Contacts of the helix formed by residues 560 - 574 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ARG* 2.8 32.9 + - - -
556A ALA* 3.8 3.2 - - - +
557A THR 2.9 6.8 + - - +
559A SER* 1.3 91.6 + - - +
561A VAL* 1.3 65.3 + - - +
562A GLU 3.2 2.2 - - - -
563A LEU* 3.2 8.2 + - + +
564A ALA* 2.9 22.2 + - - +
611A VAL* 3.5 26.9 - - + +
612A GLU* 3.9 3.8 - - - +
613A ALA* 2.9 31.1 + - - +
645A PHE* 3.9 5.2 - - - -
650A PHE* 4.1 18.2 - - + -
680A EDO 2.7 26.5 + - - -
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Residues in contact with VAL 561 (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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494A CYS* 3.6 30.7 - - + -
526A GLN* 4.1 11.9 - - + +
543A LEU* 3.6 31.0 - - + -
556A ALA* 3.6 36.6 - - + +
557A THR 3.6 3.1 + - - -
558A GLY 3.2 5.2 + - - +
560A GLU* 1.3 78.3 - - - +
562A GLU* 1.3 56.0 - - - +
564A ALA* 3.1 1.8 + - - +
565A VAL* 2.8 33.9 + - + +
580A VAL* 4.9 4.3 - - + -
582A SER* 3.8 12.3 - - - +
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Residues in contact with GLU 562 (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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354A LYS* 2.9 24.9 + - - -
522A ASN 4.8 1.7 - - - +
523A LEU* 4.5 3.1 - - - +
524A ALA* 3.3 40.2 + - + +
526A GLN* 3.9 13.3 - - - +
558A GLY 4.8 0.2 + - - -
559A SER 4.0 12.3 + - - +
561A VAL* 1.3 79.1 - - - +
563A LEU* 1.3 61.7 + - - +
565A VAL* 3.4 2.9 + - - +
566A ALA* 3.0 23.6 + - + +
680A EDO 5.9 2.5 - - - +
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Residues in contact with LEU 563 (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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559A SER 4.6 0.4 + - - -
560A GLU* 3.2 12.7 + - + +
562A GLU* 1.3 79.8 - - - +
564A ALA* 1.3 63.2 + - - +
566A ALA* 3.2 5.2 + - - +
567A ALA* 3.0 20.3 + - - +
611A VAL* 4.0 14.6 - - + -
650A PHE* 3.6 39.0 - - + +
651A THR* 3.4 7.9 - - - +
652A VAL* 3.3 39.5 - - + +
655A VAL* 3.7 19.5 - - + -
680A EDO 3.9 20.8 + - - +
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Residues in contact with ALA 564 (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 PHE* 4.2 24.7 - - + -
556A ALA* 3.6 30.7 - - + -
560A GLU 2.9 7.5 + - - +
561A VAL 3.1 4.2 + - - +
563A LEU* 1.3 77.1 - - - +
565A VAL* 1.3 58.0 + - - +
567A ALA* 3.3 7.5 + - - +
568A TYR* 2.8 28.8 + - - +
580A VAL* 3.9 9.9 - - + +
611A VAL* 4.5 9.4 - - + +
655A VAL* 5.1 0.7 - - - -
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Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLN* 3.6 25.4 - - - +
543A LEU* 3.9 20.2 - - + -
544A LYS* 3.9 29.4 - - + -
561A VAL* 2.8 21.0 + - + +
562A GLU 3.7 4.7 - - - +
564A ALA* 1.3 74.8 - - - +
566A ALA* 1.3 59.3 + - - +
568A TYR* 3.2 8.6 + - - +
569A GLU* 2.8 38.6 + - + +
580A VAL* 4.2 9.4 - - + -
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Residues in contact with ALA 566 (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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562A GLU* 3.0 13.8 + - + +
563A LEU* 3.5 9.4 - - - +
565A VAL* 1.3 77.7 - - - +
567A ALA* 1.3 60.7 + - - +
569A GLU* 3.2 9.2 + - - +
570A LYS* 3.1 26.5 + - - +
652A VAL* 3.7 26.2 - - + -
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Residues in contact with ALA 567 (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 PHE* 3.9 10.1 - - + -
