Contacts of the helix formed by residues 572 - 587 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A GLU 3.6 4.2 + - - -
571A PRO* 1.3 75.8 - - - +
573A PRO* 1.3 74.5 - - - +
574A GLU* 3.6 10.5 + - - +
575A LEU* 3.2 32.2 + - - +
576A TYR* 3.3 12.5 + - - +
598A TRP* 4.4 5.6 + - - -
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Residues in contact with PRO 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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572A SER* 1.3 86.2 - - - +
574A GLU* 1.3 66.5 + - + +
576A TYR* 3.5 9.9 - - + +
577A ALA* 3.5 19.6 + - - +
365B MET* 4.6 28.2 - - + +
393B GLU* 3.4 49.8 - - + +
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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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572A SER* 3.2 10.4 - - - +
573A PRO* 1.3 80.1 - - + +
575A LEU* 1.3 58.0 + - - +
577A ALA* 3.4 6.7 + - - +
578A GLU* 3.0 27.4 + - - +
365B MET* 6.2 0.4 - - - -
368B GLY* 5.8 0.3 - - - -
393B GLU 6.1 0.4 - - - +
396B GLU* 5.0 2.6 - - - +
397B TRP* 3.8 43.5 + - + +
400B LYS* 3.7 34.6 + - - +
401B LYS* 4.2 11.7 + - - -
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Residues in contact with LEU 575 (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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539A HIS* 4.6 1.8 - - + -
541A LYS* 3.9 28.0 - - + +
565A LEU* 3.8 28.5 - - + -
569A GLU* 5.9 0.2 - - + -
570A GLU 3.8 20.0 - - - +
571A PRO* 4.2 3.4 - - + -
572A SER* 3.2 23.0 + - - +
573A PRO 3.2 0.2 - - - -
574A GLU* 1.3 75.1 - - - +
576A TYR* 1.3 60.0 + - - +
578A GLU* 3.1 25.1 + - - +
579A VAL* 2.9 43.0 + - + +
598A TRP* 4.0 15.9 - - + -
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Residues in contact with TYR 576 (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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572A SER 3.3 8.2 + - - +
573A PRO* 3.5 15.0 - - + +
575A LEU* 1.3 77.2 - - - +
577A ALA* 1.3 62.8 + - - +
579A VAL 3.3 0.2 + - - -
580A ARG* 3.1 45.1 + - + +
594A ASP 3.7 6.8 + - - -
595A VAL* 3.3 16.5 - - - +
596A LEU* 2.9 56.2 + - + +
598A TRP* 3.6 30.4 - + - -
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Residues in contact with ALA 577 (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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573A PRO 3.5 6.5 + - - +
574A GLU* 3.4 9.0 + - - +
575A LEU 3.4 0.2 - - - -
576A TYR* 1.3 80.6 - - - +
578A GLU* 1.3 57.4 + - - +
580A ARG* 3.5 7.1 + - - +
581A ASN* 2.9 35.9 + - - -
365B MET 3.7 23.3 - - - +
366B ALA* 3.8 12.7 - - - +
367B GLU 4.5 0.4 - - - -
368B GLY* 3.7 20.4 - - - +
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Residues in contact with GLU 578 (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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539A HIS* 2.9 29.3 + - - +
540A PRO* 5.9 0.3 - - - +
541A LYS* 3.8 13.5 + - - -
574A GLU 3.0 15.9 + - - +
575A LEU* 3.1 24.7 + - - +
577A ALA* 1.3 75.5 - - - +
579A VAL* 1.3 57.1 - - - +
581A ASN* 3.4 8.1 + - + +
582A TRP* 2.9 29.7 + - + +
368B GLY* 5.5 0.6 - - - -
369B ASP* 6.0 1.6 - - - +
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Residues in contact with VAL 579 (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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536A LEU* 3.6 28.9 - - + -
539A HIS* 4.4 11.9 - - + +
542A ILE* 4.0 21.1 - - + -
563A VAL* 5.3 0.4 - - + -
565A LEU* 5.9 0.4 - - + -
575A LEU* 2.9 35.7 + - + +
578A GLU* 1.3 74.3 - - - +
580A ARG* 1.3 66.6 + - - +
582A TRP* 3.3 9.1 + - + +
583A VAL* 3.0 23.1 + - + +
596A LEU* 3.6 23.3 - - + -
598A TRP* 4.2 11.9 - - + -
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Residues in contact with ARG 580 (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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576A TYR* 3.1 37.5 + - + +
