Contacts of the helix formed by residues 651 - 663 (chain B) in PDB entry 2R5N
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 651 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B LEU* 3.4 7.6 - - - +
646B GLU* 3.9 37.5 - - + +
649B GLY* 3.0 3.7 + - - -
650B PHE* 1.3 81.0 - - - +
652B VAL* 1.3 63.5 + - - +
653B ASP* 3.7 8.3 + - - +
654B ASN* 3.0 26.9 + - - +
655B VAL* 3.0 22.3 + - - +
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Residues in contact with VAL 652 (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 LEU* 3.4 15.8 - - + +
566B ALA* 3.6 28.0 - - + +
567B ALA* 4.3 11.4 - - - +
570B LYS* 3.4 33.0 - - + +
651B THR* 1.3 72.0 - - - +
653B ASP* 1.3 59.0 + - - +
655B VAL* 3.3 2.8 + - - +
656B VAL* 2.9 41.5 + - + +
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Residues in contact with ASP 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LYS* 2.9 24.6 + - - +
651B THR* 3.3 7.2 + - - +
652B VAL* 1.3 77.6 - - - +
654B ASN* 1.3 57.6 + - - +
656B VAL* 3.5 3.0 + - - +
657B ALA* 2.9 30.4 + - - +
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Residues in contact with ASN 654 (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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630B VAL* 4.1 12.9 - - - +
648B PHE 5.2 0.2 + - - -
649B GLY* 2.8 32.8 + - - +
651B THR* 3.0 20.2 + - - +
653B ASP* 1.3 73.6 - - - +
655B VAL* 1.3 61.1 + - - +
657B ALA* 3.3 6.1 + - - +
658B LYS* 2.9 70.8 + - - +
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Residues in contact with VAL 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 3.5 30.6 - - + -
563B LEU* 3.7 27.8 - - + -
564B ALA* 5.1 3.1 - - - -
567B ALA* 3.5 16.2 - - + -
609B VAL* 4.8 1.0 - - + +
611B VAL* 4.2 12.8 - - + -
630B VAL* 4.0 29.2 - - + -
649B GLY 4.6 0.9 - - - +
651B THR 3.0 17.0 + - - +
652B VAL 3.9 2.7 - - - +
654B ASN* 1.3 76.3 - - - +
656B VAL* 1.3 60.9 + - - +
658B LYS* 3.4 2.9 + - - +
659B ALA* 3.0 23.1 + - - +
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Residues in contact with VAL 656 (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 ALA* 3.9 28.3 - - + +
570B LYS* 4.1 27.1 - - + +
571B LEU* 4.2 11.9 - - + -
574B GLU* 5.5 0.2 - - - +
652B VAL* 2.9 29.5 + - + +
653B ASP* 3.8 3.8 - - - +
655B VAL* 1.3 76.3 - - - +
657B ALA* 1.3 58.0 + - - +
659B ALA* 3.2 7.3 + - - +
660B LYS* 2.8 56.5 + - + +
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Residues in contact with ALA 657 (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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653B ASP 2.9 18.3 + - - +
654B ASN* 3.7 9.9 - - - +
656B VAL* 1.3 78.0 - - - +
658B LYS* 1.3 59.5 + - + +
660B LYS* 3.3 8.1 + - - +
661B GLU* 3.0 34.8 + - - +
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Residues in contact with LYS 658 (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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609B VAL* 5.0 1.6 - - + -
628B ALA* 4.2 19.3 - - + +
629B ILE 5.6 5.6 - - - +
630B VAL* 3.9 24.5 - - + -
654B ASN* 2.9 50.0 + - - +
655B VAL 3.8 4.3 - - - +
657B ALA* 1.3 79.0 - - - +
659B ALA* 1.3 61.4 + - - +
661B GLU* 3.4 38.6 + - - +
662B LEU* 3.5 12.6 + - - +
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Residues in contact with ALA 659 (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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552B LEU* 3.7 28.8 - - + +
554B PHE* 3.9 10.5 - - + -
571B LEU* 3.9 12.1 - - + -
609B VAL* 4.0 12.7 - - + +
655B VAL 3.0 13.9 + - - +
656B VAL 3.5 7.9 - - - +
658B LYS* 1.3 74.3 - - - +
660B LYS* 1.3 63.8 + - - +
662B LEU* 3.0 15.6 + - - +
663B LEU* 3.3 17.8 + - - +
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Residues in contact with LYS 660 (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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571B LEU* 3.8 13.2 - - + -
574B GLU* 2.6 42.1 + - - -
656B VAL* 2.8 39.3 + - + +
657B ALA* 3.8 7.0 - - - +
659B ALA* 1.3 75.3 - - - +
661B GLU* 1.3 62.9 + - - +
663B LEU* 3.2 19.8 + - + +
664B HIS* 3.1 24.0 + - + -
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Residues in contact with GLU 661 (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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657B ALA* 3.0 18.4 + - - +
658B LYS* 3.4 35.4 + - - +
660B LYS* 1.3 78.0 - - - +
662B LEU* 1.3 61.0 + - + +
664B HIS* 3.6 21.6 + - + +
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Residues in contact with LEU 662 (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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552B LEU* 4.6 1.3 - - + -
607B ALA* 4.0 17.9 - - + +
608B ARG 3.6 36.6 - - - +
609B VAL* 3.7 19.7 - - + -
626B ASN 3.5 15.3 - - - +
627B GLY* 3.5 22.4 - - - +
628B ALA* 3.8 7.4 - - + +
658B LYS 3.5 9.4 + - - +
659B ALA 3.0 8.9 + - - +
661B GLU* 1.3 77.9 - - + +
663B LEU* 1.3 59.7 + - + +
664B HIS 3.1 16.1 + - - +
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Residues in contact with LEU 663 (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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551B GLU* 3.4 36.6 - - + +
552B LEU* 4.0 17.3 - - + -
571B LEU* 5.2 3.4 - - + -
576B VAL* 4.0 31.6 - - + -
607B ALA* 4.2 10.3 - - + -
659B ALA 3.5 16.4 - - - +
660B LYS* 3.2 13.8 + - + +
662B LEU* 1.3 75.3 - - - +
664B HIS* 1.3 61.2 + - - +
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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