Contacts of the helix formed by residues 37 - 46 (chain 4) in PDB entry 4E2I
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 ASN 37 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314 CYS* 5.2 0.7 - - - -
354 GLY 3.2 9.5 + - - +
364 GLN* 1.3 74.9 + - - +
384 GLU* 1.3 75.6 + - - +
394 GLU* 3.0 17.7 + - + +
404 GLY* 3.0 6.6 + - - +
414 MET* 2.9 21.7 + - - +
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Residues in contact with GLU 38 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34 ALA* 2.6 39.8 - - + +
74 GLN* 3.6 34.4 - - + +
84 LEU* 3.7 41.5 - - + +
114 GLU* 4.2 3.8 - - + +
314 CYS* 4.5 2.8 - - - +
374 ASN* 1.3 80.7 - - - +
394 GLU* 1.3 72.4 + - + +
414 MET* 4.1 0.9 - - - -
424 VAL* 3.1 32.1 + - - +
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Residues in contact with GLU 39 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 GLN* 5.4 2.1 - - - +
114 GLU* 5.1 18.2 - - + +
374 ASN* 3.0 11.6 + - + +
384 GLU* 1.3 98.1 - - + +
404 GLY* 1.3 61.5 + - - +
424 VAL* 4.6 1.6 - - - +
434 GLY* 3.7 14.7 + - - -
548D ARG* 5.8 1.7 + - - -
549D PRO 5.9 2.2 - - - +
550D LYS* 6.4 1.6 - - - -
551D ASP* 4.6 17.1 - - - +
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Residues in contact with GLY 40 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364 GLN* 4.3 14.6 - - - -
374 ASN* 3.0 10.5 + - - +
394 GLU* 1.3 78.1 - - - +
414 MET* 1.3 62.2 + - - +
434 GLY* 3.8 1.9 - - - -
444 GLU* 3.1 34.6 + - - +
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Residues in contact with MET 41 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LEU* 4.5 7.6 - - + -
274 LEU* 4.6 7.4 - - + +
304 LEU* 3.4 44.4 - - + +
314 CYS* 3.9 17.0 - - - -
364 GLN* 3.6 42.8 - - + +
374 ASN 2.9 11.9 + - - +
384 GLU 4.3 3.8 - - - +
404 GLY* 1.3 75.5 - - - +
424 VAL* 1.3 60.9 + - + +
444 GLU* 3.2 7.4 + - + +
454 LEU* 2.8 32.1 + - - +
654 PHE* 3.7 24.5 - - + -
704 LEU* 4.2 9.4 - - + -
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Residues in contact with VAL 42 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LEU* 3.9 26.0 - - + +
114 GLU* 3.5 39.3 - - + +
124 LEU* 4.7 4.0 - - + -
154 PHE* 4.0 9.4 - - + -
174 LEU* 4.4 7.0 - - + -
274 LEU* 6.5 0.4 - - - -
384 GLU 3.1 21.2 + - - +
394 GLU 4.7 1.8 - - - +
404 GLY 3.5 0.2 - - - -
414 MET* 1.3 75.2 - - - +
434 GLY* 1.3 60.7 + - - +
454 LEU* 4.2 6.7 - - + -
464 ILE* 3.0 51.9 + - + +
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Residues in contact with GLY 43 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394 GLU 3.7 11.4 + - - -
404 GLY* 3.5 6.7 + - - -
414 MET 3.1 0.8 - - - -
424 VAL* 1.3 82.0 - - - +
444 GLU* 1.3 65.3 + - - +
464 ILE* 4.2 3.6 + - - +
474 ALA* 4.0 14.9 + - - +
620D ALA 5.5 6.8 - - - +
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Residues in contact with GLU 44 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364 GLN* 4.8 9.0 - - + +
404 GLY* 3.1 19.1 + - - +
414 MET* 3.9 7.0 - - + +
434 GLY* 1.3 79.9 - - - +
454 LEU* 1.3 66.5 + - - +
474 ALA* 3.4 19.7 + - - +
484 PHE 3.6 1.4 + - - -
654 PHE* 3.3 28.7 - - + -
694 PHE* 3.1 34.1 - - + -
704 LEU* 5.2 1.1 - - + -
734 ARG* 5.0 1.2 + - - -
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Residues in contact with LEU 45 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 LEU* 6.3 1.6 - - + -
174 LEU* 5.7 2.2 - - + -
274 LEU* 4.1 12.8 - - + -
414 MET* 2.8 18.3 + - - +
424 VAL* 3.9 8.7 - - - +
434 GLY 3.4 0.4 - - - -
444 GLU* 1.3 76.5 - - - +
464 ILE* 1.3 65.3 + - + +
474 ALA 3.1 0.2 - - - -
484 PHE* 3.0 28.4 + - + +
494 CYS* 3.6 8.7 + - - -
574 LEU* 4.2 23.8 - - + -
614 ILE* 5.1 0.4 - - + +
624 LEU* 3.5 36.1 - - + -
654 PHE* 3.6 39.2 - - + -
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Residues in contact with ILE 46 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154 PHE* 3.5 40.4 - - + -
174 LEU* 3.9 23.8 - - + -
424 VAL* 3.0 25.9 + - + +
434 GLY* 4.2 4.7 + - - +
444 GLU 3.5 0.2 - - - -
454 LEU* 1.3 74.9 - - + +
474 ALA* 1.3 57.9 + - - +
484 PHE 3.1 5.4 - - - -
494 CYS* 3.3 21.6 + - + +
504 THR* 3.2 18.0 + - - +
617D PHE* 5.4 4.3 - - + -
620D ALA* 4.5 12.3 - - + +
621D MET* 4.2 21.1 - - + +
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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