Contacts of the helix formed by residues 37 - 46 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319 CYS* 5.2 0.4 - - - -
359 GLY 3.2 9.6 + - - +
369 GLN* 1.3 75.9 + - - +
389 GLU* 1.3 75.2 + - - +
399 GLU* 3.0 18.2 + - + +
409 GLY* 3.0 6.4 + - - +
419 MET* 2.9 21.7 + - - +
551I ASP* 5.4 4.5 + - - +
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Residues in contact with GLU 38 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39 ALA* 2.6 40.1 - - + +
79 GLN* 3.6 34.5 - - + +
89 LEU* 3.7 40.6 - - + +
119 GLU* 4.2 3.4 - - + +
319 CYS* 4.4 2.5 - - - +
369 GLN 3.8 0.2 + - - -
379 ASN* 1.3 79.5 - - - +
399 GLU* 1.3 72.8 + - - +
419 MET* 4.1 0.4 - - - -
429 VAL* 3.1 31.9 + - - +
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Residues in contact with GLU 39 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79 GLN* 5.4 2.3 - - - +
119 GLU* 5.1 9.4 - - + +
379 ASN* 3.0 10.3 - - + +
389 GLU* 1.3 98.8 - - - +
409 GLY* 1.3 62.2 + - - +
429 VAL* 4.7 1.4 - - - +
439 GLY* 3.6 14.7 + - - -
548I ARG* 6.0 0.2 + - - -
549I PRO 4.8 6.5 - - - +
550I LYS* 4.8 14.1 - - + -
551I ASP* 3.4 38.8 - - + +
552I TYR* 4.4 23.9 + - + +
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Residues in contact with GLY 40 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369 GLN* 4.3 13.0 - - - -
379 ASN* 3.0 10.7 + - - +
399 GLU* 1.3 78.3 - - - +
419 MET* 1.3 63.3 + - - +
439 GLY* 3.5 2.3 + - - -
449 GLU* 3.1 34.3 + - - +
551I ASP* 5.3 1.7 + - - +
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Residues in contact with MET 41 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 LEU* 4.5 6.7 - - + -
279 LEU* 4.6 7.9 - - + +
309 LEU* 3.4 45.1 - - + +
319 CYS* 3.9 17.5 - - - -
369 GLN* 3.6 45.0 - - + +
379 ASN 2.9 12.5 + - - +
389 GLU 4.3 3.8 - - - +
399 GLU 3.4 0.2 - - - -
409 GLY* 1.3 73.8 - - - +
429 VAL* 1.3 60.0 + - - +
439 GLY 3.1 1.1 - - - -
449 GLU* 3.1 7.9 + - + +
459 LEU* 2.8 31.4 + - - +
659 PHE* 3.7 24.2 - - + -
709 LEU* 4.3 9.4 - - + -
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Residues in contact with VAL 42 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 LEU* 3.9 26.7 - - + +
119 GLU* 3.5 39.5 - - + +
129 LEU* 4.7 3.4 - - + -
159 PHE* 4.0 9.2 - - + -
179 LEU* 4.5 7.2 - - + -
279 LEU* 6.5 0.4 - - - -
389 GLU 3.1 20.4 + - - +
399 GLU 4.7 1.8 - - - +
409 GLY 3.5 0.2 - - - -
419 MET* 1.3 76.3 - - - +
439 GLY* 1.3 59.3 + - - +
459 LEU* 4.2 6.5 - - + -
469 ILE* 3.0 52.3 + - + +
620I ALA* 5.5 0.2 - - + -
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Residues in contact with GLY 43 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399 GLU 3.6 9.6 + - - -
409 GLY* 3.5 6.0 + - - -
419 MET 3.1 1.0 - - - -
429 VAL* 1.3 80.3 - - - +
449 GLU* 1.3 65.0 + - - +
479 ALA* 4.1 0.3 - - - +
620I ALA* 2.9 27.7 - - - +
621I MET* 3.1 34.4 - - - +
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Residues in contact with GLU 44 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369 GLN* 4.8 9.2 - - - +
409 GLY* 3.1 19.6 + - - +
419 MET* 3.9 6.7 - - + +
439 GLY* 1.3 80.1 - - - +
459 LEU* 1.3 65.9 + - - +
469 ILE 3.5 0.2 - - - -
479 ALA* 3.4 19.6 + - - +
489 PHE* 3.6 1.6 + - - +
659 PHE* 3.3 29.4 - - + -
699 PHE* 3.1 33.8 - - + -
709 LEU* 5.2 1.3 - - + -
739 ARG* 5.0 1.2 + - - -
621I MET 4.6 8.1 - - - +
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Residues in contact with LEU 45 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129 LEU* 6.3 2.0 - - + -
179 LEU* 5.7 1.8 - - + -
279 LEU* 4.1 12.8 - - + -
419 MET 2.8 18.0 + - - +
429 VAL* 3.9 9.2 - - + +
439 GLY 3.4 0.2 - - - -
449 GLU* 1.3 77.4 - - - +
469 ILE* 1.3 63.6 + - + +
479 ALA 3.1 0.2 - - - -
489 PHE* 3.0 27.9 + - + +
499 CYS* 3.5 9.0 + - - -
579 LEU* 4.2 23.6 - - + -
619 ILE* 5.1 0.4 - - + +
629 LEU* 3.5 37.0 - - + -
659 PHE* 3.6 39.0 - - + -
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Residues in contact with ILE 46 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159 PHE* 3.5 36.1 - - + -
179 LEU* 3.9 23.3 - - + -
429 VAL* 3.0 24.7 + - + +
459 LEU* 1.3 74.9 - - + +
479 ALA* 1.3 56.7 + - - +
489 PHE 3.1 5.4 - - - -
499 CYS* 3.3 22.9 + - + +
509 THR* 3.2 17.0 + - - +
617I PHE* 3.2 22.8 - - + -
620I ALA* 3.6 15.9 - - + -
621I MET* 3.5 9.0 - - + -
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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