Contacts of the helix formed by residues 544 - 559 (chain I) 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 ASN 544 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543I ARG* 1.3 75.3 - - - +
545I ALA* 1.3 61.5 + - - +
546I ALA* 2.7 19.4 + - - +
547I THR* 2.4 53.1 + - - -
548I TRP* 3.0 20.2 + - - -
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Residues in contact with ALA 545 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544I ASN* 1.3 75.1 - - - +
546I ALA* 1.3 57.6 + - - +
548I TRP* 3.1 29.0 - - + +
549I LYS* 2.9 48.6 + - + +
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Residues in contact with ALA 546 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544I ASN* 2.7 21.4 + - - +
545I ALA* 1.3 75.9 - - - +
547I THR* 1.3 56.7 + - - -
549I LYS* 4.4 4.1 - - - +
550I ASN* 3.5 22.2 + - - +
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Residues in contact with THR 547 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D T 3.4 37.3 + - + +
509H TYR* 4.4 0.7 - - - +
543I ARG* 4.3 16.1 - - + +
544I ASN* 2.4 47.9 + - - -
546I ALA* 1.3 72.7 - - - +
548I TRP* 1.3 62.5 + - - +
550I ASN* 3.3 7.0 + - - +
551I ALA* 3.0 25.3 + - - +
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Residues in contact with TRP 548 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 3.4 30.7 - - + +
531H TYR* 3.4 36.3 - + - -
534H PHE* 3.5 27.6 - + + -
535H THR* 3.5 23.5 - - + +
538H PHE* 3.7 41.5 - + + +
543I ARG* 4.5 0.6 - - + +
544I ASN 3.0 25.9 + - - -
545I ALA* 3.1 20.3 - - + +
547I THR* 1.3 77.2 - - - +
549I LYS* 1.3 117.8 + - + +
551I ALA* 3.6 0.5 - - - +
552I VAL* 2.8 37.2 + - + +
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Residues in contact with LYS 549 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531H TYR* 3.7 38.9 + - + +
535H THR* 4.7 4.2 + - - -
545I ALA* 2.9 32.3 + - + +
546I ALA* 4.4 3.6 - - - +
548I TRP* 1.3 117.2 - - + +
550I ASN* 1.3 62.4 - - - +
552I VAL* 3.4 2.1 + - - +
553I ARG* 3.1 37.7 + - - +
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Residues in contact with ASN 550 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C G 5.8 3.6 + - - -
8C A 5.5 3.6 - - - +
14D T 4.2 11.8 + - - +
15D T 3.5 35.3 + - - +
16D T 5.5 1.6 + - - -
546I ALA 3.5 17.9 + - - +
547I THR* 3.3 5.4 + - - +
548I TRP 3.3 0.2 - - - -
549I LYS* 1.3 80.2 - - - +
551I ALA* 1.3 66.8 + - - +
552I VAL 3.3 0.2 + - - -
553I ARG* 3.3 27.7 + - - +
554I HIS* 3.0 25.0 + - - +
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Residues in contact with ALA 551 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D G 5.1 0.4 - - + -
14D T 4.1 15.9 - - + +
509H TYR* 3.5 43.7 - - + +
547I THR 3.0 14.8 + - - +
548I TRP 3.6 0.2 - - - +
550I ASN* 1.3 82.2 + - - +
552I VAL* 1.3 57.0 + - - +
554I HIS* 3.4 6.5 + - - +
555I ASN* 2.9 38.1 + - - +
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Residues in contact with VAL 552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509H TYR* 4.1 4.0 - - + -
513H ILE* 4.0 12.3 - - + +
527H LEU* 4.4 0.9 - - + -
530H ILE* 4.0 22.9 - - + -
531H TYR* 4.3 14.8 - - + -
534H PHE* 3.7 41.3 - - + -
548I TRP* 2.8 29.8 + - + +
549I LYS 3.7 4.7 - - - +
550I ASN 3.2 0.4 - - - -
551I ALA* 1.3 71.2 - - - +
553I ARG* 1.3 66.2 + - - +
555I ASN* 3.4 1.9 + - - +
556I LEU* 3.1 36.6 + - + +
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Residues in contact with ARG 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C T 4.4 30.1 + - - +
7C G 3.0 35.9 + - - +
527H LEU* 4.5 16.6 - - + -
531H TYR* 3.2 28.7 + - + +
549I LYS* 3.1 34.5 + - - +
550I ASN* 3.7 24.5 - - - +
552I VAL* 1.3 76.5 - - - +
554I HIS* 1.3 63.3 + - - +
556I LEU* 3.3 8.6 + - - +
557I SER* 3.2 25.3 + - - -
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Residues in contact with HIS 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C A 5.8 2.7 - - - -
9C A 4.2 13.6 + - - -
10C A 4.2 6.9 + - - -
13D G 4.1 18.6 + + - -
14D T 3.0 37.2 + + + +
15D T 5.0 1.8 - - - -
550I ASN* 3.0 22.3 + - - +
551I ALA* 3.4 8.7 - - - +
553I ARG* 1.3 78.9 - - - +
555I ASN* 1.3 68.7 + - - +
557I SER* 3.3 7.3 + - - -
558I LEU* 3.1 64.4 + - + +
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Residues in contact with ASN 555 (chain I).
