Contacts of the helix formed by residues 501 - 518 (chain B) in PDB entry 3ODO
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 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B LEU* 2.9 44.2 + - + +
500B PHE* 1.3 79.4 - - - +
502B GLY* 1.3 76.4 + - - +
503B ALA 3.5 1.9 + - - -
504B GLU* 3.6 11.1 + - - +
505B GLY 3.4 6.4 + - - -
590B LEU* 4.2 17.2 - - - +
594B CYS* 4.1 12.2 - - - -
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PHE 4.2 1.0 + - - -
501B ASP* 1.3 82.4 + - - +
503B ALA* 1.3 52.6 + - - -
505B GLY* 3.0 2.4 + - - -
506B SER* 2.8 39.2 + - - -
594B CYS* 5.4 1.0 - - - -
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ASP 3.5 1.0 + - - -
502B GLY* 1.3 70.5 - - - -
504B GLU* 1.3 66.3 + - - +
506B SER* 2.9 11.0 + - - -
507B TRP* 2.7 35.1 + - - +
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ARG* 6.1 0.9 - - - +
497B LEU 4.6 1.6 - - - +
498B ALA* 3.3 31.5 - - - +
499B ARG* 3.2 37.7 + - - +
500B PHE 4.5 1.1 - - - -
501B ASP 3.8 11.4 - - - +
502B GLY 3.5 0.8 - - - -
503B ALA* 1.3 86.0 + - - +
505B GLY* 1.3 52.9 + - - +
507B TRP* 3.3 3.6 + - - +
508B PHE* 2.8 29.9 + - - +
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Residues in contact with GLY 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B PHE* 3.3 34.9 - - - -
501B ASP 3.4 4.8 + - - -
502B GLY 3.0 6.3 + - - -
504B GLU* 1.3 75.3 - - - +
506B SER* 1.3 54.9 + - - +
508B PHE* 3.1 4.7 + - - +
509B GLN* 2.7 37.3 + - - +
598B ILE* 4.2 7.9 - - - +
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Residues in contact with SER 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLY 2.8 19.4 + - - -
503B ALA* 2.9 11.2 + - - -
505B GLY* 1.3 70.8 - - - +
507B TRP* 1.3 55.8 + - - +
509B GLN* 3.5 12.3 + - - +
510B LYS* 3.1 25.5 + - - +
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Residues in contact with TRP 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B GLU* 4.3 24.0 + - + -
470B VAL* 3.3 25.8 - - + +
499B ARG* 3.2 26.6 - - - +
503B ALA 2.7 16.1 + - - +
504B GLU* 3.6 8.5 - - - +
506B SER* 1.3 68.7 - - - +
508B PHE* 1.3 61.6 + - - +
509B GLN 3.0 1.6 - - - -
510B LYS* 2.9 43.1 + - - +
511B ILE* 3.0 41.3 + - + +
514B ARG* 5.7 0.7 - - - -
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Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B VAL* 3.7 22.7 - - + -
471B HIS* 3.5 42.2 - + - -
474B PHE* 6.3 1.8 - + - -
499B ARG* 3.0 40.2 - - + +
500B PHE* 3.9 22.0 - + - -
504B GLU 2.8 12.5 + - - +
505B GLY* 3.5 5.6 - - - +
507B TRP* 1.3 74.6 - - - +
509B GLN* 1.3 67.0 + - - +
511B ILE* 4.0 2.0 - - - +
512B SER* 3.1 30.7 + - - -
561B GLU* 4.9 0.4 - - - -
565B LEU* 3.7 27.4 - - + -
568B TYR* 4.1 6.5 - + - -
598B ILE* 4.3 17.0 - - + -
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Residues in contact with GLN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B GLY 2.7 16.7 + - - +
506B SER* 3.5 10.7 + - - +
508B PHE* 1.3 81.5 - - - +
510B LYS* 1.3 66.0 + - - +
512B SER* 3.9 1.1 - - - -
513B SER* 2.8 28.1 + - - -
597B GLU* 4.3 3.8 - - - +
598B ILE* 3.9 35.8 + - + +
601B HIS* 3.3 54.6 + - + +
602B VAL* 4.4 4.6 - - + +
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Residues in contact with LYS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B SER 3.1 10.5 + - - +
507B TRP* 2.9 36.0 + - - +
509B GLN* 1.3 83.0 - - - +
511B ILE* 1.3 63.0 + - - +
513B SER* 3.7 5.7 + - - -
514B ARG* 3.1 56.1 + - - +
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Residues in contact with ILE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B PRO 5.0 1.2 - - - +