563A LEU 3.0 10.2 + - - +
564A ALA 3.6 7.4 - - - +
566A ALA* 1.3 72.5 - - - +
568A TYR* 1.3 66.2 + - - +
570A LYS* 3.2 2.6 + - - +
571A LEU* 3.0 30.9 + - - +
652A VAL* 4.2 3.7 - - + +
655A VAL* 3.6 33.4 - - + -
656A VAL* 3.9 20.9 - - + -
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Residues in contact with TYR 568 (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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544A LYS* 3.5 31.2 - - + +
545A ASP 2.8 22.3 + - - -
546A CYS* 5.7 0.2 - - + -
554A PHE* 4.0 12.5 - - + -
564A ALA 2.8 6.5 + - - +
565A VAL 3.3 9.4 - - - +
567A ALA* 1.3 77.6 - - - +
569A GLU* 1.3 83.0 + - + +
571A LEU* 3.5 2.4 + - - +
572A THR* 2.7 60.6 + - + +
578A ALA* 3.2 39.2 - - + +
579A ARG 4.1 0.4 - - - -
580A VAL* 3.3 32.3 - - + -
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Residues in contact with GLU 569 (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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544A LYS* 4.4 13.3 + - - -
565A VAL* 2.8 28.4 + - + +
566A ALA* 3.6 9.4 - - - +
567A ALA 3.2 0.4 - - - -
568A TYR* 1.3 95.8 - - + +
570A LYS* 1.3 63.1 + - + +
572A THR* 3.4 8.3 + - - +
573A ALA* 3.0 25.5 + - - +
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Residues in contact with LYS 570 (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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566A ALA 3.1 18.0 + - - +
567A ALA 3.2 6.7 + - - +
569A GLU* 1.3 75.1 - - + +
571A LEU* 1.3 63.6 + - + +
573A ALA* 3.2 8.1 + - + +
574A GLU* 3.2 32.4 + - - +
652A VAL* 3.9 21.8 - - + -
653A ASP* 6.1 1.3 - - - -
656A VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 571 (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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552A LEU* 3.7 14.8 - - + -
554A PHE* 3.5 32.8 - - + -
567A ALA 3.0 17.7 + - - +
568A TYR* 4.0 3.4 - - - +
570A LYS* 1.3 77.0 - - - +
572A THR* 1.3 63.3 + - - +
574A GLU* 3.0 13.4 + - - +
575A GLY 3.2 0.2 + - - -
576A VAL* 3.0 50.9 + - + +
578A ALA* 4.9 4.3 - - + -
656A VAL* 4.2 13.7 - - + -
659A ALA* 3.9 9.0 - - + -
660A LYS* 3.8 40.4 - - + +
663A LEU* 5.4 1.8 - - + -
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Residues in contact with THR 572 (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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568A TYR* 2.7 54.7 + - + +
569A GLU* 3.7 11.4 - - - +
571A LEU* 1.3 76.2 - - - +
573A ALA* 1.3 59.4 + - - +
575A GLY* 3.0 19.9 + - - -
576A VAL 3.6 15.6 + - - +
578A ALA* 4.4 3.1 + - - +
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Residues in contact with ALA 573 (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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569A GLU 3.0 17.0 + - - +
570A LYS* 3.5 9.0 - - + +
571A LEU 3.2 0.2 - - - -
572A THR* 1.3 75.8 - - - +
574A GLU* 1.3 61.6 + - + +
575A GLY 3.2 1.0 + - - -
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Residues in contact with GLU 574 (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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570A LYS* 3.2 20.1 + - - +
571A LEU* 3.0 12.4 + - - +
573A ALA* 1.3 78.1 - - + +
575A GLY* 1.3 60.3 + - - +
576A VAL* 3.4 7.3 + - + +
656A VAL* 5.4 2.5 - - - +
660A LYS* 2.6 41.0 + - - -
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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