Contacts of the helix formed by residues 552 - 565 (chain B) in PDB entry 3E0D
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 ASP 552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513B ILE* 5.8 0.2 - - - +
548B GLU 4.2 1.2 + - - -
549B MET 2.8 23.0 + - - +
551B LYS* 1.3 80.4 - - + +
553B GLU* 1.3 70.3 + - - +
554B ARG* 3.3 30.6 + - - +
555B ILE* 3.6 30.6 + - + +
556B ARG* 3.4 10.1 + - - -
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Residues in contact with GLU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B GLU 6.1 0.2 - - - +
551B LYS 4.0 2.3 + - - +
552B ASP* 1.3 75.3 + - - +
554B ARG* 1.3 64.9 + - - +
556B ARG* 3.2 49.8 + - - +
557B GLN* 3.6 10.4 + - - +
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Residues in contact with ARG 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B THR* 5.0 4.4 - - - +
236B LEU* 5.4 5.8 - - - +
237B ASP* 4.4 16.0 + - - -
511B TYR* 2.8 58.2 + - - +
513B ILE* 4.9 10.1 - - + -
552B ASP* 3.3 22.7 + - - +
553B GLU* 1.3 79.7 - - - +
555B ILE* 1.3 62.7 + - + +
557B GLN* 3.4 9.1 + - - +
558B VAL* 3.4 23.6 + - - +
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Residues in contact with ILE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ILE* 4.5 15.0 - - + -
521B LEU* 4.0 30.3 - - + -
548B GLU* 3.7 28.0 - - + +
549B MET* 4.9 5.6 - - - -
552B ASP* 3.6 32.9 + - + +
553B GLU 3.3 0.6 - - - -
554B ARG* 1.3 73.2 - - - +
556B ARG* 1.3 65.2 + - - +
557B GLN 3.3 0.2 - - - -
558B VAL* 3.8 12.6 - - + -
559B ILE* 3.1 44.7 + - + +
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Residues in contact with ARG 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B MET* 3.2 43.5 + - + +
550B GLU* 4.0 23.2 + - - +
552B ASP 3.4 6.3 + - - +
553B GLU* 3.2 41.8 + - - +
555B ILE* 1.3 80.3 - - - +
557B GLN* 1.3 66.2 + - + +
560B GLU* 3.3 33.6 + - - +
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Residues in contact with GLN 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 4.4 16.1 + - - +
236B LEU* 5.3 3.2 - - - +
511B TYR* 3.3 37.4 + - + +
553B GLU 3.6 8.8 + - - +
554B ARG* 3.4 9.5 + - - +
555B ILE 3.3 0.2 - - - -
556B ARG* 1.3 77.5 - - + +
558B VAL* 1.3 67.3 + - - +
560B GLU* 2.8 11.8 + - - +
561B VAL* 2.7 33.2 + - + +
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Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 3.8 20.6 - - + -
507B VAL* 3.7 21.4 - - + +
508B ALA* 4.1 17.9 - - + +
511B TYR* 3.7 26.2 - - + -
513B ILE* 3.8 23.3 - - + -
521B LEU* 6.1 2.5 - - + -
554B ARG 3.4 15.2 + - - +
555B ILE* 3.5 14.3 + - + +
557B GLN* 1.3 77.0 - - - +
559B ILE* 1.3 57.6 + - + +
561B VAL* 4.6 0.2 - - - -
562B ALA* 3.0 29.5 + - - +
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B LEU* 4.2 19.3 - - + -
521B LEU* 4.4 6.3 - - + -
535B LEU* 3.4 6.9 - - + +
539B PHE* 2.5 50.3 - - + -
545B LEU* 3.9 22.9 - - + -
548B GLU* 5.2 1.1 - - + -
549B MET* 3.4 35.2 - - + +
555B ILE* 3.1 30.4 + - + +
557B GLN 2.9 3.8 + - - -
558B VAL* 1.3 71.8 - - - +
560B GLU* 1.3 63.8 + - - +
562B ALA 3.5 0.2 + - - -
563B MET* 3.3 25.0 + - + +
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B MET* 3.5 20.0 - - + +
556B ARG* 3.3 24.7 + - - +
557B GLN* 2.8 14.4 + - - +
559B ILE* 1.3 73.7 - - + +
561B VAL* 1.3 61.2 + - + +
563B MET* 3.0 32.3 - - + +
564B ARG* 3.1 10.9 + - - +
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Residues in contact with VAL 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ALA* 5.8 3.1 - - + -
226B VAL* 4.1 27.1 - - + -
507B VAL* 4.2 13.9 - - + -
511B TYR* 3.9 20.2 - - + +
557B GLN* 2.7 35.0 + - + +
558B VAL 3.9 3.1 - - - +
560B GLU* 1.3 74.2 - - + +
562B ALA* 1.3 57.3 + - - +
564B ARG* 3.0 11.4 + - + +
565B LEU* 3.0 36.4 + - + +
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Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B ALA* 3.8 12.1 - - + +
504B LEU* 4.0 32.3 - - + +
507B VAL* 4.1 10.1 - - + +
535B LEU* 3.3 22.1 - - + +
558B VAL 3.0 19.2 + - - +
559B ILE 3.9 0.4 - - - +
560B GLU 3.3 0.2 - - - -
561B VAL* 1.3 76.2 - - - +
563B MET* 1.3 56.3 + - - +
565B LEU* 3.5 3.0 + - - +
566B GLU* 3.2 24.6 + - - +
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Residues in contact with MET 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 5.8 0.5 + - - -
535B LEU* 3.1 48.9 - - + +
536B GLN* 4.5 17.9 - - + +
539B PHE* 3.5 27.4 - - + -
559B ILE* 3.4 17.0 - - + +
560B GLU* 3.0 31.6 - - + +
562B ALA* 1.3 75.1 - - - +
564B ARG* 1.3 62.0 + - - +
565B LEU 3.2 0.7 - - - -
566B GLU* 3.8 17.3 + - + +
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Residues in contact with ARG 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 4.2 12.2 + - - -
217B ARG* 5.2 10.3 - - - +
219B GLU* 5.9 4.0 - - - +
220B ASP* 4.9 10.9 + - - -
223B ALA* 4.9 16.1 - - + +
560B GLU 3.1 12.4 + - - +
561B VAL* 3.0 16.5 + - + +
563B MET* 1.3 78.4 - - - +
565B LEU* 1.3 64.5 + - + +
566B GLU 3.5 0.4 - - - -
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 4.4 2.7 - - - +
223B ALA* 3.9 34.8 - - + +
226B VAL* 3.9 18.4 - - + -
227B LEU* 5.4 5.2 - - + +
230B ILE* 4.2 14.1 - - + -
498B LEU* 3.2 27.5 - - + +
503B ALA* 5.5 0.4 - - + -
507B VAL* 3.8 27.1 - - + -
561B VAL* 3.0 17.5 + - + +
562B ALA* 3.5 5.6 + - - +
563B MET 3.2 0.2 - - - -
564B ARG* 1.3 81.7 - - + +
566B GLU* 1.3 62.1 + - - +
567B GLY 3.5 2.4 + - - -
568B LEU* 3.8 26.5 - - + +
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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