Contacts of the helix formed by residues 550 - 558 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116 GLU* 3.3 22.1 + - - +
146 ILE* 3.6 9.5 - - - +
396 GLU* 5.0 13.9 - - + -
396F CYS 3.6 0.6 + - - -
397F LEU 2.8 32.5 + - - +
398F LEU* 4.0 4.3 - - - +
399F PRO* 4.7 4.0 - - - +
430F SER 5.4 0.4 + - - -
548F ARG* 2.7 35.3 + - + +
549F PRO* 1.3 73.8 - - - +
551F ASP* 1.3 63.3 + - - +
552F TYR* 3.0 44.0 + - + +
553F LEU* 3.6 26.6 + - + +
554F LYS* 3.6 15.9 + - - +
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Residues in contact with ASP 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396 GLU* 5.1 17.3 + - - +
406 GLY* 5.3 3.8 - - - -
549F PRO 4.7 5.7 - - - +
550F LYS* 1.3 69.8 - - - +
552F TYR* 1.3 61.3 + - + +
553F LEU 3.0 4.5 - - - -
554F LYS* 2.8 28.6 + - - +
555F HIS* 3.0 34.1 + - + +
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Residues in contact with TYR 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116 GLU* 3.1 26.6 + - - -
146 ILE* 3.8 6.2 - - - +
156 PHE* 3.7 20.3 - + - -
396 GLU* 5.0 12.8 - - + -
426 VAL* 6.4 0.2 - - + -
436 GLY* 5.5 8.7 - - - -
396F CYS 2.7 20.7 + - - -
550F LYS* 3.0 36.0 + - + +
551F ASP* 1.3 79.2 - - - +
553F LEU* 1.3 73.6 - - + +
555F HIS* 4.2 7.9 - - - -
556F CYS* 3.1 27.2 + - - +
619F VAL* 3.1 41.3 - - + +
620F ALA* 3.8 15.7 - - - +
621F MET 4.8 1.1 - - - +
622F GLY* 3.9 7.2 - - - -
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Residues in contact with LEU 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F TRP* 3.2 49.0 + - + +
396F CYS 3.4 23.6 - - - +
397F LEU* 3.6 27.1 - - + -
430F SER 4.5 5.8 - - - +
548F ARG 4.9 0.2 - - - +
550F LYS* 3.6 39.9 + - + +
551F ASP 3.0 0.4 - - - -
552F TYR* 1.3 92.8 - - + +
554F LYS* 1.3 66.5 + - - +
556F CYS* 3.2 14.9 - - - +
557F LEU* 3.2 9.6 + - - +
619F VAL* 4.1 2.7 - - + -
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Residues in contact with LYS 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550F LYS 3.6 6.6 + - - +
551F ASP* 2.8 18.6 + - - +
553F LEU* 1.3 76.6 - - - +
555F HIS* 1.3 82.5 + - + +
556F CYS 3.1 1.0 + - - -
557F LEU* 3.2 16.3 + - - +
558F GLU* 3.1 35.8 + - + +
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Residues in contact with HIS 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551F ASP* 3.0 40.1 + - + +
552F TYR* 4.1 3.6 - - - -
554F LYS* 1.3 92.4 - - + +
556F CYS* 1.3 62.5 + - - +
558F GLU* 2.9 45.2 + - - +
559F ARG* 3.3 8.8 + - - +
621F MET 5.6 1.8 - - - -
622F GLY* 2.8 36.8 - - - +
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Residues in contact with CYS 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F TRP* 3.4 22.9 - - + -
552F TYR 3.1 22.5 + - - +
553F LEU* 3.2 8.5 - - - +
554F LYS 3.0 0.4 - - - -
555F HIS* 1.3 78.0 - - - +
557F LEU* 1.3 62.5 + - - +
558F GLU 3.1 0.2 - - - -
559F ARG* 3.2 8.8 + - - -
560F SER* 3.1 21.2 + - - -
563F LEU* 5.3 0.2 - - - -
619F VAL* 4.0 12.1 - - + -
622F GLY 4.2 1.3 - - - -
623F ILE 3.8 19.4 - - - +
625F VAL* 3.4 32.8 - - - -
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Residues in contact with LEU 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E LYS* 6.2 1.8 - - - -
393F TRP* 3.7 36.1 - - + +
553F LEU 3.2 10.7 + - - +
554F LYS* 3.2 9.9 + - - +
556F CYS* 1.3 74.7 - - - +
558F GLU* 1.3 56.4 + - - +
559F ARG 3.0 5.6 - - - -
560F SER* 3.2 11.2 + - - +
561F GLU* 2.8 21.3 + - - +
563F LEU* 3.6 38.8 - - + -
564F LEU* 4.1 37.0 - - + +
569F ILE* 4.3 6.5 - - + -
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Residues in contact with GLU 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F LYS* 3.1 32.7 - - + +
555F HIS* 2.9 41.5 + - - +
556F CYS 3.1 0.4 - - - -
557F LEU* 1.3 77.4 - - - +
559F ARG* 1.3 71.5 + - - +
561F GLU* 3.3 14.1 - - - +
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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