Contacts of the helix formed by residues 550 - 558 (chain I) 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 LYS 550 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119 GLU* 4.0 12.9 + - - +
149 ILE* 4.4 8.1 - - - +
399 GLU* 4.8 11.4 - - + -
396I CYS 3.6 1.4 + - - -
397I LEU 2.8 32.4 + - - +
398I LEU* 4.0 6.6 - - - +
399I PRO* 4.7 5.7 - - - +
430I SER* 5.4 0.6 + - - +
548I ARG* 2.7 36.9 + - + +
549I PRO* 1.3 73.7 - - - +
551I ASP* 1.3 63.9 + - - +
552I TYR* 3.0 44.0 + - + +
553I LEU* 3.6 28.1 + - + +
554I LYS* 3.6 15.6 + - - +
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Residues in contact with ASP 551 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379 ASN* 5.4 4.9 + - - +
399 GLU* 3.4 35.2 - - + +
409 GLY* 5.3 1.2 + - - -
549I PRO 4.7 4.3 - - - +
550I LYS* 1.3 69.1 - - - +
552I TYR* 1.3 62.5 + - - +
553I LEU 3.0 4.7 - - - -
554I LYS* 2.8 29.8 + - - +
555I HIS* 3.0 33.9 + - + +
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Residues in contact with TYR 552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119 GLU* 3.0 32.8 + - - -
149 ILE* 3.9 5.4 - - + +
159 PHE* 4.9 4.7 - + - -
399 GLU* 4.4 22.3 + - + +
396I CYS* 2.7 24.1 + - + +
550I LYS* 3.0 40.3 + - + +
551I ASP* 1.3 78.4 - - - +
553I LEU* 1.3 74.2 + - + +
555I HIS* 4.1 8.5 - - - -
556I CYS* 3.1 26.8 + - - +
619I VAL* 3.1 44.4 - - + +
620I ALA* 3.8 17.0 - - - +
621I MET 4.8 1.8 - - - +
622I GLY* 3.9 6.9 - - - -
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Residues in contact with LEU 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I TRP* 3.2 48.5 + - + +
396I CYS 3.4 24.0 - - - +
397I LEU* 3.6 26.9 - - + -
430I SER 4.5 5.2 - - - +
548I ARG 4.9 0.7 - - - +
550I LYS* 3.6 39.9 - - + +
551I ASP 2.9 0.8 + - - -
552I TYR* 1.3 94.1 - - + +
554I LYS* 1.3 65.8 + - - +
556I CYS* 3.2 14.5 - - - +
557I LEU* 3.2 9.9 + - - +
619I VAL* 4.1 2.9 - - + -
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Residues in contact with LYS 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550I LYS 3.6 7.0 + - - +
551I ASP* 2.8 18.4 + - - +
553I LEU* 1.3 76.1 - - - +
555I HIS* 1.3 83.6 + - + +
556I CYS 3.0 2.6 + - - -
557I LEU* 3.2 16.0 + - - +
558I GLU* 3.1 34.7 + - + +
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Residues in contact with HIS 555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551I ASP* 3.0 39.4 + - + +
552I TYR* 4.1 3.6 - - - -
554I LYS* 1.3 94.0 - - + +
556I CYS* 1.3 62.2 + - - +
558I GLU* 2.9 44.6 + - - +
559I ARG* 3.3 8.7 + - - +
621I MET 5.6 1.6 - - - -
622I GLY* 2.8 36.4 - - - +
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Residues in contact with CYS 556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I TRP* 3.4 21.5 - - + -
552I TYR 3.1 22.9 + - - +
553I LEU* 3.2 9.2 - - - +
554I LYS 3.0 0.2 - - - -
555I HIS* 1.3 78.7 - - - +
557I LEU* 1.3 61.4 + - - +
559I ARG* 3.2 9.4 + - - -
560I SER* 3.2 20.9 + - - -
563I LEU* 5.3 0.2 - - - -
619I VAL* 4.0 12.6 - - - -
622I GLY 3.8 1.5 + - - -
623I ILE 3.8 19.5 - - - +
625I VAL* 3.4 33.9 - - - -
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Residues in contact with LEU 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I TRP* 3.7 37.0 - - + +
553I LEU 3.2 11.0 + - - +
554I LYS* 3.2 8.8 + - - +
556I CYS* 1.3 75.6 - - - +
558I GLU* 1.3 56.7 + - - +
559I ARG 3.0 5.8 - - - -
560I SER* 3.2 11.8 + - - +
561I GLU* 2.8 21.0 + - - +
563I LEU* 3.6 38.6 - - + -
564I LEU* 4.1 36.4 - - + +
569I ILE* 4.3 7.2 - - + -
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Residues in contact with GLU 558 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554I LYS* 3.1 32.5 + - + +
555I HIS* 2.9 42.8 + - - +
556I CYS 3.1 0.6 - - - -
557I LEU* 1.3 77.4 - - - +
559I ARG* 1.3 71.1 + - + +
561I GLU* 3.3 14.9 - - - +
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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
------------------------------------------------------------
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