Contacts of the helix formed by residues 503 - 521 (chain A) in PDB entry 2IVF
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 MET 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A TYR* 3.8 21.8 - - + -
494A MET* 3.7 13.5 - - - -
498A THR* 3.8 25.7 + - + +
501A GLY 3.1 1.0 - - - -
502A GLY* 1.3 75.8 - - - +
504A ASP* 1.3 61.8 + - - +
505A GLU 3.4 1.8 - - - -
506A LEU* 3.3 8.7 + - - +
507A HIS* 2.8 55.2 + - + +
746A ILE* 3.8 27.8 - - + -
749A ALA* 3.8 24.7 - - + -
750A VAL* 3.8 16.4 - - + -
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Residues in contact with ASP 504 (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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496A LYS* 5.8 0.3 + - - -
501A GLY* 3.0 31.6 + - - +
502A GLY 3.4 0.2 - - - -
503A MET* 1.3 78.9 + - - +
505A GLU* 1.3 59.6 + - + +
507A HIS* 3.3 4.9 + - - +
508A GLN* 2.8 36.7 + - - +
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Residues in contact with GLU 505 (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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495A SER* 5.6 2.3 + - - -
501A GLY 4.7 0.8 + - - -
502A GLY 4.8 4.1 + - - +
503A MET 3.4 0.4 - - - -
504A ASP* 1.3 80.2 - - + +
506A LEU* 1.3 59.3 + - + +
508A GLN* 3.1 25.7 + - - +
509A MET* 2.9 31.9 + - - +
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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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490A TYR* 3.6 37.5 - - + +
493A VAL* 3.8 29.4 - - + -
494A MET* 4.1 13.0 - - + -
502A GLY 4.3 7.6 + - - +
503A MET* 3.3 5.7 + - - +
505A GLU* 1.3 79.8 - - + +
507A HIS* 1.3 59.5 + - - +
509A MET* 3.4 14.6 + - - +
510A ALA* 2.9 30.7 + - - +
533A PHE* 4.2 24.0 - - + -
537A VAL* 5.9 1.1 - - + -
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Residues in contact with HIS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A TYR* 3.0 37.3 + + - -
503A MET* 2.8 38.0 + - + +
504A ASP* 3.8 5.4 - - - +
506A LEU* 1.3 80.4 - - - +
508A GLN* 1.3 58.2 + - - +
510A ALA* 3.5 8.8 - - - +
511A GLU* 3.3 29.6 + - - +
749A ALA 5.6 2.6 + - - -
750A VAL* 4.9 1.8 - - - +
775A THR* 4.5 17.5 - - + +
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Residues in contact with GLN 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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504A ASP* 2.8 16.0 + - - +
505A GLU* 3.1 45.3 + - - +
507A HIS* 1.3 75.4 - - - +
509A MET* 1.3 62.9 + - + +
511A GLU* 3.4 17.9 + - - +
512A GLY* 3.1 17.8 + - - -
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Residues in contact with MET 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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505A GLU 2.9 19.3 + - - +
506A LEU* 3.6 13.7 - - - +
508A GLN* 1.3 74.1 - - + +
510A ALA* 1.3 65.0 + - - +
512A GLY* 3.1 4.9 + - - +
513A PHE* 3.0 51.8 + - + -
516A ARG* 5.3 0.8 + - - +
533A PHE* 4.0 13.5 - - + -
536A VAL* 4.6 8.3 - - + -
537A VAL* 3.7 26.2 - - + -
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Residues in contact with ALA 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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506A LEU 2.9 18.3 + - - +
507A HIS* 3.5 11.7 - - - +
509A MET* 1.3 76.2 - - - +
511A GLU* 1.3 59.6 + - + +
513A PHE* 3.4 4.5 + - - +
514A ASN* 3.2 27.4 + - - +
533A PHE* 3.9 23.8 - - + +
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Residues in contact with GLU 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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507A HIS* 3.3 18.3 + - - +
508A GLN* 3.6 16.8 - - - +
509A MET 3.2 0.4 - - - -
510A ALA* 1.3 74.7 - - + +
512A GLY* 1.3 66.2 + - - +
514A ASN* 2.9 10.9 + - - +
515A LYS* 2.8 24.3 + - - +
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Residues in contact with GLY 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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508A GLN 3.1 14.6 + - - -