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 6.0 0.7 - - - +
13D G 4.4 12.1 + - - +
14D T 5.9 0.4 - - - +
509H TYR* 3.4 25.7 - - - +
510H ALA* 3.9 11.1 + - - +
513H ILE* 3.8 19.3 - - + -
551I ALA* 2.9 29.9 + - - +
552I VAL 3.9 0.2 - - - +
554I HIS* 1.3 86.6 + - - +
556I LEU* 1.3 64.8 + - - +
558I LEU* 4.4 0.9 - - - -
559I HIS* 2.9 58.1 + - + -
562I PHE* 3.5 8.5 - - + -
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Residues in contact with LEU 556 (chain I).
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* 4.0 21.5 - - + -
517H ILE* 5.4 0.2 - - + -
527H LEU* 3.8 28.5 - - + -
530H ILE* 4.2 5.2 - - + -
552I VAL* 3.1 27.6 + - + +
553I ARG* 3.8 5.8 - - - +
555I ASN* 1.3 77.7 - - - +
557I SER* 1.3 58.8 + - - +
558I LEU 3.8 0.3 + - - -
559I HIS 3.8 5.0 - - - +
562I PHE* 3.8 38.1 - - + +
573I TRP* 3.5 62.4 - - + +
603I MG 3.8 2.1 - - - -
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Residues in contact with SER 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C G 4.9 9.3 + - - +
8C A 3.6 24.6 + - - -
553I ARG 3.2 16.7 + - - -
554I HIS* 3.3 8.7 + - - -
556I LEU* 1.3 74.3 - - - +
558I LEU* 1.3 56.0 + - - +
573I TRP* 5.2 4.7 - - - -
603I MG 3.1 15.1 - - - -
583K ARG* 5.3 8.9 + - - +
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Residues in contact with LEU 558 (chain I).
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 5.1 8.5 - - + -
554I HIS* 3.1 46.1 + - + +
555I ASN* 4.2 2.9 - - - +
556I LEU 3.4 0.2 - - - -
557I SER* 1.3 78.1 - - - +
559I HIS* 1.3 81.1 + - + +
560I LYS* 3.7 6.4 + - - +
603I MG 3.2 10.2 - - - -
558K LEU* 4.3 37.5 - - + -
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Residues in contact with HIS 559 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D T 6.3 0.7 - - + -
12D T 4.6 22.7 + + + +
510H ALA* 4.4 10.2 - - + +
554I HIS* 5.9 0.2 - - - -
555I ASN* 2.9 52.6 + - + +
556I LEU 3.8 1.9 - - - +
558I LEU* 1.3 98.7 + - + +
560I LYS* 1.3 63.8 + - - +
561I CYS* 3.9 20.9 - - - -
562I PHE* 3.3 27.1 + + + +
583I ARG* 6.1 0.6 + - - -
603I MG 3.1 8.3 - - - -
558K LEU* 6.3 0.9 - - + -
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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