Contacts of the helix formed by residues 572 - 587 (chain B) in PDB entry 2P2F
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 SER 572 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLU* 5.5 0.9 - - - -
570B GLU 3.7 3.4 + - - -
571B PRO* 1.3 75.8 - - - +
573B PRO* 1.3 74.6 - - - +
574B GLU* 3.3 11.7 + - - +
575B LEU* 2.9 26.1 + - - +
576B TYR* 3.0 21.5 + - - +
598B TRP* 4.4 3.6 + - - -
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Residues in contact with PRO 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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365A MET* 4.3 30.6 - - + +
393A GLU* 3.7 54.7 - - + +
397A TRP* 5.9 1.3 - - + -
572B SER* 1.3 85.7 - - - +
574B GLU* 1.3 61.3 + - + +
576B TYR* 3.3 10.6 - - + +
577B ALA* 3.3 21.8 + - - +
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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
----------------------------------------------------------
368A GLY* 5.5 1.3 - - - -
369A ASP* 6.0 0.2 - - - +
397A TRP* 4.4 20.9 - - + +
400A LYS* 2.9 42.1 + - - +
401A LYS* 3.3 27.0 + - - -
572B SER* 3.0 10.6 + - - +
573B PRO* 1.3 83.2 - - + +
575B LEU* 1.3 63.7 + - + +
577B ALA* 3.4 5.5 + - - +
578B GLU* 3.0 30.6 + - + +
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B HIS* 4.3 4.3 - - + -
541B LYS* 4.1 30.3 - - + +
565B LEU* 3.8 30.5 - - + -
569B GLU* 5.5 0.2 - - + -
570B GLU 3.7 20.6 - - - +
571B PRO* 4.3 1.6 - - + -
572B SER* 2.9 21.7 + - - +
574B GLU* 1.3 79.0 - - + +
576B TYR* 1.3 53.7 + - - +
578B GLU* 3.1 23.5 + - - +
579B VAL* 2.7 46.6 + - + +
598B TRP* 4.1 11.7 - - + -
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Residues in contact with TYR 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ALA* 5.9 1.1 - - - -
572B SER 3.0 12.9 + - - +
573B PRO* 3.3 17.0 - - + +
575B LEU* 1.3 77.8 - - - +
577B ALA* 1.3 64.3 + - + +
579B VAL 3.3 0.2 + - - -
580B ARG* 3.0 42.4 + - + +
594B ASP 3.9 5.1 + - - -
595B VAL* 3.6 10.9 - - - +
596B LEU* 3.0 61.4 + - + +
598B TRP* 3.8 27.9 - + + -
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Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET 3.5 8.5 - - - +
366A ALA* 3.5 26.0 - - - +
367A GLU 4.2 0.2 - - - -
368A GLY* 3.5 27.4 - - - +
397A TRP* 6.0 0.2 - - - +
573B PRO 3.3 7.3 + - - +
574B GLU* 3.9 6.3 - - - +
576B TYR* 1.3 80.8 - - + +
578B GLU* 1.3 58.0 + - - +
580B ARG* 3.8 5.5 - - - +
581B ASN* 2.9 36.2 + - - -
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Residues in contact with GLU 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLY* 5.3 1.1 - - - -
369A ASP* 6.0 2.9 - - - +
539B HIS* 2.7 31.3 + - + +
541B LYS* 4.2 15.1 + - - -
574B GLU* 3.0 24.3 + - + +
575B LEU* 3.1 18.5 + - - +
577B ALA* 1.3 78.0 - - - +
579B VAL* 1.3 57.1 + - - +
581B ASN* 3.5 7.4 + - + +
582B TRP* 2.9 28.9 + - + +
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Residues in contact with VAL 579 (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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536B LEU* 3.4 27.8 - - + -
539B HIS* 4.5 7.9 - - + +
542B ILE* 3.7 25.8 - - + -
563B VAL* 4.8 3.4 - - + -
565B LEU* 5.6 0.2 - - + -
575B LEU* 2.7 37.3 + - + +
576B TYR 3.9 3.1 - - - +
578B GLU* 1.3 69.6 - - - +
580B ARG* 1.3 66.5 + - - +
582B TRP* 3.1 17.7 + - + +
583B VAL* 3.3 14.0 + - - +
593B PRO* 6.1 0.2 - - + -
596B LEU* 3.9 21.5 - - + -
598B TRP* 4.2 11.4 - - + -
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Residues in contact with ARG 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ALA* 4.1 22.3 + - - +
367A GLU* 4.3 16.0 + - - -
576B TYR* 3.0 38.7 + - + +
577B ALA* 3.8 4.9 - - - +
578B GLU 3.3 0.2 - - - -
579B VAL* 1.3 76.6 - - - +
581B ASN* 1.3 61.9 + - - +
