3.4 9.0 + - - -
253A VAL* 3.1 26.2 + - - +
254A LEU* 3.0 22.5 + - - +
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Residues in contact with PRO 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLU* 4.3 0.2 - - - +
126A TRP* 3.3 35.4 - - + +
213A TYR* 3.8 20.4 - - + -
249A ILE 4.5 0.7 - - - +
250A SER* 1.4 84.8 - - - +
252A THR* 1.3 56.6 + - - +
254A LEU* 3.3 6.1 + - + +
255A LYS* 2.9 34.0 + - - +
261A PHE* 3.7 27.8 - - + -
263A ARG* 3.7 16.2 - - - +
406A EDO 3.7 18.4 - - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A SER* 3.2 8.8 + - - -
251A PRO* 1.3 81.4 - - - +
253A VAL* 1.4 59.1 + - + +
255A LYS* 3.4 5.7 + - - +
256A GLU* 2.9 52.1 + - + +
406A EDO 3.6 22.9 + - - -
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLY* 3.8 15.0 - - - +
85A VAL* 4.0 17.3 - - + -
226A LEU* 4.8 0.9 - - + -
230A LEU* 4.0 11.2 - - + -
249A ILE* 3.6 20.9 - - + -
250A SER* 3.1 21.0 + - - +
252A THR* 1.4 75.5 - - + +
254A LEU* 1.4 66.9 + - - +
256A GLU* 3.3 18.4 + - - +
257A ASN* 2.9 42.6 + - - +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 3.6 29.4 - - + -
213A TYR* 5.6 0.9 - - + -
215A VAL* 5.3 0.2 - - + -
223A LEU* 3.8 25.8 - - + -
226A LEU* 4.0 10.3 - - + -
249A ILE* 3.7 22.7 - - + +
250A SER 3.0 18.0 + - - +
251A PRO* 3.7 10.1 - - + +
253A VAL* 1.4 77.9 - - - +
255A LYS* 1.3 61.6 + - - +
257A ASN 3.2 2.6 + - - -
258A GLY 3.1 4.5 + - - -
259A ILE* 3.0 40.4 + - + +
261A PHE* 3.7 36.1 - - + -
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PRO 2.9 20.1 + - - +
252A THR* 3.6 6.1 - - - +
254A LEU* 1.3 75.3 - - - +
256A GLU* 1.3 64.8 + - + +
258A GLY* 3.1 14.5 + - - +
259A ILE 5.1 2.0 - - - +
261A PHE* 3.7 18.2 - - + -
263A ARG* 5.3 0.2 - - - +
406A EDO 3.9 16.4 - - - +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A THR* 2.9 36.1 + - + +
253A VAL* 3.6 24.0 - - - +
254A LEU 3.2 0.2 - - - -
255A LYS* 1.3 76.5 - - - +
257A ASN* 1.4 65.1 + - - +
258A GLY 3.5 0.6 + - - -
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Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.6 37.2 - - + +
229A GLU* 4.9 2.8 - - - +
230A LEU* 5.4 2.2 - - - +
253A VAL* 2.9 39.7 + - - +
254A LEU 3.2 1.5 + - - +
255A LYS 3.1 0.2 - - - -
256A GLU* 1.4 86.1 + - - +
258A GLY* 1.3 60.8 + - - +
259A ILE* 3.3 12.4 + - + +
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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