Contacts of the helix formed by residues 507 - 522 (chain A) in PDB entry 3TT9
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 ASP 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LEU* 4.5 14.2 - - + +
456A LYS* 2.8 34.9 + - - -
491A PHE* 3.5 14.3 - - - -
506A LEU* 1.3 77.2 - - - +
508A PHE* 1.3 64.8 + - - +
509A ASP* 3.2 13.5 + - - +
510A ILE* 3.2 17.3 + - - +
511A PHE* 3.1 21.0 + - - +
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Residues in contact with PHE 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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491A PHE* 3.6 21.0 - + + -
507A ASP* 1.3 76.8 - - - +
509A ASP* 1.3 71.5 + - - +
511A PHE* 3.2 3.2 + + - +
512A TYR* 2.8 47.0 + + + +
545A TYR* 3.5 25.8 - - - -
557A ASP* 3.6 22.7 - - - -
558A LYS* 4.5 7.2 - - + -
559A ALA* 3.7 22.4 - - + -
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Residues in contact with ASP 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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1A GOL 3.9 22.8 + - - -
456A LYS* 2.9 43.5 + - + +
507A ASP* 3.2 4.0 + - - +
508A PHE* 1.3 90.8 - - - +
510A ILE* 1.3 63.9 + - - +
512A TYR* 3.4 5.6 + - - +
513A ASN* 3.0 30.3 + - - +
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Residues in contact with ILE 510 (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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446A LEU* 5.3 0.9 - - + -
452A LEU* 3.7 29.8 - - + +
455A LYS* 3.6 30.5 - - + -
456A LYS* 3.5 23.8 - - + +
459A THR* 4.0 17.3 - - + +
487A ILE* 4.0 27.4 - - + -
506A LEU* 4.1 10.5 - - + -
507A ASP* 3.2 25.8 + - - +
509A ASP* 1.3 75.7 - - - +
511A PHE* 1.3 64.3 + - - +
513A ASN* 3.4 2.9 + - - +
514A VAL* 3.1 23.0 + - - +
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Residues in contact with PHE 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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487A ILE* 3.8 13.0 - - + +
488A ILE* 3.6 46.2 - - + -
491A PHE* 3.3 45.1 - + + -
492A SER* 4.5 2.5 - - - -
507A ASP 3.1 9.0 + - - +
508A PHE* 3.6 7.6 - + - +
510A ILE* 1.3 78.3 - - - +
512A TYR* 1.3 55.7 + - - +
514A VAL* 3.1 3.3 + - - +
515A THR* 2.8 49.2 + - + +
542A LEU* 5.0 0.9 - - + -
545A TYR* 3.7 51.4 - + + -
559A ALA* 3.9 13.9 - - + -
563A CYS* 4.5 4.5 - - - -
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Residues in contact with TYR 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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1A GOL 4.0 18.4 - - - -
463A TRP* 3.6 31.6 - + - -
508A PHE* 2.8 39.4 + + + +
509A ASP* 3.6 5.8 - - - +
510A ILE 3.3 0.2 - - - -
511A PHE* 1.3 73.1 - - - +
513A ASN* 1.3 72.5 + - - +
515A THR* 2.8 21.0 + - - -
516A GLY* 3.0 7.8 + - - -
558A LYS* 3.5 40.7 - - + +
559A ALA* 3.7 20.6 - - - -
562A ASN* 3.5 20.5 + - - -
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Residues in contact with ASN 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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1A GOL 2.7 49.5 + - - -
456A LYS* 3.1 12.7 + - - +
459A THR* 2.9 45.2 - - + +
460A GLY* 3.5 8.4 - - - +
463A TRP* 3.6 20.4 - - + -
509A ASP 3.0 14.4 + - - +
510A ILE 3.4 0.2 + - - -
512A TYR* 1.3 76.3 - - - +
514A VAL* 1.3 56.4 + - - +
516A GLY* 3.2 2.9 + - - -
517A CYS* 3.0 29.7 + - - -
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Residues in contact with VAL 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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459A THR* 3.0 28.5 - - - +
483A LEU* 3.8 37.2 - - + +
487A ILE* 3.8 25.4 - - + -
488A ILE* 3.7 23.3 - - + -
510A ILE 3.1 14.0 + - - +
511A PHE 3.7 3.6 - - - +
513A ASN* 1.3 72.5 - - - +
515A THR* 1.3 61.3 + - - +
517A CYS* 3.1 7.5 - - - +
518A LEU* 2.8 31.5 + - + +
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Residues in contact with THR 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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488A ILE* 3.9 14.4 - - + -
