Contacts of the helix formed by residues 361 - 374 (chain B) in PDB entry 1EGE
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 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ARG* 3.9 24.9 - - - +
273B GLU* 3.4 31.6 - - + +
351B LEU* 5.5 1.3 - - + -
359B GLU 4.4 2.5 - - - +
360B TYR* 1.3 94.8 - - + +
362B VAL* 1.3 66.7 + - + +
363B GLU 3.4 0.3 + - - -
364B LYS* 3.5 14.8 + - + +
365B LEU* 3.3 20.3 + - - +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLU* 3.7 27.8 - - + -
344B ALA 4.2 1.4 - - - +
347B ALA* 4.0 14.1 - - + -
348B VAL* 3.6 28.4 - - + +
351B LEU* 3.8 27.4 - - + -
355B GLY* 3.1 35.0 - - - +
360B TYR* 4.6 2.0 - - + -
361B PRO* 1.3 76.7 - - + +
363B GLU* 1.3 66.7 + - - +
365B LEU* 3.1 25.4 + - + +
366B MET 3.4 5.0 + - - -
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 3.6 44.4 - - + +
218B ARG* 5.3 0.2 + - - -
348B VAL* 4.1 7.6 - - + -
355B GLY 3.3 18.2 - - - +
356B PHE* 3.9 6.7 - - - +
357B ASN 3.8 10.3 - - - +
358B THR* 3.8 25.3 - - - +
360B TYR 3.8 6.1 + - - +
361B PRO 3.4 0.6 - - - -
362B VAL* 1.3 81.7 - - - +
364B LYS* 1.3 66.6 + - - +
366B MET* 3.1 18.5 + - - +
367B ARG* 2.9 39.2 + - - +
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.6 11.0 - - + +
40B ALA* 4.9 10.1 - - + +
43B ASP* 3.5 42.4 - - + +
90B GLY 5.1 1.6 + - - -
91B CYS* 3.3 37.6 - - - +
93B GLY* 5.5 0.2 - - - -
217B GLN* 6.2 0.8 - - - +
360B TYR 4.2 2.2 + - - +
361B PRO* 3.5 13.1 + - + +
362B VAL 3.3 0.6 - - - -
363B GLU* 1.3 82.9 + - - +
365B LEU* 1.3 68.0 + - + +
367B ARG* 3.2 22.2 + - - +
368B ASP* 3.1 53.1 + - - +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR 5.7 0.4 - - - +
90B GLY 6.0 0.7 - - - +
91B CYS* 6.4 1.6 - - - -
266B LEU* 3.9 18.9 - - + +
269B ARG* 3.8 39.0 - - + +
270B ALA* 3.8 26.2 - - + +
273B GLU* 5.0 2.9 - - + -
344B ALA* 3.7 13.7 - - + -
361B PRO 3.3 19.1 - - - +
362B VAL* 3.1 16.3 + - + +
364B LYS* 1.3 82.6 - - + +
366B MET* 1.3 60.3 + - - +
368B ASP* 3.6 12.7 - - - +
369B ALA* 2.8 35.2 + - - +
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Residues in contact with MET 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 3.6 31.9 - - + -
341A ASN* 4.5 5.2 - - - +
366A MET* 4.0 35.9 - - + +
370A LYS* 3.8 29.2 - - + -
215B MET* 4.5 1.9 - - - +
341B ASN* 4.6 4.5 + - - +
344B ALA* 3.9 9.6 - - - +
345B THR* 3.8 27.1 - - + +
348B VAL* 3.9 27.6 - - + -
362B VAL 3.4 2.4 + - - -
363B GLU 3.1 11.7 + - - +
365B LEU* 1.3 79.2 - - - +
367B ARG* 1.3 62.6 + - - +
369B ALA* 3.9 2.6 + - - +
370B LYS* 3.9 14.2 + - - +
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Residues in contact with ARG 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 4.5 11.9 - - - -
356A PHE* 3.2 24.9 - - - -
367A ARG* 4.6 11.2 - - + +
43B ASP* 3.0 34.3 + - - -
215B MET* 3.0 52.6 + - + +
216B GLY* 3.8 8.0 - - - -
218B ARG* 2.8 45.6 - - - +
358B THR* 6.3 0.8 - - - +
363B GLU* 2.9 36.1 + - - +
364B LYS* 3.2 22.8 + - - +
365B LEU 3.2 0.2 - - - -
366B MET* 1.3 76.0 - - - +
368B ASP* 1.3 65.0 + - - +
370B LYS 3.6 1.6 + - - -
