Contacts of the helix formed by residues 526 - 538 (chain J) 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 526 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525J LEU* 1.3 78.0 - - - +
527J LEU* 1.3 64.9 + - - +
528J ASN* 3.6 7.1 + - - +
529J GLU* 2.9 43.1 + - - +
530J ILE* 3.0 18.7 + - - +
571J ALA 3.8 22.9 - - - +
572J VAL* 4.2 10.1 - - + +
573J TRP* 4.4 1.1 - - - +
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Residues in contact with LEU 527 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B A 3.4 48.7 - - + +
9B A 3.4 15.7 + - - +
526J THR* 1.3 72.5 - - - +
528J ASN* 1.3 63.9 + - - +
530J ILE* 3.0 8.8 + - + +
531J TYR* 3.0 59.9 + - + +
552J VAL* 4.2 5.2 - - + -
553J ARG* 4.0 14.4 - - + -
556J LEU* 3.7 26.9 - - + -
571J ALA 4.8 1.2 + - - -
573J TRP* 4.0 10.8 - - - +
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Residues in contact with ASN 528 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B A 4.1 19.1 + - - +
526J THR* 3.3 6.8 + - - +
527J LEU* 1.3 79.8 - - - +
529J GLU* 1.3 58.3 + - + +
531J TYR* 3.3 25.4 + - - +
532J SER* 3.0 37.2 + - - -
549J LYS* 5.5 2.0 - - - +
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Residues in contact with GLU 529 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524J GLN 4.4 1.0 - - - +
525J LEU* 3.3 31.4 - - + +
526J THR* 2.9 47.1 + - - +
528J ASN* 1.3 74.3 - - + +
530J ILE* 1.3 64.9 + - - +
532J SER* 3.4 8.7 + - - -
533J TRP* 3.1 21.8 + - - +
536J ARG* 4.8 2.3 + - - -
572J VAL* 5.5 0.5 - - - +
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Residues in contact with ILE 530 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J ILE* 4.5 8.7 - - + -
516J ALA* 4.8 4.0 - - + -
517J ILE* 4.5 11.4 - - + -
525J LEU* 3.7 26.5 - - + +
526J THR 3.0 17.1 + - - +
527J LEU* 3.0 8.8 + - - +
529J GLU* 1.3 74.3 - - - +
531J TYR* 1.3 66.7 + - - +
533J TRP* 3.2 4.5 + - - +
534J PHE* 3.1 49.3 + - + -
552J VAL* 4.0 17.9 - - + -
556J LEU* 4.2 16.6 - - + -
573J TRP* 3.9 33.4 - - + -
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Residues in contact with TYR 531 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B A 3.7 19.9 + - - -
527J LEU* 3.0 42.0 + - + +
528J ASN* 3.3 26.0 + - - +
530J ILE* 1.3 77.2 - - - +
532J SER* 1.3 63.4 + - - +
534J PHE* 3.1 6.1 + - - +
535J THR* 3.0 25.5 + - + +
548J TRP* 3.9 18.2 - + + -
549J LYS* 3.7 57.4 - - + +
552J VAL* 4.3 8.5 - - + -
553J ARG* 2.9 36.6 + - - +
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Residues in contact with SER 532 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528J ASN* 3.0 22.4 + - - -
529J GLU* 3.6 12.0 - - - -
530J ILE 3.2 0.2 - - - -
531J TYR* 1.3 77.1 - - - +
533J TRP* 1.3 57.5 + - - +
535J THR* 3.2 8.9 + - - -
536J ARG* 2.9 47.5 + - - +
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Residues in contact with TRP 533 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512J LEU* 3.5 31.6 - - + -
515J GLN* 3.7 28.3 - - + -
516J ALA* 3.5 31.6 - - + +
519J GLU* 3.0 26.0 + - + -
525J LEU* 5.0 3.6 - - + -
529J GLU 3.1 13.6 + - - +
530J ILE* 3.2 8.0 + - - +
532J SER* 1.3 74.6 - - - +
534J PHE* 1.3 82.7 + + - +
536J ARG* 3.7 27.9 - - - +
537J THR* 2.6 49.1 + - + -
538J PHE* 3.8 29.8 - + - -
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Residues in contact with PHE 534 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509J TYR* 3.9 14.6 - + - -
512J LEU* 3.6 31.9 - - + -
513J ILE* 3.9 22.4 - - + -
516J ALA* 5.0 0.2 - - + -
530J ILE* 3.1 41.2 + - + -
531J TYR 3.1 9.3 + - - +
533J TRP* 1.3 99.7 - + - +
535J THR* 1.3 61.9 + - - +
537J THR* 4.8 0.4 - - - -
538J PHE* 3.1 25.3 + - - +
541J PHE* 3.5 50.9 - + + +
548J TRP* 3.7 20.2 - + + -
552J VAL* 4.0 10.8 - - + -
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Residues in contact with THR 535 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531J TYR* 3.0 11.3 + - + +
532J SER* 3.2 13.2 + - - -
534J PHE* 1.3 75.2 - - - +
536J ARG* 1.3 63.8 + - - +
538J PHE 3.7 1.7 - - - +
541J PHE* 3.4 16.8 - - - +
542J ARG* 2.8 38.6 + - - +
548J TRP* 3.4 31.4 - - + -
549J LYS* 5.6 1.8 - - - -
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Residues in contact with ARG 536 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529J GLU 4.8 2.0 + - - -
532J SER* 2.9 37.8 + - - +
533J TRP* 3.7 31.0 - - - +
535J THR* 1.3 78.8 + - - +
537J THR* 1.3 64.7 + - - +
542J ARG* 3.2 14.8 + - - +
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Residues in contact with THR 537 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533J TRP* 2.6 47.9 + - + -
536J ARG* 1.3 86.0 - - - +
538J PHE* 1.3 96.2 + - + +
542J ARG* 4.1 3.0 + - - -
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Residues in contact with PHE 538 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503J VAL 5.6 2.2 - - - +
505J PRO* 3.3 41.1 - - + -
507J PHE* 5.7 4.7 - + - -
512J LEU* 4.5 11.7 - - + -
533J TRP* 3.8 24.9 - + - -
534J PHE 3.1 12.8 + - - +
535J THR 3.7 7.4 - - - +
536J ARG 3.7 0.6 - - - -
537J THR* 1.3 110.2 - - + +
539J ALA* 1.3 64.8 + - - +
540J TYR* 4.1 6.3 - - + +
541J PHE* 3.1 34.2 + + + -
542J ARG* 3.7 6.3 + - - +
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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