Contacts of the helix formed by residues 505 - 516 (chain A) in PDB entry 1IEQ
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 GLY 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A VAL* 3.7 23.5 - - - +
485A GLY 5.8 0.2 - - - -
501A ILE* 4.4 6.5 - - - -
502A PRO 3.9 7.6 - - - -
503A GLU* 3.0 10.4 + - - -
504A PRO* 1.3 76.0 - - - +
506A LEU* 1.3 66.7 + - - +
507A SER* 3.3 1.4 + - - +
508A THR* 3.3 5.0 + - - -
509A VAL* 3.2 27.2 + - - +
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Residues in contact with LEU 506 (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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501A ILE* 4.5 5.9 - - + +
503A GLU* 3.0 17.5 + - - +
505A GLY* 1.3 73.6 - - - +
507A SER* 1.3 59.6 + - - +
509A VAL* 3.2 2.5 + - + +
510A GLN* 2.8 66.1 + - + +
532A PRO* 3.6 44.9 - - + +
533A LEU* 4.0 20.2 - - + +
536A ALA* 5.3 0.2 - - + -
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Residues in contact with SER 507 (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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503A GLU* 3.3 16.4 + - - -
504A PRO* 3.7 17.5 - - - +
506A LEU* 1.3 80.2 - - - +
508A THR* 1.3 59.0 + - - +
510A GLN* 3.4 12.4 + - - +
511A ALA* 2.8 30.1 + - - +
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Residues in contact with THR 508 (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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417A GLY* 4.4 3.9 - - - +
418A SER 5.8 0.3 + - - -
465A GLU 3.7 16.2 - - - +
466A ASN* 2.3 36.4 + - - +
467A PRO* 4.2 10.8 - - + -
482A VAL* 4.1 19.5 - - + -
484A VAL* 4.7 2.7 - - - -
504A PRO* 3.7 12.5 + - - +
505A GLY* 3.3 8.9 + - - -
506A LEU 3.3 0.6 - - - -
507A SER* 1.3 78.2 + - - +
509A VAL* 1.3 59.0 + - - +
511A ALA* 3.2 5.1 + - - +
512A VAL* 2.8 44.8 + - + +
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Residues in contact with VAL 509 (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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482A VAL* 3.9 22.2 - - + -
484A VAL* 4.0 10.1 - - + -
505A GLY 3.2 13.3 + - - +
506A LEU 3.6 7.6 - - - +
508A THR* 1.3 76.4 - - - +
510A GLN* 1.3 59.6 + - + +
512A VAL* 4.6 1.6 - - - -
513A CYS* 2.8 53.6 + - - +
520A THR* 3.6 11.9 - - + +
533A LEU* 3.7 25.8 - - + -
536A ALA* 4.0 10.8 - - + -
537A SER* 3.6 15.9 - - - +
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Residues in contact with GLN 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 2.8 55.2 + - + +
507A SER* 3.8 11.4 - - - +
509A VAL* 1.3 76.7 - - - +
511A ALA* 1.3 62.1 + - - +
513A CYS* 4.8 0.2 - - - -
514A GLY* 3.1 20.4 + - - -
532A PRO* 4.9 6.1 + - - +
536A ALA* 4.0 18.7 - - + +
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Residues in contact with ALA 511 (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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467A PRO 3.5 22.7 - - - +
468A ASP* 4.2 2.0 - - - -
469A ALA* 3.9 34.9 - - + +
472A VAL* 4.3 2.5 - - - +
507A SER 2.8 17.5 + - - +
508A THR* 3.5 5.2 - - - +
510A GLN* 1.3 79.8 - - - +
512A VAL* 1.3 64.6 + - - +
514A GLY* 3.4 5.2 + - - -
515A GLY* 3.5 7.4 + - - -
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Residues in contact with VAL 512 (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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414A LEU* 4.2 14.6 - - + -
416A ALA* 4.3 12.1 - - + -
467A PRO* 4.5 6.1 - - + -
472A VAL* 3.7 14.2 - - + +
480A ALA* 3.5 26.2 - - + -
482A VAL* 3.4 33.0 - - + -
508A THR* 2.8 35.4 + - + +
509A VAL 4.0 0.4 - - - +
511A ALA* 1.3 73.4 - - + +
513A CYS* 1.3 58.5 + - - +
515A GLY* 2.9 19.2 + - - -
516A VAL* 3.1 12.1 + - + +
518A CYS* 4.4 3.4 - - + -
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Residues in contact with CYS 513 (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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396A LYS* 4.9 7.7 + - - -
482A VAL* 5.2 1.1 - - - -
509A VAL* 2.8 46.5 + - - +
510A GLN 4.6 0.2 - - - +
512A VAL* 1.3 74.6 - - - +
514A GLY* 1.3 61.3 + - - +
516A VAL 3.3 20.7 + - - +
517A ARG* 5.1 0.7 - - - -
518A CYS* 2.0 42.4 - - - -
520A THR* 4.2 1.1 - - - -
536A ALA* 2.9 29.3 - - + +
537A SER* 3.9 1.6 - - - -
538A ASP* 5.2 1.9 - - - +
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Residues in contact with GLY 514 (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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469A ALA* 6.2 1.3 - - - -
473A LYS* 4.4 13.0 - - - -
510A GLN 3.1 19.9 + - - -
511A ALA 3.9 1.8 - - - -
512A VAL 3.1 0.4 - - - -
513A CYS* 1.3 78.9 - - - +
515A GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 515 (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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472A VAL* 3.9 15.1 - - - +
473A LYS* 3.9 29.0 - - - +
511A ALA 3.5 6.3 + - - -
512A VAL 2.9 7.5 + - - -
514A GLY* 1.3 80.0 - - - +
516A VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 516 (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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472A VAL* 3.6 23.1 - - + +
477A PHE* 3.6 28.7 - - + +
478A SER 3.8 4.3 - - - +
479A TYR* 3.6 25.6 - - - +
480A ALA* 3.8 24.0 - - + -
512A VAL 3.1 3.8 + - - +
513A CYS* 3.3 20.8 - - - +
514A GLY 3.7 1.4 - - - -
515A GLY* 1.3 78.6 - - - +
517A ARG* 1.3 72.2 + - + +
518A CYS* 3.2 2.8 + - - +
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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