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Residues in contact with ASP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.8 0.2 - - - -
43B ASP* 4.8 1.7 - - - +
91B CYS* 5.3 0.2 - - - -
92B THR* 3.2 20.6 + - - +
93B GLY 4.7 0.3 + - - -
216B GLY* 3.7 6.5 - - - -
217B GLN* 3.3 26.5 + - + +
266B LEU* 3.3 21.1 - - + +
364B LYS* 3.1 47.5 + - - +
365B LEU* 3.6 7.1 - - - +
367B ARG* 1.3 74.4 - - - +
369B ALA* 1.3 66.8 + - - +
370B LYS 3.0 1.7 + - - -
371B ILE* 3.2 28.0 - - - +
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.4 24.8 - - + +
340B ALA* 4.1 0.8 - - - +
341B ASN* 3.1 40.0 - - - +
344B ALA* 3.9 5.4 - - + -
365B LEU 2.8 20.4 + - - +
366B MET 4.0 2.7 - - - +
367B ARG 3.5 0.2 - - - -
368B ASP* 1.3 72.5 - - - +
370B LYS* 1.3 52.3 + - - +
372B TYR* 2.8 38.9 + - - +
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 3.1 40.2 + - - -
348A VAL* 3.7 21.5 - - + +
349A GLN* 2.5 37.6 - - - +
356A PHE* 3.5 5.6 - - + -
366A MET* 3.7 13.2 - - + -
215B MET* 3.4 35.7 - - + -
341B ASN* 3.4 14.6 + - - +
366B MET 3.9 2.3 + - - +
367B ARG 3.6 1.0 + - - +
368B ASP 3.0 2.4 + - - -
369B ALA* 1.3 76.5 - - - +
371B ILE* 1.3 61.8 + - - +
372B TYR 3.0 1.6 + - - -
373B GLN* 2.9 24.8 + - - +
374B ILE* 3.6 7.3 + - + +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 3.4 42.3 - - + -
217B GLN* 3.0 42.0 - - - +
368B ASP 3.2 18.6 - - - +
370B LYS* 1.3 75.6 - - - +
372B TYR* 1.3 74.0 + - + +
373B GLN 3.0 3.0 + - - -
374B ILE* 3.6 6.7 - - + +
375B TYR* 2.9 45.6 + - + -
399B FAD 3.7 29.2 - - + -
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.5 32.1 - - + +
95B GLN* 4.0 6.4 + - - -
96B THR* 3.7 12.3 + - - -
217B GLN* 3.6 7.2 - - - -
259B VAL* 3.2 36.3 - - + -
262B GLY* 3.9 14.3 - - - -
263B ALA* 3.6 24.9 - - + -
266B LEU* 4.7 3.1 - - + -
333B LYS* 3.5 20.7 - - + +
337B GLY* 3.1 30.3 - - - +
340B ALA* 4.9 2.2 - - + -
368B ASP 4.1 3.1 - - - -
369B ALA* 2.8 20.9 + - - +
371B ILE* 1.3 100.9 - - + +
373B GLN* 1.3 59.3 + - - +
375B TYR* 3.8 20.4 + + - -
379B SER* 4.8 0.2 + - - -
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A THR* 4.3 4.1 + - - -
349A GLN* 2.8 30.7 + - - +
333B LYS* 5.1 0.7 - - - +
337B GLY* 3.6 10.8 - - - +
338B ASP* 3.9 21.8 + - - +
341B ASN* 3.3 40.5 + - - +
342B GLN* 6.0 0.4 - - - +
370B LYS* 2.9 16.5 + - - +
371B ILE 3.0 0.4 - - - -
372B TYR* 1.3 77.6 - - - +
374B ILE* 1.3 61.6 + - - +
375B TYR 5.0 0.2 - - - -
377B GLY 4.1 2.6 - - - +
378B THR* 3.2 4.4 - - - -
379B SER* 2.8 45.3 + - - +
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A VAL* 3.9 27.4 - - + +
349A GLN* 3.5 24.5 - - - +
352A GLY* 3.6 40.2 - - - +
353A GLY* 3.7 9.6 - - - +
356A PHE* 4.5 13.5 - - + -
370B LYS* 3.9 17.9 - - + +
371B ILE* 3.2 6.0 + - + +
373B GLN* 1.3 78.6 - - - +
375B TYR* 1.3 66.3 + - - +
376B GLU 3.8 0.5 + - - -
378B THR* 3.1 29.1 + - + +
399B FAD 3.8 19.7 - - + +
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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
------------------------------------------------------------
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