Contacts of the helix formed by residues 245 - 256 (chain A) in PDB entry 5JEI
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 GLY 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ASN 3.0 14.1 + - - -
243A GLU 3.3 1.6 + - - -
244A GLN* 1.3 78.6 - - - +
246A LEU* 1.3 63.2 + - - +
247A LEU 3.4 2.2 - - - -
248A ASP* 3.4 16.0 + - - +
249A LYS* 3.1 29.7 + - - +
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Residues in contact with LEU 246 (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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39A LEU* 5.1 0.2 - - + -
42A GLU* 4.1 26.7 - - + +
241A LEU* 3.0 33.7 + - + +
244A GLN* 3.4 8.0 + - + +
245A GLY* 1.3 76.9 - - - +
247A LEU* 1.3 76.8 + - + +
249A LYS* 3.2 23.4 + - - +
250A LEU* 2.9 55.3 + - + +
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Residues in contact with LEU 247 (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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35A TYR* 3.7 22.2 + - + +
39A LEU* 3.7 29.8 - - + -
105A PRO 5.1 0.2 - - - +
106A PHE* 3.5 32.1 - - + +
238A VAL* 4.1 8.1 - - + +
241A LEU* 3.5 12.4 + - + -
242A ASN* 3.6 43.0 - - + +
245A GLY 3.4 0.4 - - - -
246A LEU* 1.3 81.2 - - + +
248A ASP* 1.3 58.3 + - - +
250A LEU* 3.3 5.0 + - + +
251A LYS* 2.9 28.9 + - - +
306A TOE 4.0 14.9 - - - +
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Residues in contact with ASP 248 (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 ASN* 4.6 7.0 + - - +
245A GLY* 3.4 18.2 + - - +
246A LEU 3.2 0.6 - - - -
247A LEU* 1.3 79.2 - - - +
249A LYS* 1.3 56.5 + - + +
251A LYS* 3.3 2.3 + - - +
252A ASN* 2.9 39.9 + - - +
306A TOE 2.8 44.7 - - - +
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Residues in contact with LYS 249 (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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244A GLN 5.7 1.1 - - - +
245A GLY 3.1 23.0 + - - +
246A LEU* 3.2 23.2 + - + +
248A ASP* 1.3 75.7 - - + +
250A LEU* 1.3 59.7 + - + +
252A ASN* 3.3 8.6 + - - +
253A LYS* 2.9 28.5 + - - +
257A ASP* 4.9 0.7 - - - +
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Residues in contact with LEU 250 (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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35A TYR* 3.6 25.3 - - + +
38A ASP* 3.7 42.6 - - + +
39A LEU* 4.1 18.4 - - + +
42A GLU* 5.2 1.3 - - + -
246A LEU* 2.9 50.7 + - + +
247A LEU* 3.8 1.6 - - - +
249A LYS* 1.3 75.0 - - + +
251A LYS* 1.3 67.7 + - - +
253A LYS* 4.2 10.8 - - + +
254A TRP* 3.1 32.3 + - + +
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Residues in contact with LYS 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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35A TYR* 3.6 5.5 - - + -
107A MET* 3.7 29.8 - - + +
108A SER 5.3 1.4 + - - -
195A THR* 4.5 12.0 - - - +
198A GLU* 4.7 7.1 + - - -
247A LEU 2.9 16.9 + - - +
248A ASP 3.6 4.5 - - - +
250A LEU* 1.3 76.7 - - - +
252A ASN* 1.3 65.6 + - - +
255A TRP* 2.9 74.1 + - + +
256A TYR* 4.3 21.4 + - + -
306A TOE 3.9 33.0 - - - +
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Residues in contact with ASN 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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248A ASP* 2.9 28.2 + - - +
249A LYS* 3.8 6.3 - - - +
251A LYS* 1.3 77.7 - - - +
253A LYS* 1.3 63.4 + - - +
256A TYR* 3.0 30.5 + - + -
257A ASP* 2.9 43.4 + - - +
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Residues in contact with LYS 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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38A ASP* 2.9 25.6 + - - +
249A LYS 2.9 17.7 + - - +
250A LEU* 3.5 12.5 - - + +
251A LYS 3.2 0.2 - - - -
252A ASN* 1.3 79.9 - - - +
254A TRP* 1.3 96.0 + - + +
256A TYR 4.6 0.2 + - - -
257A ASP* 3.5 23.0 + - - +
258A LYS* 4.6 10.0 + - - +
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Residues in contact with TRP 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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15A PRO* 3.9 10.1 - - + +
18A MET* 3.6 29.2 - - + -
33A GLU* 3.9 18.8 - - + -
34A GLY* 3.4 26.0 - - - -
35A TYR* 3.4 24.6 - - - +
38A ASP* 2.8 27.4 + - - -
199A TYR* 3.6 22.3 - - - -
203A ARG* 5.3 3.1 + - - -
250A LEU* 3.1 27.0 + - + +
253A LYS* 1.3 112.0 - - + +
255A TRP* 1.3 78.3 + - + +
311A PEG 4.0 17.0 - - - -
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Residues in contact with TRP 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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15A PRO* 3.6 26.0 - - + -
16A TYR* 3.6 44.6 - + - -
35A TYR* 3.8 25.4 - + + -
107A MET* 3.9 10.3 - - + -
195A THR* 2.8 24.2 + - - +
198A GLU* 3.9 6.5 - - + -
199A TYR* 3.5 28.5 - - + +
202A GLN* 3.4 27.2 - - - +
203A ARG* 5.3 2.8 + - - -
251A LYS* 2.9 50.9 + - + +
253A LYS 5.0 0.2 - - - -
254A TRP* 1.3 89.5 - - + +
256A TYR* 1.3 82.6 + - + +
258A LYS 5.3 0.7 - - - -
259A GLY* 4.5 3.6 + - - -
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Residues in contact with TYR 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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198A GLU* 4.1 16.5 + - + +
202A GLN* 3.7 37.6 - - + +
251A LYS* 4.3 16.1 + - + -
252A ASN* 3.0 31.7 + - - +
255A TRP* 1.3 106.5 - + + +
257A ASP* 1.3 71.8 + - - +
258A LYS 3.1 2.7 - - - -
259A GLY* 3.0 14.1 + - - -
304A PG4 6.2 3.5 - - - -
310A ETE 4.7 13.5 - - - -
314A NA 4.1 14.7 - - - -
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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