Contacts of the helix formed by residues 550 - 558 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101 GLU* 6.1 2.3 - - - +
111 GLU* 4.1 10.9 + - - -
141 ILE* 4.5 5.5 - - - +
391 GLU* 4.9 12.8 - - + -
396A CYS 3.6 1.4 + - - -
397A LEU 2.8 31.5 + - - -
398A LEU* 4.0 7.2 - - - +
399A PRO* 4.8 5.9 - - - +
430A SER* 5.4 0.6 + - - +
548A ARG* 2.7 37.2 + - + +
549A PRO* 1.3 73.0 - - - +
551A ASP* 1.3 62.8 + - - +
552A TYR* 3.0 44.3 + - + +
553A LEU* 3.6 28.2 + - + +
554A LYS* 3.6 15.4 + - - +
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Residues in contact with ASP 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 ASN* 5.7 2.6 + - - +
391 GLU* 3.7 27.2 - - + +
549A PRO 4.7 5.2 - - - +
550A LYS* 1.3 70.4 - - - +
552A TYR* 1.3 60.9 + - - +
553A LEU 3.0 4.9 - - - -
554A LYS* 2.8 28.9 + - - +
555A HIS* 3.0 33.9 + - + +
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Residues in contact with TYR 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111 GLU* 3.1 37.6 + - - -
141 ILE* 3.8 4.9 - - + +
151 PHE* 5.0 2.9 - + - -
391 GLU* 4.4 24.8 - - + +
396A CYS* 2.7 24.9 + - + -
550A LYS* 3.0 36.6 + - + +
551A ASP* 1.3 78.1 - - - +
553A LEU* 1.3 74.5 + - + +
555A HIS* 4.1 8.5 - - - -
556A CYS* 3.1 27.0 + - - +
619A VAL* 3.1 44.4 - - + +
620A ALA* 3.8 16.8 - - - +
621A MET 4.8 1.3 - - - +
622A GLY* 3.9 6.8 - - - -
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A TRP* 3.2 48.9 + - + +
396A CYS 3.4 23.3 - - - +
397A LEU* 3.6 27.1 - - + -
430A SER 4.5 6.1 - - - +
548A ARG 4.9 0.2 - - - +
550A LYS* 3.6 39.2 + - + +
551A ASP 3.0 0.4 - - - -
552A TYR* 1.3 93.8 - - + +
554A LYS* 1.3 66.0 + - - +
556A CYS* 3.2 15.1 - - - +
557A LEU* 3.2 9.8 + - - +
619A VAL* 4.1 3.1 - - + -
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LYS 3.6 6.6 + - - +
551A ASP* 2.8 17.8 + - - +
553A LEU* 1.3 77.2 - - - +
555A HIS* 1.3 81.8 + - + +
556A CYS 3.1 0.7 + - - -
557A LEU* 3.2 16.4 + - - +
558A GLU* 3.1 35.7 + - + +
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Residues in contact with HIS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A ASP* 3.0 39.3 + - + +
552A TYR* 4.1 4.0 - - - -
554A LYS* 1.3 95.6 - - + +
556A CYS* 1.3 62.2 + - - +
558A GLU* 2.9 44.0 + - - +
559A ARG* 3.3 8.8 + - - +
621A MET 5.6 1.3 - - - -
622A GLY* 2.9 35.7 - - - +
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Residues in contact with CYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A TRP* 3.4 21.5 - - + -
552A TYR 3.1 22.5 + - - +
553A LEU* 3.2 9.4 - - - +
554A LYS 3.0 0.2 - - - -
555A HIS* 1.3 77.1 - - - +
557A LEU* 1.3 62.1 + - - +
558A GLU 3.1 0.2 - - - -
559A ARG* 3.2 9.4 + - - -
560A SER* 3.1 21.6 + - - -
563A LEU* 5.3 0.4 - - - -
619A VAL* 4.0 13.5 - - + -
622A GLY 4.2 1.6 - - - -
623A ILE 3.8 19.3 - - - +
625A VAL* 3.4 33.2 - - - -
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A TRP* 3.7 36.1 - - + +
553A LEU 3.2 11.4 + - - +
554A LYS* 3.2 9.0 + - - +
556A CYS* 1.3 74.5 - - - +
558A GLU* 1.3 56.4 + - - +
559A ARG 3.0 6.0 + - - -
560A SER* 3.2 12.1 + - - +
561A GLU* 2.8 21.3 - - - +
563A LEU* 3.7 38.8 - - + -
564A LEU* 4.1 38.0 - - + +
569A ILE* 4.3 6.5 - - + -
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A LYS* 3.1 31.7 - - + +
555A HIS* 2.9 42.4 + - - +
556A CYS 3.1 0.8 - - - -
557A LEU* 1.3 77.8 - - - +
559A ARG* 1.3 71.1 + - - +
561A 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