577A ALA* 3.8 5.7 - - - +
579A VAL* 1.3 75.9 - - - +
581A ASN* 1.3 60.9 + - - +
583A VAL* 3.2 5.7 + - - +
584A ARG* 3.1 27.1 + - - +
592A THR* 3.3 35.0 + - + +
593A PRO* 3.1 31.2 + - + +
594A ASP* 4.5 9.8 + - - +
596A LEU* 3.8 13.9 - - + -
366B ALA* 4.0 23.6 + - - +
367B GLU* 4.9 11.9 + - - -
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Residues in contact with ASN 581 (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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577A ALA* 2.9 28.5 + - - +
578A GLU* 3.6 7.0 - - - +
580A ARG* 1.3 72.5 - - - +
582A TRP* 1.3 56.4 + - - +
584A ARG* 3.4 24.1 + - - +
585A LYS* 3.1 28.4 + - - +
366B ALA 5.3 0.4 + - - -
367B GLU* 3.1 32.2 + - - +
368B GLY* 4.0 5.1 - - - -
369B ASP* 4.3 4.8 - - - +
370B LYS* 3.6 27.7 - - - +
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Residues in contact with TRP 582 (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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535A ALA 2.7 31.3 + - - -
536A LEU* 4.8 1.8 - - + -
538A ALA* 3.4 24.9 - - + -
539A HIS* 3.6 37.4 - + + +
540A PRO* 4.4 11.0 - - + -
542A ILE* 6.0 0.4 - - + -
578A GLU* 2.9 16.6 + - + +
579A VAL* 3.4 10.3 - - + +
580A ARG 3.2 0.4 - - - -
581A ASN* 1.3 74.7 - - - +
583A VAL* 1.3 69.3 + - + +
585A LYS* 3.1 22.2 + - + +
586A GLU* 2.9 52.1 + - + +
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Residues in contact with VAL 583 (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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532A ILE* 4.5 11.0 - - + -
535A ALA* 4.6 9.0 - - + -
536A LEU* 3.6 35.7 - - + +
579A VAL 3.0 15.1 + - - +
580A ARG 3.8 4.9 - - - +
582A TRP* 1.3 81.1 - - + +
584A ARG* 1.3 57.0 + - - +
586A GLU* 3.1 6.0 + - - +
587A ILE* 3.0 29.4 + - + -
588A GLY 3.5 3.0 + - - -
591A ALA* 3.3 35.0 - - + +
592A THR* 4.8 0.4 - - - -
593A PRO* 3.9 16.2 - - + -
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Residues in contact with ARG 584 (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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167A SER* 3.6 5.7 - - - -
580A ARG* 3.1 18.1 + - - +
581A ASN* 3.4 30.1 + - - +
583A VAL* 1.3 78.0 - - - +
585A LYS* 1.3 56.0 + - - +
588A GLY* 2.9 34.0 + - - -
589A PRO* 4.0 25.1 - - + +
592A THR* 3.4 29.1 + - - +
990A COA 2.7 42.4 + - - -
367B GLU* 5.3 11.2 + - - -
370B LYS* 5.3 13.9 - - - +
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Residues in contact with LYS 585 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A SER* 2.8 25.8 + - - -
168A PRO* 4.8 4.5 - - + +
169A GLU* 3.5 11.7 + - + +
581A ASN 3.1 16.1 + - - +
582A TRP* 3.1 24.4 + - + +
584A ARG* 1.3 75.5 - - + +
586A GLU* 1.3 66.4 + - - +
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Residues in contact with GLU 586 (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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167A SER* 3.4 3.0 + - - -
169A GLU* 3.3 40.5 - - - +
170A ALA* 3.9 4.9 + - - +
535A ALA* 3.7 25.9 - - + -
538A ALA* 4.1 14.4 - - - +
582A TRP* 2.9 58.1 + - + +
583A VAL 3.5 4.5 - - - +
585A LYS* 1.3 87.5 - - - +
587A ILE* 1.3 62.0 + - + +
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Residues in contact with ILE 587 (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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166A PHE* 3.6 20.2 - - + -
167A SER* 2.8 26.6 + - - -
170A ALA* 3.6 9.0 - - + +
527A LEU* 4.9 4.9 - - + -
531A GLU* 3.6 51.1 - - + +
532A ILE* 4.3 5.4 - - + -
535A ALA* 3.7 15.7 - - + -
583A VAL* 3.0 10.3 + - + +
586A GLU* 1.3 84.2 - - + +
588A GLY* 1.3 60.7 + - - +
590A LEU* 3.8 12.1 - - + -
591A ALA* 3.8 26.2 - - + -
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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