511A PHE* 2.8 43.8 + - + +
512A TYR* 2.8 22.2 + - - -
514A VAL* 1.3 77.7 - - - +
516A GLY* 1.3 55.0 + - - +
518A LEU* 4.6 1.1 - - - -
519A ARG* 2.9 29.8 + - - +
542A LEU* 4.6 3.1 - - + -
559A ALA* 3.9 5.6 - - - +
562A ASN* 3.1 27.7 + - - +
563A CYS* 4.1 14.1 - - - -
566A ILE* 3.6 12.4 - - - +
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Residues in contact with GLY 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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463A TRP* 3.3 36.9 + - - -
512A TYR 3.0 11.6 + - - -
513A ASN 3.2 1.3 + - - -
515A THR* 1.3 74.4 + - - +
517A CYS* 1.3 66.0 + - - +
519A ARG* 3.3 6.0 + - - +
520A ASN* 3.1 21.3 + - - -
562A ASN* 3.6 13.9 - - - -
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Residues in contact with CYS 517 (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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459A THR 3.7 7.4 - - - -
462A LEU* 3.5 15.9 - - - -
463A TRP* 3.2 34.5 - - - -
466A SER* 3.6 11.2 + - - -
475A MET* 4.9 1.8 - - - -
483A LEU* 4.2 21.3 - - + -
513A ASN 3.0 14.4 + - - -
514A VAL* 3.1 15.9 - - - +
516A GLY* 1.3 75.0 - - - +
518A LEU* 1.3 58.3 + - - +
520A ASN* 3.2 5.4 + - - +
521A MET* 2.9 36.6 + - - +
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Residues in contact with LEU 518 (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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480A LEU* 4.0 12.8 - - + -
483A LEU* 4.6 13.5 - - + -
484A THR* 4.8 3.4 - - - +
488A ILE* 3.6 34.5 - - + -
514A VAL* 2.8 25.5 + - + +
517A CYS* 1.3 76.0 - - + +
519A ARG* 1.3 60.9 + - - +
521A MET* 3.8 28.5 - - + -
522A SER* 2.9 31.5 + - - -
532A MET* 3.7 18.1 - - + +
538A LEU* 3.9 17.3 - - + -
542A LEU* 5.2 0.4 - - + -
566A ILE* 3.7 19.5 - - + +
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Residues in contact with ARG 519 (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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515A THR 2.9 18.7 + - - +
516A GLY* 3.5 7.2 - - - +
517A CYS 3.3 0.2 - - - -
518A LEU* 1.3 77.7 - - - +
520A ASN* 1.3 70.4 + - - +
522A SER* 2.8 19.4 + - - +
523A SER* 3.7 5.2 + - - -
561A GLU* 4.1 9.1 + - - +
562A ASN* 2.8 34.1 + - - +
565A CYS* 3.1 46.2 - - + +
566A ILE* 3.5 15.2 - - + +
569A ASN* 4.1 4.9 + - - +
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Residues in contact with ASN 520 (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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463A TRP* 3.6 16.8 + - - +
466A SER* 3.0 41.5 + - - +
467A SER* 3.6 21.2 + - - +
472A LYS* 3.3 14.6 - - - +
516A GLY 3.1 12.6 + - - -
517A CYS 3.6 1.1 - - - +
519A ARG* 1.3 85.8 - - - +
521A MET* 1.3 62.2 + - - +
523A SER* 2.8 26.5 + - - -
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Residues in contact with MET 521 (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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466A SER* 4.3 7.0 - - - -
472A LYS* 4.3 11.7 - - - +
475A MET* 3.6 51.4 - - + +
476A ILE* 3.6 22.8 - - + +
479A ALA 4.8 0.9 - - - -
480A LEU* 4.1 15.3 - - + +
483A LEU* 4.5 7.2 - - + -
517A CYS* 2.9 31.5 + - - +
518A LEU* 3.2 30.3 + - + +
520A ASN* 1.3 76.9 - - - +
522A SER* 1.3 56.2 + - - +
523A SER 3.1 0.2 - - - -
524A ALA* 3.1 28.9 + - - +
532A MET* 3.7 9.5 - - + +
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Residues in contact with SER 522 (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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518A LEU 2.9 15.0 + - - -
519A ARG* 2.8 22.0 + - - -
521A MET* 1.3 75.9 - - - +
523A SER* 1.3 55.4 + - - +
524A ALA 3.2 2.0 - - - -
529A ARG* 3.6 19.4 - - - +
532A MET* 3.6 13.6 - - - -
566A ILE* 3.8 9.7 - - - -
569A ASN* 2.9 38.8 + - - +
570A LEU* 3.9 18.6 - - - -
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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