Contacts of the helix formed by residues 508 - 519 (chain H) in PDB entry 2A07
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 508 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D T 4.1 31.9 + - - +
13D G 3.2 20.4 - - - +
506H PRO* 5.6 2.5 - - + -
507H PHE* 1.3 80.1 - - - +
509H TYR* 1.3 65.7 + - - +
510H ALA* 3.2 10.9 + - - +
511H THR* 3.0 44.7 + - + +
512H LEU* 3.0 12.2 + - - +
540I TYR* 3.4 5.8 - - - -
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Residues in contact with TYR 509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D G 3.2 33.2 + - + +
14D T 4.3 2.0 + - - -
508H THR* 1.3 73.9 - - - +
510H ALA* 1.3 57.2 + - - +
512H LEU* 3.4 5.5 + - + +
513H ILE* 2.8 38.5 + - + +
534H PHE* 3.7 22.2 - + - -
538H PHE* 4.1 5.0 - + - -
540I TYR* 3.4 16.4 + + - -
543I ARG* 3.1 35.3 + - - -
547I THR* 4.4 0.2 - - - +
548I TRP* 3.4 36.1 + - + +
551I ALA* 3.5 31.7 - - + +
552I VAL* 4.1 7.4 - - + -
555I ASN* 3.4 24.2 - - + +
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Residues in contact with ALA 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D T 5.8 3.6 - - - +
508H THR* 3.1 8.6 + - - +
509H TYR* 1.3 77.5 - - - +
511H THR* 1.3 66.9 + - + +
513H ILE 3.4 0.2 + - - -
514H ARG* 3.0 18.5 + - - +
555I ASN* 3.9 11.7 + - - +
559I HIS* 4.4 11.0 - - + +
561I CYS* 5.5 1.1 - - - -
562I PHE* 3.3 31.0 - - + -
580I TYR* 3.3 16.3 + - + +
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Residues in contact with THR 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H PRO 4.3 6.1 + - - +
507H PHE* 3.5 15.3 - - - +
508H THR* 3.0 39.7 + - + +
510H ALA* 1.3 75.8 - - + +
512H LEU* 1.3 61.3 + - - +
514H ARG* 3.3 4.0 + - - +
515H GLN* 2.8 30.1 + - - +
580I TYR* 3.1 17.7 - - + +
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Residues in contact with LEU 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507H PHE* 3.9 24.0 - - + -
508H THR 3.0 17.3 + - - +
509H TYR* 3.7 6.3 - - + +
511H THR* 1.3 82.4 + - - +
513H ILE* 1.3 65.0 + - - +
515H GLN* 3.2 6.9 + - - +
516H ALA* 3.0 23.6 + - - +
533H TRP* 3.7 25.9 - - + -
534H PHE* 3.7 27.1 - - + -
538H PHE* 4.9 2.7 - - + -
507I PHE* 3.9 12.1 - - + -
540I TYR* 4.0 19.3 - - + +
541I PHE* 3.8 26.7 - - + -
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Residues in contact with ILE 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 2.8 29.7 + - + +
512H LEU* 1.3 73.2 - - - +
514H ARG* 1.3 61.2 + - - +
516H ALA* 3.5 3.4 + - - +
517H ILE* 3.1 36.7 + - + +
530H ILE* 4.5 9.2 - - + -
534H PHE* 3.8 23.3 - - + -
552I VAL* 4.0 26.2 - - + +
555I ASN* 3.8 27.6 - - + -
556I LEU* 4.0 16.8 - - + -
562I PHE* 3.7 29.2 - - + -
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Residues in contact with ARG 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510H ALA 3.0 18.3 + - - +
511H THR* 3.6 4.8 + - - +
513H ILE* 1.3 75.5 - - - +
515H GLN* 1.3 60.3 + - - +
517H ILE* 3.4 0.3 + - - +
518H MET* 2.7 69.2 + - + +
562I PHE* 4.2 1.5 - - + -
575I VAL* 4.2 23.3 - - + -
577I GLU* 3.0 35.4 + - - -
580I TYR* 3.1 43.2 - - + +
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Residues in contact with GLN 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507H PHE* 4.6 3.6 - - - -
511H THR 2.8 18.5 + - - +
512H LEU* 3.2 12.7 + - - +
514H ARG* 1.3 81.9 - - - +
516H ALA* 1.3 56.9 + - - +
518H MET* 4.3 4.3 - - - -
519H GLU* 2.9 63.4 + - - +
533H TRP* 3.8 11.2 - - + -
506I PRO 3.3 24.5 + - - -
507I PHE* 3.1 34.1 - - - -
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Residues in contact with ALA 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512H LEU 3.0 9.9 + - - +
513H ILE* 3.6 10.8 - - - +
514H ARG 3.2 0.2 - - - -
515H GLN* 1.3 74.9 - - - +
517H ILE* 1.3 64.6 + - + +
519H GLU 3.1 22.9 + - - +
525H LEU* 3.6 18.9 - - + +
530H ILE* 5.3 4.3 - - + -
533H TRP* 3.4 48.7 + - + +
534H PHE* 5.1 2.5 - - + -
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Residues in contact with ILE 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513H ILE* 3.1 29.2 + - + +
514H ARG 3.9 2.2 - - - +
516H ALA* 1.3 79.3 - - - +
518H MET* 1.3 62.8 + - - +
520H SER* 2.6 21.9 + - - -
523H ARG* 3.2 35.1 - - + +
524H GLN* 4.2 0.9 - - - +
525H LEU* 3.6 22.0 - - + -
530H ILE* 4.4 5.8 - - + -
562I PHE* 4.8 1.8 - - + -
573I TRP* 3.7 35.4 - - + +
574I THR* 4.2 5.4 - - - +
575I VAL* 3.6 31.6 - - + +
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Residues in contact with MET 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514H ARG* 2.7 55.6 + - + +
515H GLN* 3.8 5.6 - - - +
517H ILE* 1.3 73.9 - - - +
519H GLU* 1.3 63.1 + - + +
520H SER 3.4 6.5 + - - +
523H ARG* 4.1 41.7 + - - +
575I VAL* 5.1 8.3 - - + +
577I GLU* 3.1 30.7 - - + +
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Residues in contact with GLU 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515H GLN* 2.9 49.0 + - + +
516H ALA* 3.1 9.1 + - - +
518H MET* 1.3 82.0 - - + +
520H SER* 1.3 61.1 + - - +
533H TRP* 4.9 12.9 + - - +
584H ARG* 4.9 11.6 + - - -
506I PRO* 4.5 8.7 - - - +
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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