Contacts of the helix formed by residues 20 - 34 (chain 7) 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 GLU 20 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187 ASP* 5.4 1.2 + - - -
197 CYS* 1.3 77.4 - - - +
217 GLU* 1.3 68.1 + - - +
227 ALA* 3.8 19.0 + - - +
237 LEU* 3.0 36.1 + - + +
247 ILE* 3.0 11.2 + - - +
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Residues in contact with GLU 21 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207 GLU* 1.3 74.5 + - - +
227 ALA* 1.3 59.3 + - - +
247 ILE* 3.7 8.2 + - + +
257 GLU* 3.1 41.3 + - - +
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Residues in contact with ALA 22 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207 GLU* 3.1 20.4 + - + +
217 GLU* 1.3 80.4 - - - +
237 LEU* 1.3 63.9 + - + +
257 GLU* 3.8 9.6 + - - +
267 LYS* 3.4 19.6 + - - +
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Residues in contact with LEU 23 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 ASP* 4.3 2.2 - - - +
197 CYS* 3.5 28.0 - - + -
207 GLU* 3.0 37.1 + - + +
227 ALA* 1.3 78.7 - - + +
247 ILE* 1.3 64.2 + - - +
267 LYS* 3.1 22.6 + - + +
277 LEU* 3.1 14.6 - - + +
577 LEU 3.9 17.3 - - - +
587 THR* 3.6 22.4 - - - +
597 SER* 3.4 26.7 - - - +
627 LEU* 5.4 3.5 - - + +
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Residues in contact with ILE 24 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57 ALA* 3.5 35.7 - - + +
87 LEU* 4.6 4.5 - - + +
97 ALA* 3.9 24.7 - - + +
127 LEU* 3.8 16.2 - - + -
197 CYS* 3.2 29.6 - - + +
207 GLU 3.0 16.0 + - - +
217 GLU* 4.2 7.0 - - + +
237 LEU* 1.3 75.3 - - - +
257 GLU* 1.3 62.1 + - - +
267 LYS 3.1 0.2 - - - -
277 LEU* 3.3 16.8 + - - +
287 VAL* 3.2 13.1 + - - +
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Residues in contact with GLU 25 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57 ALA* 4.4 13.5 - - + -
217 GLU* 3.1 31.8 + - + +
227 ALA* 4.1 8.2 - - - +
237 LEU 3.3 0.2 - - - -
247 ILE* 1.3 74.2 - - - +
267 LYS* 1.3 62.6 + - - +
277 LEU 3.2 0.4 - - - -
287 VAL* 3.4 24.5 + - + +
297 GLU* 3.7 13.6 + - - +
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Residues in contact with LYS 26 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227 ALA 3.4 12.9 + - - +
237 LEU* 3.1 19.1 - - + +
247 ILE 3.1 0.2 - - - -
257 GLU* 1.3 82.2 - - - +
277 LEU* 1.3 59.7 + - + +
297 GLU* 3.6 31.5 + - - +
307 LEU* 4.0 7.6 + - + +
597 SER* 4.8 13.0 - - - +
627 LEU* 3.2 36.1 + - + +
637 ASN* 3.4 28.2 + - - +
667 GLU* 3.1 25.3 + - - +
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Residues in contact with LEU 27 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 3.6 32.3 - - + -
127 LEU* 5.8 5.6 - - + -
197 CYS* 5.7 4.9 - - - -
237 LEU* 3.1 20.4 - - + +
247 ILE* 3.3 8.3 + - - +
257 GLU 3.2 0.4 - - - -
267 LYS* 1.3 76.8 - - + +
287 VAL* 1.3 65.7 + - - +
297 GLU 3.0 2.2 - - - -
307 LEU* 3.0 44.8 + - + +
317 CYS* 3.3 11.6 - - - -
417 MET* 4.6 8.0 - - + +
427 VAL* 6.5 0.2 - - - -
457 LEU* 4.1 12.8 - - + -