509A MET* 3.1 6.0 + - - -
511A GLU* 1.3 75.2 - - - +
513A PHE* 1.3 56.8 + - - +
515A LYS* 3.1 6.7 + - - +
516A ARG* 2.9 45.3 + - - +
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Residues in contact with PHE 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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509A MET* 3.0 50.7 + - + -
510A ALA 3.7 6.7 - - - +
511A GLU 3.2 0.4 - - - -
512A GLY* 1.3 74.6 - - - +
514A ASN* 1.3 54.6 + - - +
516A ARG* 3.7 32.0 - - + +
517A THR* 2.6 38.9 + - - +
529A GLY 4.1 6.7 - - - +
532A GLU* 3.8 15.0 - - + -
533A PHE* 3.5 39.9 - + + -
536A VAL* 3.4 44.9 - - + -
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Residues in contact with ASN 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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510A ALA 3.2 14.8 + - - +
511A GLU* 2.9 12.6 + - - +
513A PHE* 1.3 76.0 - - - +
515A LYS* 1.3 62.9 + - - +
517A THR* 3.1 6.6 + - - -
518A LEU* 2.9 30.7 + - + +
526A ASP* 4.5 21.0 + - - +
529A GLY* 3.6 25.3 - - - -
530A ASN* 4.1 2.3 + - - -
780A TYR* 5.8 2.2 + - - -
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Residues in contact with LYS 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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511A GLU 2.8 15.8 + - - +
512A GLY* 3.6 9.4 - - - +
514A ASN* 1.3 73.6 - - - +
516A ARG* 1.3 62.4 + - + +
518A LEU* 3.4 7.5 + - - +
519A GLU* 3.0 50.5 + - + +
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Residues in contact with ARG 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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509A MET* 5.3 0.8 + - - +
512A GLY* 2.9 28.0 + - - +
513A PHE* 3.7 46.9 - - + +
515A LYS* 1.3 73.5 - - + +
517A THR* 1.3 58.5 + - - +
519A GLU* 3.4 14.6 + - - +
520A ALA* 2.9 28.1 + - - +
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Residues in contact with THR 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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513A PHE* 2.6 24.2 + - - -
514A ASN* 3.1 4.7 + - - -
516A ARG* 1.3 74.2 - - - +
518A LEU* 1.3 60.5 + - - +
520A ALA* 3.1 8.6 + - + +
521A ASP* 2.8 26.7 + - - +
524A SER* 3.5 27.2 + - - +
525A THR 4.9 0.7 - - - +
528A MET* 4.3 6.3 - - + +
529A GLY* 3.6 30.4 - - - +
532A GLU* 3.8 19.2 - - + +
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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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514A ASN* 2.9 21.4 + - + +
515A LYS* 3.8 7.2 - - + +
517A THR* 1.3 75.8 - - + +
519A GLU* 1.3 59.0 + - + +
521A ASP 2.9 6.5 - - - +
522A PRO* 2.9 51.4 - - + +
524A SER* 3.5 27.1 - - - +
525A THR 6.0 0.9 - - - -
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Residues in contact with GLU 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 LYS* 3.0 56.6 + - + +
516A ARG* 3.4 12.7 + - - +
517A THR 3.2 0.2 - - - -
518A LEU* 1.3 76.9 - - + +
520A ALA* 1.3 66.4 + - - +
521A ASP* 4.3 0.3 - - - -
522A PRO* 4.5 5.4 - - - +
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Residues in contact with ALA 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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516A ARG 2.9 14.8 + - - +
517A THR* 3.4 11.0 - - + +
519A GLU* 1.3 76.1 - - - +
521A ASP* 1.3 62.6 + - + +
522A PRO* 4.4 2.1 - - - +
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Residues in contact with ASP 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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371A ARG* 2.8 22.7 + - - -
517A THR 2.8 6.0 + - - +
518A LEU* 2.9 7.8 + - - +
520A ALA* 1.3 81.7 - - + +
522A PRO* 1.3 63.6 - - - +
523A THR* 2.5 28.0 + - - +
524A SER* 2.8 41.2 + - - +
810A ARG* 2.7 27.8 + - - +
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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