Contacts of the helix formed by residues 550 - 558 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396L CYS 3.6 1.6 + - - -
397L LEU 2.8 32.3 + - - +
398L LEU* 4.0 6.4 - - - +
399L PRO* 4.8 7.1 - - - +
430L SER 5.4 0.6 + - - -
548L ARG* 2.7 37.1 + - + +
549L PRO* 1.3 74.1 - - - +
551L ASP* 1.3 63.2 + - - +
552L TYR* 3.0 44.9 + - + +
553L LEU* 3.6 28.5 + - + +
554L LYS* 3.6 15.6 + - - +
11W GLU* 5.5 4.9 + - - -
39W GLU* 4.0 19.7 - - + +
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Residues in contact with ASP 551 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549L PRO 4.7 5.7 - - - +
550L LYS* 1.3 70.1 - - - +
552L TYR* 1.3 59.6 + - - +
553L LEU 3.0 4.9 - - - -
554L LYS* 2.8 29.8 + - - +
555L HIS* 3.0 34.5 + - + +
37W ASN* 3.1 31.0 + - - +
39W GLU* 4.5 7.7 + - + +
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Residues in contact with TYR 552 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396L CYS* 2.7 25.9 + - + +
550L LYS* 3.0 31.4 + - + +
551L ASP* 1.3 77.4 - - - +
553L LEU* 1.3 73.9 + - + +
555L HIS* 4.2 8.3 - - - -
556L CYS* 3.1 26.8 + - - +
619L VAL* 3.1 44.0 - - + +
620L ALA* 3.8 19.3 - - - +
621L MET 4.8 1.8 - - - +
622L GLY* 3.9 6.6 - - - -
11W GLU* 5.0 10.5 + - - -
39W GLU* 3.3 50.0 - - + +
40W GLY* 5.8 2.0 - - - -
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Residues in contact with LEU 553 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393L TRP* 3.2 49.2 + - + +
396L CYS 3.4 22.4 - - - +
397L LEU* 3.6 26.5 - - + -
430L SER 4.5 6.1 - - - +
548L ARG 4.9 0.4 - - - +
550L LYS* 3.6 40.5 + - + +
551L ASP 3.0 0.4 - - - -
552L TYR* 1.3 93.2 - - + +
554L LYS* 1.3 66.7 + - - +
556L CYS* 3.2 14.5 - - - +
557L LEU* 3.2 10.1 + - - +
619L VAL* 4.1 2.7 - - + -
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Residues in contact with LYS 554 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550L LYS 3.6 7.2 + - - +
551L ASP* 2.8 18.4 + - - +
553L LEU* 1.3 75.7 - - - +
555L HIS* 1.3 82.6 + - + +
556L CYS 3.1 0.9 + - - -
557L LEU* 3.2 16.0 + - - +
558L GLU* 3.1 34.0 + - + +
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Residues in contact with HIS 555 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551L ASP* 3.0 40.2 + - + +
552L TYR* 4.1 3.8 - - - -
554L LYS* 1.3 94.5 - - + +
556L CYS* 1.3 61.6 + - - +
558L GLU* 2.9 44.4 + - - +
559L ARG* 3.3 8.5 + - - +
621L MET 5.5 1.6 - - - -
622L GLY* 2.8 36.9 - - - +
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Residues in contact with CYS 556 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393L TRP* 3.4 22.7 - - + -
552L TYR 3.1 21.0 + - - +
553L LEU* 3.2 9.4 - - - +
554L LYS 3.0 0.2 - - - -
555L HIS* 1.3 78.1 - - - +
557L LEU* 1.3 62.2 - - - +
559L ARG* 3.2 8.7 + - - -
560L SER* 3.1 22.1 + - - -
563L LEU* 5.3 0.2 - - - -
619L VAL* 4.0 12.6 - - + -
622L GLY 4.2 1.8 - - - -
623L ILE 3.8 19.4 - - - +
625L VAL* 3.4 32.8 - - - -
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Residues in contact with LEU 557 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K LYS* 6.5 0.4 - - - -
393L TRP* 3.7 37.0 - - + +
553L LEU 3.2 10.7 + - - +
554L LYS* 3.2 9.7 + - - +
556L CYS* 1.3 74.1 - - - +
558L GLU* 1.3 56.4 + - + +
559L ARG 3.0 5.3 + - - -
560L SER* 3.2 12.3 + - - +
561L GLU* 2.8 21.5 - - - +
563L LEU* 3.6 38.8 - - + -
564L LEU* 4.1 37.1 - - + +
569L ILE* 4.3 6.5 - - + -
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Residues in contact with GLU 558 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554L LYS* 3.1 31.8 + - + +
555L HIS* 2.9 42.6 + - - +
556L CYS 3.1 0.8 - - - -
557L LEU* 1.3 77.2 - - - +
559L ARG* 1.3 70.8 + - - +
561L 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