Contacts of the helix formed by residues 560 - 575 (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 GLU 560 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ARG* 2.8 26.2 + - - -
556B ALA* 3.8 3.0 - - - +
557B THR 3.0 5.9 + - - +
559B SER* 1.3 93.3 + - - +
561B VAL* 1.3 65.2 + - - +
562B GLU 3.3 1.8 - - - -
563B LEU* 3.3 7.3 + - + +
564B ALA* 3.0 22.2 + - - +
611B VAL* 3.5 27.0 - - + +
612B GLU* 3.9 2.9 - - - -
613B ALA* 2.8 37.9 + - - +
645B PHE* 3.6 6.4 - - - -
650B PHE* 4.0 17.7 - - + -
677B EDO 2.8 26.9 + - - -
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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
----------------------------------------------------------
494B CYS* 3.5 31.4 - - + -
526B GLN* 4.0 14.8 - - + +
543B LEU* 3.5 32.5 - - + -
556B ALA* 3.7 31.0 - - + +
557B THR 3.6 6.7 + - - -
558B GLY 3.2 4.5 + - - +
560B GLU* 1.3 78.5 - - - +
562B GLU* 1.3 58.5 + - - +
564B ALA* 3.1 2.6 + - - +
565B VAL* 2.8 29.4 + - + +
580B VAL* 4.9 4.3 - - + -
582B SER* 3.8 11.2 - - - +
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Residues in contact with GLU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LYS* 4.7 13.9 + - - -
522B ASN 5.5 0.7 - - - +
523B LEU* 5.4 0.5 - - - -
524B ALA* 3.5 36.9 + - + +
526B GLN* 4.0 16.9 - - - +
558B GLY 4.9 0.4 + - - -
559B SER 4.1 9.8 + - - +
560B GLU 3.3 0.8 - - - -
561B VAL* 1.3 77.3 - - - +
563B LEU* 1.3 58.0 + - - +
565B VAL* 3.2 5.2 + - + +
566B ALA* 2.9 28.3 + - + +
677B EDO 6.4 0.9 - - - -
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Residues in contact with LEU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B SER 4.8 0.6 + - - -
560B GLU* 3.3 10.6 + - + +
561B VAL 3.2 0.2 - - - -
562B GLU* 1.3 78.2 - - - +
564B ALA* 1.3 62.6 + - - +
566B ALA* 3.1 8.2 + - - +
567B ALA* 3.0 20.6 + - - +
611B VAL* 3.9 15.5 - - + -
650B PHE* 3.7 39.7 - - + +
651B THR* 3.4 32.1 - - - +
652B VAL* 3.4 15.7 - - + +
655B VAL* 3.7 18.6 - - + -
677B EDO 4.2 20.3 - - - +
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 4.1 24.6 - - + -
556B ALA* 3.6 27.6 - - + -
560B GLU 3.0 6.4 + - - +
561B VAL 3.5 7.6 - - - +
563B LEU* 1.3 76.2 - - - +
565B VAL* 1.3 58.2 + - - +
567B ALA* 3.2 8.5 + - - +
568B TYR* 2.9 28.6 + - - +
580B VAL* 3.9 10.4 - - + +
611B VAL* 4.5 9.4 - - + +
655B VAL* 5.1 0.7 - - - -
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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
----------------------------------------------------------
526B GLN* 3.8 24.9 - - - +
543B LEU* 4.0 18.2 - - + -
544B LYS* 3.9 30.3 - - + -
561B VAL* 2.8 18.2 + - + +
562B GLU* 3.5 9.9 - - + +
564B ALA* 1.3 76.8 - - - +
566B ALA* 1.3 57.3 + - - +
568B TYR* 3.2 8.7 + - - +
569B GLU* 2.9 40.6 + - + +
580B VAL* 4.2 5.4 - - + -
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Residues in contact with ALA 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 GLU* 2.9 13.7 + - + +
563B LEU* 3.1 9.8 + - - +
565B VAL* 1.3 76.0 - - - +
567B ALA* 1.3 63.3 + - - +
569B GLU* 3.3 9.4 + - - +
570B LYS* 3.2 21.0 + - - +
652B VAL* 3.6 27.0 - - + +
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Residues in contact with ALA 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 3.8 12.8 - - + -
563B LEU 3.0 8.9 + - - +
564B ALA 3.5 7.6 - - - +
566B ALA* 1.3 74.2 - - - +
