Contacts of the helix formed by residues 250 - 255 (chain A) in PDB entry 1EG4
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 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN* 4.4 0.5 - - - +
104A SER* 4.9 0.5 - - - -
107A ARG* 2.9 40.0 + - - +
108A THR* 3.4 29.7 + - + +
111A LYS* 2.8 29.6 + - + +
245A PRO 3.1 10.7 + - - +
248A LEU* 3.8 16.4 - - + +
249A GLY* 1.3 82.7 - - - +
251A VAL* 1.3 65.2 + - - +
252A ALA* 3.0 4.7 + - - -
253A SER* 3.1 17.4 + - - -
254A PHE* 3.2 17.2 - - + -
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Residues in contact with VAL 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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242A ILE* 3.7 26.9 - - + +
245A PRO 3.8 2.2 + - - -
246A ARG* 3.7 35.7 - - + +
249A GLY 3.6 2.6 - - - -
250A GLU* 1.3 77.2 - - - +
252A ALA* 1.4 61.9 + - + +
254A PHE* 3.0 23.5 + - - -
256A GLY* 3.1 35.0 + - - -
257A SER* 3.8 17.0 - - - +
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Residues in contact with ALA 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 GLU 3.0 2.0 + - - -
251A VAL* 1.4 82.4 - - + +
253A SER* 1.3 59.8 + - - +
254A PHE 3.6 0.3 + - - -
255A GLY* 4.0 6.1 + - - -
256A GLY* 4.5 7.0 + - - +
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Residues in contact with SER 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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104A SER* 3.2 36.4 + - - -
107A ARG* 4.5 4.7 + - - -
250A GLU* 3.1 15.3 + - - -
252A ALA* 1.3 76.3 - - - +
254A PHE* 1.3 63.2 + - - +
255A GLY 3.5 2.7 - - - -
290A GLN* 2.7 30.5 - - - +
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Residues in contact with PHE 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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104A SER* 4.0 10.8 - - - -
105A ALA* 4.1 7.9 - - + -
108A THR* 3.4 44.9 - - + -
242A ILE* 3.6 26.3 - - + +
245A PRO* 3.8 14.4 - - + -
250A GLU* 3.2 29.2 - - + -
251A VAL* 3.0 4.9 + - - +
253A SER* 1.3 86.9 - - - +
255A GLY* 1.3 59.3 - - - +
256A GLY 3.3 2.8 - - - +
259A ILE* 5.7 0.2 - - - +
290A GLN* 3.1 29.6 - - - +
291A SER* 3.3 22.1 + - - +
293A VAL* 3.6 22.2 - - + -
294A TRP* 3.8 22.4 - + + -
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Residues in contact with GLY 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 VAL 3.7 0.2 + - - -
252A ALA 4.0 5.5 + - - -
253A SER 3.5 3.0 - - - -
254A PHE* 1.3 77.3 - - - +
256A GLY* 1.3 60.5 + - - +
258A ASN 4.3 8.9 + - - +
261A PRO* 5.8 2.3 - - - +
262A SER* 5.9 2.5 - - - -
290A GLN* 4.3 9.4 - - - +
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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