583B VAL* 3.3 7.6 + - - +
584B ARG* 3.2 20.7 + - - +
592B THR* 3.5 32.0 + - + +
593B PRO* 3.0 36.8 + - + +
594B ASP* 4.3 13.7 + - - +
596B LEU* 3.9 18.2 - - + -
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Residues in contact with ASN 581 (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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367A GLU* 2.9 36.0 + - - +
369A ASP* 4.0 11.3 - - - +
370A LYS* 4.4 17.1 - - - +
577B ALA 2.9 22.6 + - - +
578B GLU* 3.7 7.5 - - + +
580B ARG* 1.3 72.9 - - - +
582B TRP* 1.3 63.1 + - - +
584B ARG* 3.3 30.8 + - - +
585B LYS* 3.1 23.6 + - - +
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Residues in contact with TRP 582 (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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535B ALA 2.9 30.6 + - - -
536B LEU* 4.6 3.6 - - + -
538B ALA* 3.5 24.2 - - + -
539B HIS* 3.5 36.7 - + + +
540B PRO* 4.2 15.0 - - + -
542B ILE* 5.8 0.2 - - + -
578B GLU* 2.9 16.7 + - + +
579B VAL* 3.1 12.2 + - - +
581B ASN* 1.3 74.4 - - - +
583B VAL* 1.3 66.9 + - + +
585B LYS* 3.2 36.8 + - + +
586B GLU* 3.0 44.3 + - + +
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Residues in contact with VAL 583 (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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532B ILE* 4.6 7.6 - - + -
535B ALA* 4.6 6.1 - - + -
536B LEU* 3.6 30.5 - - + -
579B VAL 3.6 12.8 - - - +
580B ARG 3.3 6.9 + - - +
582B TRP* 1.3 77.9 - - + +
584B ARG* 1.3 60.9 + - - +
586B GLU* 3.1 6.8 + - - +
587B ILE* 2.9 39.8 + - + -
588B GLY 3.6 3.8 + - - -
591B ALA* 3.3 36.3 - - + +
592B THR* 4.6 0.4 - - - -
593B PRO* 4.0 14.1 - - + -
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Residues in contact with ARG 584 (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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367A GLU* 4.7 12.2 + - - -
370A LYS* 4.9 20.2 - - - +
167B SER* 3.6 5.9 - - - -
580B ARG* 3.2 10.3 + - - +
581B ASN* 3.3 35.1 + - - +
583B VAL* 1.3 76.7 - - - +
585B LYS* 1.3 57.4 + - - +
588B GLY* 3.1 33.7 + - - -
589B PRO* 4.0 26.5 - - + +
592B THR* 3.8 26.8 + - - +
991B COA 2.7 45.9 + - - -
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Residues in contact with LYS 585 (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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167B SER* 2.7 23.1 + - - -
168B PRO* 4.9 4.1 - - + +
169B GLU* 3.4 13.1 + - + +
581B ASN 3.1 15.3 + - - +
582B TRP* 3.2 47.8 + - + +
584B ARG* 1.3 76.1 - - - +
586B GLU* 1.3 81.7 + - - +
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Residues in contact with GLU 586 (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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167B SER* 3.4 6.3 + - - -
169B GLU* 3.5 36.4 - - - +
170B ALA* 3.7 6.6 + - - +
270B LYS* 5.7 2.1 + - - -
535B ALA* 3.9 26.1 - - + -
538B ALA* 4.4 15.4 - - - +
582B TRP* 3.0 46.4 + - + +
583B VAL 3.7 3.8 - - - +
585B LYS* 1.3 104.4 + - - +
587B ILE* 1.3 62.5 + - + +
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Residues in contact with ILE 587 (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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166B PHE* 3.4 27.9 - - + -
167B SER* 2.8 25.7 + - - -
170B ALA* 3.6 4.4 - - + +
270B LYS* 6.3 1.3 - - - +
527B LEU* 4.6 7.0 - - + -
531B GLU* 3.8 31.4 - - + +
532B ILE* 4.3 6.7 - - + +
535B ALA* 3.8 24.2 - - + -
583B VAL* 2.9 12.6 + - + +
585B LYS 3.5 0.2 - - - -
586B GLU* 1.3 88.4 - - + +
588B GLY* 1.3 57.4 + - - +
590B LEU* 4.0 10.8 - - + -
591B ALA* 3.8 27.4 - - + -
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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