Contacts of the helix formed by residues 550 - 558 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113 GLU* 4.6 11.0 - - - +
143 ILE* 4.2 11.3 - - - +
393 GLU* 6.0 6.7 - - + -
396C CYS 3.6 1.0 + - - -
397C LEU 2.8 32.3 + - - -
398C LEU* 4.0 6.6 - - - +
399C PRO* 4.8 4.9 - - - +
430C SER 5.4 0.4 + - - -
548C ARG* 2.7 37.0 + - + +
549C PRO* 1.3 73.8 - - - +
551C ASP* 1.3 64.3 + - - +
552C TYR* 3.0 46.1 + - + +
553C LEU* 3.6 28.0 + - + +
554C LYS* 3.6 15.6 + - - +
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Residues in contact with ASP 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393 GLU* 4.2 28.8 - - + +
549C PRO 4.7 5.9 - - - +
550C LYS* 1.3 69.8 - - - +
552C TYR* 1.3 61.9 + - - +
553C LEU 3.0 4.7 - - - -
554C LYS* 2.8 29.8 + - + +
555C HIS* 3.0 34.0 + - + +
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Residues in contact with TYR 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113 GLU* 3.5 24.2 - - - -
143 ILE* 4.1 10.0 - - - +
153 PHE* 4.7 8.7 - + - -
393 GLU* 5.3 16.8 - - + +
396C CYS* 2.7 24.9 + - + +
550C LYS* 3.0 41.2 + - + +
551C ASP* 1.3 80.1 - - - +
553C LEU* 1.3 74.2 + - + +
555C HIS* 4.1 8.3 - - - -
556C CYS* 3.1 26.4 + - - +
619C VAL* 3.1 44.8 - - + +
620C ALA* 3.8 17.0 - - - +
621C MET 4.8 1.6 - - - +
622C GLY* 3.9 7.6 - - - -
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Residues in contact with LEU 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C TRP* 3.2 50.2 + - + +
396C CYS 3.4 23.1 - - - +
397C LEU* 3.6 26.9 - - + -
430C SER 4.5 5.6 - - - +
550C LYS* 3.6 39.2 + - + +
551C ASP 3.0 0.8 - - - -
552C TYR* 1.3 94.4 - - + +
554C LYS* 1.3 65.5 + - - +
556C CYS* 3.2 14.4 - - - +
557C LEU* 3.2 9.9 + - - +
619C VAL* 4.1 2.9 - - + -
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Residues in contact with LYS 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C LYS 3.6 6.5 + - - +
551C ASP* 2.8 19.1 + - - +
553C LEU* 1.3 75.9 - - - +
555C HIS* 1.3 82.4 + - + +
556C CYS 3.1 1.0 + - - -
557C LEU* 3.2 16.7 + - - +
558C GLU* 3.1 35.6 + - + +
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Residues in contact with HIS 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C ASP* 3.0 40.0 + - + +
552C TYR* 4.1 3.1 - - - -
554C LYS* 1.3 93.8 - - + +
556C CYS* 1.3 61.6 + - - +
558C GLU* 2.9 45.0 + - - +
559C ARG* 3.3 8.5 + - - +
621C MET 5.6 1.3 - - - -
622C GLY* 2.9 36.7 - - - +
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Residues in contact with CYS 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C TRP* 3.4 21.8 - - + -
552C TYR 3.1 20.7 + - - +
553C LEU 3.2 9.4 - - - +
554C LYS 3.0 0.4 - - - -
555C HIS* 1.3 78.2 - - - +
557C LEU* 1.3 62.2 + - - +
558C GLU 3.1 0.2 - - - -
559C ARG* 3.2 9.2 + - - -
560C SER* 3.1 21.8 + - - -
563C LEU* 5.3 0.2 - - - -
619C VAL* 4.0 13.7 - - + +
622C GLY 3.8 1.5 + - - -
623C ILE 3.8 19.1 - - - +
625C VAL* 3.4 33.7 - - - -
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Residues in contact with LEU 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LYS* 6.5 0.2 - - - -
393C TRP* 3.7 36.8 - - + +
553C LEU 3.2 10.1 + - - +
554C LYS* 3.2 9.9 + - - +
556C CYS* 1.3 74.6 - - - +
558C GLU* 1.3 56.4 + - - +
559C ARG 3.0 6.5 + - - -
560C SER* 3.2 12.6 + - - +
561C GLU* 2.8 21.1 - - - +
563C LEU* 3.6 39.0 - - + -
564C LEU* 4.1 36.6 - - + +
569C ILE* 4.3 7.0 - - + -
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Residues in contact with GLU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C LYS* 3.1 32.6 + - + +
555C HIS* 2.9 42.9 + - - +
556C CYS 3.1 1.0 - - - -
557C LEU* 1.3 76.7 - - - +
559C ARG* 1.3 70.2 + - - +
561C GLU* 3.3 13.7 - - - +
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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