627 LEU* 3.6 38.4 - - + -
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Residues in contact with VAL 28 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27 SER* 4.0 12.6 - - - -
37 ALA* 3.6 29.8 - - + +
47 SER 4.4 2.0 - - - +
57 ALA* 3.6 27.1 - - + +
87 LEU* 4.8 3.8 - - + -
247 ILE 3.2 17.3 - - - +
257 GLU* 3.4 20.4 - - + +
267 LYS 3.3 0.4 - - - -
277 LEU* 1.3 78.4 - - - +
297 GLU* 1.3 61.9 + - + +
317 CYS* 3.3 15.1 + - - +
327 VAL* 3.2 18.2 - - + +
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Residues in contact with GLU 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257 GLU 3.7 12.3 - - - +
267 LYS* 3.6 30.6 - - - +
277 LEU 3.0 0.4 - - - -
287 VAL* 1.3 77.3 - - + +
307 LEU* 1.3 53.8 + - - +
317 CYS 3.1 0.4 - - - -
327 VAL* 3.0 8.0 + - - +
337 GLN* 2.8 49.0 + - + +
667 GLU* 5.4 5.8 - - - +
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Residues in contact with LEU 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267 LYS* 4.0 4.5 + - + +
277 LEU* 3.0 40.2 + - + +
297 GLU* 1.3 79.4 - - - +
317 CYS* 1.3 57.9 + - - +
327 VAL 3.2 0.2 - - - -
337 GLN* 4.0 2.0 - - - -
347 TYR* 3.5 48.7 + - + +
357 GLY 4.0 1.2 + - - -
367 GLN* 4.0 6.2 + - - +
417 MET* 3.4 28.7 - - + -
627 LEU 4.7 7.4 - - - +
657 PHE* 3.7 20.0 - - + -
667 GLU* 3.5 37.7 - - + +
707 LEU* 4.5 2.7 - - + -
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Residues in contact with CYS 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37 ALA* 3.5 25.0 - - + +
87 LEU* 3.6 23.3 - - - -
277 LEU 3.3 16.4 - - - -
287 VAL 3.3 8.0 + - - +
297 GLU 3.1 1.0 - - - -
307 LEU* 1.3 77.1 - - - +
327 VAL* 1.3 60.5 + - - +
357 GLY* 3.3 21.8 - - - -
367 GLN 3.2 26.2 - - - +
377 ASN* 5.2 0.7 - - - -
387 GLU* 4.5 9.0 - - - +
417 MET* 3.9 8.1 - - - -
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Residues in contact with VAL 32 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17 MET 4.7 9.2 - - - +
27 SER* 4.5 26.2 - - - +
287 VAL* 3.2 20.2 - - + +
297 GLU* 3.0 8.0 + - - +
317 CYS* 1.3 83.1 - - + +
337 GLN* 1.3 70.7 + - - +
347 TYR 3.4 1.6 - - - -
357 GLY* 4.2 1.3 - - - -
767 LYS* 3.9 12.2 + - - +
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Residues in contact with GLN 33 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297 GLU* 2.8 27.9 + - + +
307 LEU* 4.6 0.4 - - - -
327 VAL* 1.3 88.6 + - - +
347 TYR* 1.3 84.0 + - + +
667 GLU* 4.6 9.2 - - - +
747 LEU* 4.5 4.0 - - - +
767 LYS* 3.6 18.4 - - - +
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Residues in contact with TYR 34 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307 LEU* 3.5 40.0 + - + +
337 GLN* 1.3 87.8 - - + +
357 GLY* 1.3 63.1 + - - +
367 GLN* 3.4 20.5 + - + +
667 GLU* 3.8 31.4 + - - +
707 LEU* 3.5 49.4 + - + +
717 SER* 4.7 1.0 - - - -
737 ARG 5.2 0.2 - - - -
747 LEU* 3.5 37.4 - - + +
757 SER* 4.2 14.6 + - - +
767 LYS* 3.2 22.8 - - - +
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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