Contacts of the helix formed by residues 37 - 46 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315 CYS* 5.2 0.7 - - - -
355 GLY 3.2 10.9 + - - +
365 GLN* 1.3 75.9 + - - +
385 GLU* 1.3 75.5 + - - +
395 GLU* 3.0 17.9 + - + +
405 GLY* 3.0 6.6 + - - +
415 MET* 2.9 21.7 + - - +
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Residues in contact with GLU 38 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35 ALA* 2.6 40.8 - - + +
75 GLN* 3.6 33.8 - - + +
85 LEU* 3.7 41.1 - - + +
115 GLU* 4.2 3.8 - - + +
315 CYS* 4.5 3.4 - - - +
365 GLN 3.8 0.2 + - - -
375 ASN* 1.3 79.1 - - - +
395 GLU* 1.3 72.7 + - - +
415 MET* 4.1 0.7 - - - -
425 VAL* 3.1 32.2 + - - +
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Residues in contact with GLU 39 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75 GLN* 5.4 2.3 - - - +
115 GLU* 5.1 16.7 - - + +
375 ASN* 3.0 12.4 + - + +
385 GLU* 1.3 97.7 - - + +
405 GLY* 1.3 61.2 + - - +
415 MET 3.4 0.2 - - - -
425 VAL* 4.6 1.7 - - - +
435 GLY* 3.6 14.2 + - - -
550E LYS* 6.1 3.4 - - + -
551E ASP* 3.8 30.7 - - + +
552E TYR* 5.5 14.8 - - + +
620E ALA 5.3 0.9 - - - +
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Residues in contact with GLY 40 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 GLN* 4.3 13.7 - - - -
375 ASN* 3.0 10.7 + - - +
395 GLU* 1.3 78.1 - - - +
415 MET* 1.3 61.6 + - - +
435 GLY* 3.5 2.0 + - - -
445 GLU* 3.1 34.7 + - - +
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Residues in contact with MET 41 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 LEU* 4.5 7.4 - - + -
275 LEU* 4.6 7.4 - - + +
305 LEU* 3.4 44.4 - - + +
315 CYS* 3.9 17.5 - - - -
345 TYR* 5.7 0.2 - - + -
365 GLN* 3.6 43.9 - - + +
375 ASN 2.9 11.9 + - - +
385 GLU 4.3 3.8 - - - +
405 GLY* 1.3 75.5 - - - +
425 VAL* 1.3 61.6 + - + +
445 GLU* 3.2 8.3 + - + +
455 LEU* 2.8 32.3 + - - +
655 PHE* 3.7 23.6 - - + -
705 LEU* 4.3 9.4 - - + -
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Residues in contact with VAL 42 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 LEU* 3.9 26.7 - - + +
115 GLU* 3.5 40.2 - - + +
125 LEU* 4.7 4.0 - - + -
155 PHE* 4.0 9.6 - - + -
175 LEU* 4.5 7.0 - - + -
275 LEU* 6.5 0.4 - - - -
385 GLU 3.1 20.3 + - - +
395 GLU 4.7 2.5 - - - +
405 GLY 3.5 0.2 - - - -
415 MET* 1.3 75.3 - - - +
435 GLY* 1.3 59.2 + - - +
455 LEU* 4.2 5.8 - - + -
465 ILE* 3.0 51.9 + - + +
620E ALA* 5.6 0.4 - - + -
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Residues in contact with GLY 43 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395 GLU 3.6 10.3 + - - -
405 GLY* 3.5 6.0 + - - -
415 MET 3.1 1.0 - - - -
425 VAL* 1.3 80.8 - - - +
445 GLU* 1.3 64.1 + - - +
455 LEU 3.8 0.2 + - - -
620E ALA* 3.4 25.1 - - - -
621E MET* 3.0 37.0 - - - +
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Residues in contact with GLU 44 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365 GLN* 4.8 9.2 - - + +
405 GLY* 3.1 18.9 + - - +
415 MET* 3.9 6.7 - - + +
435 GLY* 1.3 79.5 - - - +
455 LEU* 1.3 65.6 + - - +
475 ALA* 3.3 19.6 + - - +
485 PHE 3.6 1.4 + - - -
655 PHE* 3.3 28.3 - - + -
695 PHE* 3.1 34.0 - - + -
705 LEU* 5.2 0.9 - - + -
735 ARG* 5.0 1.1 + - - -
621E MET* 5.3 4.2 - - - +
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Residues in contact with LEU 45 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125 LEU* 6.3 2.0 - - + -
175 LEU* 5.7 2.2 - - + -
275 LEU* 4.1 12.8 - - + -
305 LEU* 5.0 0.2 - - + -
415 MET 2.8 18.3 + - - +
425 VAL* 3.9 8.7 - - + +
445 GLU* 1.3 78.6 - - - +
465 ILE* 1.3 63.6 + - + +
475 ALA 3.1 0.2 - - - -
485 PHE* 3.0 28.0 + - + +
495 CYS* 3.5 8.7 + - - -
575 LEU* 4.2 23.3 - - + -
615 ILE* 5.1 0.4 - - + +
625 LEU* 3.5 36.6 - - + -
655 PHE* 3.6 40.6 - - + -
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Residues in contact with ILE 46 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155 PHE* 3.5 36.3 - - + -
175 LEU* 3.9 24.0 - - + -
425 VAL* 3.0 24.3 + - + +
455 LEU* 1.3 75.3 - - + +
475 ALA* 1.3 59.2 + - - +
485 PHE 3.1 5.4 - - - -
495 CYS* 3.3 22.1 + - + +
505 THR* 3.2 7.3 + - - -
617E PHE* 3.0 34.1 - - + -
620E ALA* 3.6 15.7 - - + -
621E MET* 3.8 8.1 - - + -
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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