Contacts of the helix formed by residues 251 - 255 (chain A) in PDB entry 4PE5
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 GLU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ARG* 2.4 35.2 + - - +
144A TYR* 4.6 7.4 - - + -
147A GLN* 2.8 18.6 + - - +
250A GLY* 1.3 71.4 - - - -
252A ARG* 1.3 67.0 + - - +
253A GLU* 3.0 3.3 + - - -
254A ILE* 3.1 11.7 + - + +
255A SER* 3.0 28.7 + - - +
269A LEU 3.3 14.6 - - - +
270A GLN* 3.6 13.0 - - + +
271A LEU* 2.9 28.9 + - - +
274A GLY* 6.0 0.7 - - - -
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 4.5 17.4 - - - +
144A TYR* 3.4 49.1 - - + +
147A GLN* 5.4 0.4 - - - +
168A SER* 4.8 5.1 + - - -
170A ASP* 5.2 2.4 + - - -
172A GLU* 3.9 28.9 - - - +
222A SER* 4.7 4.2 + - - -
223A ALA* 3.6 40.4 + - - +
224A SER* 3.3 23.7 + - - +
225A GLU* 3.7 32.1 - - + +
251A GLU* 1.3 76.7 - - - +
253A GLU* 1.3 65.6 + - - +
254A ILE 3.2 1.4 + - - -
255A SER* 3.6 13.4 + - - -
258A ALA* 4.0 1.0 - - - +
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Residues in contact with GLU 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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147A GLN* 5.1 1.9 + - - -
151A TRP* 5.3 1.2 - - - -
221A LEU* 3.5 22.7 - - + +
222A SER* 3.2 10.7 + - - -
223A ALA 3.0 37.9 + - - +
228A ALA* 3.7 11.9 - - + -
232A TYR* 2.8 46.4 + - - +
249A VAL* 3.8 9.4 - - + -
250A GLY* 3.1 31.3 + - - -
251A GLU 3.0 0.4 + - - -
252A ARG* 1.3 82.3 + - - +
254A ILE* 1.3 60.2 + - - +
255A SER 3.7 0.9 - - - -
258A ALA* 4.0 5.7 - - - +
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Residues in contact with ILE 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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232A TYR* 4.5 0.4 - - - +
249A VAL* 3.8 18.8 - - + -
250A GLY 3.3 11.4 - - - +
251A GLU* 3.4 8.3 - - + +
253A GLU* 1.3 85.8 - - - +
255A SER* 1.3 57.8 + - - +
258A ALA* 4.9 1.1 - - - -
259A LEU* 3.5 38.4 - - + +
262A ALA* 5.4 0.9 - - + -
266A ILE* 4.3 20.4 - - + -
268A GLY* 3.7 7.6 - - - -
269A LEU 3.5 37.2 - - - +
270A GLN* 4.4 17.1 + - + +
354A MET* 4.6 7.6 - - + -
361A LEU* 4.4 11.2 - - + +
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Residues in contact with SER 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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225A GLU* 3.6 21.9 - - - -
251A GLU* 3.0 29.0 + - - +
252A ARG* 3.6 10.0 + - - -
253A GLU 3.7 0.4 - - - -
254A ILE* 1.3 79.3 + - - +
256A GLY* 1.3 68.1 + - - +
257A ASN 3.3 0.5 + - - -
258A ALA* 3.0 20.0 + - - +
259A LEU* 4.3 1.6 - - - -
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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