Contacts of the helix formed by residues 557 - 573 (chain B) in PDB entry 2N5T
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 THR 557 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A VAL* 4.1 11.8 - - - +
397A GLU* 2.7 33.2 + - + +
400A ARG* 4.4 10.4 + - - +
479B PRO* 4.0 5.1 - - - +
555B GLN* 3.2 3.7 + - - +
556B PRO* 1.3 89.6 + - - +
558B THR* 1.3 65.2 + - - +
559B ASP* 3.8 20.4 - - + +
560B GLU* 3.3 27.8 + - + +
561B LEU* 3.2 21.3 + - - +
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Residues in contact with THR 558 (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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397A GLU* 2.7 16.9 + - - -
475B GLN* 4.7 18.6 - - + +
477B MET* 3.1 29.0 + - + +
478B SER* 3.8 6.8 + - - -
479B PRO* 3.7 12.7 - - - +
557B THR* 1.3 67.4 - - - +
559B ASP* 1.3 72.1 + - - +
561B LEU* 2.8 13.5 + - + +
562B MET* 2.7 36.3 + - + +
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Residues in contact with ASP 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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397A GLU* 4.0 4.7 + - - +
557B THR* 3.3 14.2 - - + +
558B THR* 1.3 81.9 - - - +
560B GLU* 1.3 58.5 + - + +
562B MET* 3.1 11.1 + - - +
563B THR* 2.9 31.6 + - - +
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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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400A ARG* 5.0 7.4 + - - -
555B GLN* 3.3 27.9 + - - +
556B PRO* 3.2 27.5 - - - +
557B THR* 3.3 27.7 + - + +
558B THR 3.1 0.4 - - - -
559B ASP* 1.3 77.3 - - + +
561B LEU* 1.3 60.6 + - - +
563B THR* 3.4 19.7 - - - -
564B LEU* 3.5 15.4 + - - +
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Residues in contact with LEU 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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477B MET* 3.5 36.8 - - + +
479B PRO* 4.0 28.5 - - + -
482B LEU* 3.5 30.7 - - + -
514B LEU* 5.0 2.9 - - + -
552B ALA* 3.5 30.9 - - + +
555B GLN* 3.9 13.9 - - + +
557B THR 3.2 4.4 + - - +
558B THR* 2.8 15.6 + - + +
560B GLU* 1.3 76.3 - - - +
562B MET* 1.3 63.8 + - + +
563B THR 3.2 0.4 + - - -
564B LEU* 3.4 7.3 + - - +
565B VAL* 3.3 26.1 + - + +
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Residues in contact with MET 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B MET* 3.6 34.3 - - - +
510B ARG* 4.3 26.5 - - + +
558B THR* 2.7 35.0 + - + +
559B ASP* 3.4 13.2 - - - +
561B LEU* 1.3 74.3 - - + +
563B THR* 1.3 63.1 + - - +
565B VAL* 3.4 12.3 + - + +
566B ASN* 3.0 43.6 + - - +
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Residues in contact with THR 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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559B ASP 2.9 15.5 + - - -
560B GLU* 3.4 12.4 - - - -
561B LEU 3.2 0.2 - - - -
562B MET* 1.3 76.1 - - - +
564B LEU* 1.3 64.9 + - + +
566B ASN* 3.1 8.9 + - - +
567B LYS* 2.9 53.3 + - + +
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Residues in contact with LEU 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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548B LEU* 3.7 15.9 - - + +
551B GLN* 3.0 47.6 - - + +
552B ALA* 4.6 4.9 - - + +
555B GLN* 3.8 28.9 - - + +
560B GLU 3.5 21.2 + - - +
561B LEU* 3.4 8.0 + - - +
563B THR* 1.3 79.2 - - + +
565B VAL* 1.3 64.8 + - + +
567B LYS* 3.2 9.7 + - + +
568B PHE* 3.0 23.6 + - - +
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Residues in contact with VAL 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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477B MET* 5.0 3.6 - - + -
510B ARG* 4.0 22.0 - - + +
513B LEU* 4.9 7.0 - - + -
514B LEU* 3.9 39.0 - - + -
548B LEU* 3.8 10.3 - - + +
561B LEU 3.3 15.0 + - - +
562B MET* 3.5 17.0 - - + +
564B LEU* 1.3 78.6 - - + +
566B ASN* 1.3 67.0 + - - +
568B PHE* 3.1 6.1 - - - +
569B ILE* 3.0 39.4 + - + +
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Residues in contact with ASN 566 (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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562B MET* 3.0 35.5 + - - +
563B THR* 3.6 9.9 - - + +
565B VAL* 1.3 79.2 - - - +
567B LYS* 1.3 66.4 + - + +
568B PHE 3.0 2.0 - - - -
569B ILE* 3.1 13.9 + - - +
570B GLU* 3.0 32.5 + - + +
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Residues in contact with LYS 567 (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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563B THR* 2.9 42.6 + - + +
564B LEU* 3.9 10.3 - - + +
566B ASN* 1.3 73.4 - - + +
568B PHE* 1.3 61.4 + - - +
570B GLU* 3.4 22.2 - - - +
571B GLU* 3.0 30.0 + - - +
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Residues in contact with PHE 568 (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 LEU* 3.3 35.2 - - + -
540B THR* 4.4 8.7 - - + -
541B ASN 5.6 0.4 - - - -
544B ASP* 3.5 45.8 - - + -
545B ALA* 3.7 12.6 - - - -
548B LEU* 3.7 26.5 - - + -
564B LEU 3.0 12.2 + - - +
565B VAL* 3.1 12.3 - - - +
567B LYS* 1.3 77.3 - - - +
569B ILE* 1.3 56.0 + - - +
571B GLU* 2.9 2.3 + - - -
572B LYS* 2.7 69.1 + - + +
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Residues in contact with ILE 569 (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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509B GLU 5.5 6.1 - - - +
510B ARG* 6.1 1.1 - - - -
513B LEU* 4.1 17.0 - - + -
565B VAL* 3.0 30.6 + - + +
566B ASN* 3.6 15.0 - - - +
568B PHE* 1.3 81.2 - - - +
570B GLU* 1.3 63.6 + - + +
573B THR* 3.5 27.7 + - - +
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Residues in contact with GLU 570 (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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566B ASN* 3.0 21.3 + - + +
567B LYS* 3.4 27.2 - - - +
569B ILE* 1.3 81.5 - - + +
571B GLU* 1.3 62.1 - - + +
573B THR 4.5 4.5 + - - -
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Residues in contact with GLU 571 (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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567B LYS* 3.0 15.5 + - - +
568B PHE 2.9 2.2 + - - -
570B GLU* 1.3 80.7 - - + +
572B LYS* 1.3 88.0 + - + +
573B THR 3.9 0.2 - - - -
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Residues in contact with LYS 572 (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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539B ASN 4.5 2.1 - - - +
544B ASP* 4.1 27.1 - - - +
568B PHE* 2.7 64.7 + - + +
569B ILE* 5.2 0.4 - - - -
571B GLU* 1.3 107.8 + - + +
573B THR* 1.3 69.3 + - - +
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Residues in contact with THR 573 (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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539B ASN* 3.1 39.0 + - + +
540B THR* 5.2 0.2 - - - -
569B ILE* 3.5 23.8 + - - +
570B GLU 4.9 4.0 - - - -
571B GLU 3.9 0.8 - - - -
572B LYS* 1.3 91.0 + - - +
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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