463B SER* 4.2 10.5 - - - +
466B GLU* 3.9 18.6 - - + +
467B LEU* 3.7 37.2 - - + +
470B VAL* 4.6 7.9 - - + -
507B TRP* 3.0 63.4 + - + +
508B PHE 4.5 2.0 - - - +
510B LYS* 1.3 73.9 - - + +
512B SER* 1.3 67.0 + - - +
514B ARG* 3.2 36.7 + - - +
515B PHE* 3.3 12.0 + - - +
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Residues in contact with SER 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LEU* 4.1 13.3 - - - +
470B VAL* 5.7 0.2 - - - +
508B PHE* 3.1 28.8 + - - -
509B GLN* 3.9 2.5 - - - -
511B ILE* 1.3 76.2 - - - +
513B SER* 1.3 62.7 + - - +
515B PHE* 3.1 5.3 + - - +
516B CYS* 2.9 25.8 + - - -
561B GLU* 3.1 25.7 + - - +
565B LEU* 3.5 27.3 - - - +
598B ILE* 5.6 0.4 - - - -
602B VAL* 4.7 1.3 - - - -
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Residues in contact with SER 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLN* 2.8 23.0 + - - -
510B LYS* 3.7 6.4 + - - -
512B SER* 1.3 68.1 - - - +
514B ARG* 1.3 67.8 + - - +
516B CYS* 4.2 0.2 - - - +
517B SER* 2.9 30.7 + - - -
601B HIS* 5.0 6.9 + - - -
602B VAL* 3.9 26.7 - - - +
605B ALA* 3.6 22.3 - - - +
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B PRO* 3.7 25.5 - - + +
463B SER* 3.4 26.0 + - - +
507B TRP* 5.7 0.4 - - - -
510B LYS* 3.1 51.4 + - - +
511B ILE* 3.2 22.5 + - - +
513B SER* 1.3 79.8 + - - +
515B PHE* 1.3 68.6 + - - +
517B SER* 3.2 11.8 + - - -
518B ARG* 3.9 3.8 + - - +
609B MET* 5.6 1.3 - - - +
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Residues in contact with PHE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B LEU* 5.1 5.6 - - + -
438B LEU* 4.3 18.2 - - + -
460B ILE 5.1 2.9 - - - -
461B PHE* 4.4 13.9 - + - -
462B PRO* 4.0 30.9 + - + +
464B LEU* 3.7 29.6 - - + -
467B LEU* 3.6 27.8 - - + -
511B ILE 3.3 5.5 + - - +
512B SER 3.1 7.8 + - - +
514B ARG* 1.3 82.5 - - - +
516B CYS* 1.3 68.7 + - - +
517B SER 2.9 1.7 + - - -
518B ARG* 3.1 13.3 + - - +
519B GLN* 4.0 4.6 + - + -
557B MET 5.4 0.7 - - - -
558B ILE* 3.6 34.5 - - + -
561B GLU* 4.0 20.2 - - + -
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Residues in contact with CYS 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B SER 2.9 19.2 + - - +
513B SER 4.2 0.2 - - - +
515B PHE* 1.3 77.4 - - - +
517B SER* 1.3 61.6 + - - +
519B GLN* 3.2 25.3 + - - +
561B GLU* 3.5 31.6 - - - -
562B MET* 3.6 31.8 - - + +
565B LEU* 4.2 6.3 - - - -
602B VAL* 3.8 27.1 - - + -
606B VAL* 3.4 10.1 - - + +
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Residues in contact with SER 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B SER* 2.9 20.4 + - - -
514B ARG* 3.2 9.5 + - - -
515B PHE 2.9 0.4 + - - -
516B CYS* 1.3 79.8 - - - +
518B ARG* 1.3 58.2 + - - +
519B GLN 3.3 3.1 + - - -
520B SER* 4.8 3.3 + - - -
602B VAL* 6.2 0.2 - - - -
605B ALA* 3.9 12.3 - - - -
606B VAL* 3.5 34.6 - - - +
609B MET* 3.5 37.5 - - - +
610B GLU 5.1 0.7 + - - -
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Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ASN* 2.7 55.4 + - - +
460B ILE 4.8 1.1 - - - +
462B PRO* 4.1 15.3 - - + -
514B ARG 4.4 1.8 - - - +
515B PHE 3.1 11.8 + - - +
517B SER* 1.3 80.9 + - - +
519B GLN* 1.3 62.3 + - - -
520B SER 3.3 2.7 - - - -
521B PHE* 3.1 49.5 + - + -
522B ALA* 3.0 23.4 + - - +
609B MET* 4.3 27.9 - - + +
612B LEU* 5.9 0.8 - - - +
613B LEU* 3.9 26.1 - - - +
616B LYS* 6.1 1.0 - - - +
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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
------------------------------------------------------------
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