568B TYR* 1.3 65.9 + - - +
570B LYS* 3.2 4.0 + - - +
571B LEU* 3.0 26.9 + - - +
652B VAL* 4.3 5.3 - - + +
655B VAL* 3.5 33.0 - - + -
656B VAL* 3.9 21.5 - - + +
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Residues in contact with TYR 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LYS* 3.5 29.9 - - + +
545B ASP 2.7 24.9 + - - -
554B PHE* 3.9 11.6 - - + -
564B ALA 2.9 6.0 + - - +
565B VAL 3.3 8.7 - - - +
567B ALA* 1.3 75.8 - - - +
569B GLU* 1.3 83.9 + - - +
571B LEU* 3.3 1.0 + - - +
572B THR* 2.7 61.3 + - + +
578B ALA* 3.2 39.3 - - + -
579B ARG 4.0 0.9 - - - -
580B VAL* 3.4 31.2 - - + -
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Residues in contact with GLU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LYS* 4.8 7.4 + - - +
565B VAL* 2.9 31.1 + - + +
566B ALA* 3.7 9.0 - - - +
567B ALA 3.3 0.2 - - - -
568B TYR* 1.3 99.0 - - - +
570B LYS* 1.3 62.4 - - - +
572B THR* 3.8 6.9 - - - +
573B ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 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 ALA 3.2 10.2 + - - +
567B ALA 3.2 8.5 + - - +
569B GLU* 1.3 79.0 - - - +
571B LEU* 1.3 63.1 + - + +
573B ALA* 3.4 6.5 + - - +
574B GLU* 3.3 29.8 + - + +
652B VAL* 3.4 28.8 - - + +
653B ASP* 2.9 33.3 + - - +
656B VAL* 4.1 23.3 - - + +
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Residues in contact with LEU 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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552B LEU* 3.6 15.0 - - + -
554B PHE* 3.6 31.0 - - + -
567B ALA 3.0 16.1 + - - +
568B TYR 4.1 2.2 - - - +
570B LYS* 1.3 73.5 - - - +
572B THR* 1.3 67.3 + - - +
574B GLU* 3.1 20.4 + - - +
575B GLY 3.2 0.5 + - - -
576B VAL* 3.0 44.4 + - + +
578B ALA* 4.7 5.4 - - + -
656B VAL* 4.2 15.3 - - + -
659B ALA* 3.9 10.1 - - + -
660B LYS* 3.8 37.7 - - + -
663B LEU* 5.2 2.2 - - + -
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Residues in contact with THR 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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545B ASP 5.9 0.4 - - - +
568B TYR* 2.7 60.1 + - + +
569B GLU* 3.8 9.2 - - - +
571B LEU* 1.3 72.1 - - - +
573B ALA* 1.3 56.8 - - - +
575B GLY* 2.9 21.1 + - - -
576B VAL 3.7 12.4 + - - +
578B ALA* 4.0 7.3 + - - +
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Residues in contact with ALA 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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569B GLU 3.0 18.1 + - - +
570B LYS* 3.7 7.9 - - - +
571B LEU 3.2 0.4 - - - -
572B THR* 1.3 76.5 - - - +
574B GLU* 1.3 59.1 + - - +
575B GLY* 3.2 0.7 + - - -
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Residues in contact with GLU 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LYS* 3.3 18.8 + - + +
571B LEU* 3.1 19.1 + - - +
573B ALA* 1.3 76.9 - - + +
575B GLY* 1.3 58.8 + - - +
576B VAL* 4.5 8.0 - - + +
656B VAL* 5.5 0.5 - - - +
660B LYS* 2.6 41.5 + - - -
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Residues in contact with GLY 575 (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* 4.2 3.5 - - - +
572B THR 2.9 13.6 + - - -
573B ALA 3.2 1.4 + - - -
574B GLU* 1.3 80.0 - - - +
576B VAL* 1.3 64.1 + - - +
577B LYS* 3.7 6.4 + - - +
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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