Contacts of the helix formed by residues 495 - 506 (chain C) in PDB entry 5DO7
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 GLU 495 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488C TRP* 5.0 0.7 - - - -
493C HIS* 2.9 13.2 + - + +
494C PRO* 1.3 75.4 - - - +
496C VAL* 1.3 98.4 + - - +
497C ALA* 4.1 13.5 - - + +
498C ARG* 2.8 28.2 + - + +
499C PHE 3.1 9.0 + - - -
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Residues in contact with VAL 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C TRP* 4.1 21.1 - - + -
494C PRO 3.5 1.4 + - - -
495C GLU* 1.3 93.4 + - - +
497C ALA* 1.3 78.8 + - + +
499C PHE* 2.8 19.0 + - + +
500C GLY* 2.6 21.2 + - - -
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Residues in contact with ALA 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C GLU* 3.1 10.7 + - + +
496C VAL* 1.3 83.5 - - + +
498C ARG* 1.3 64.3 + - + +
500C GLY* 2.8 6.2 + - - +
501C TYR* 2.8 41.4 + - + -
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Residues in contact with ARG 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C TYR* 4.0 5.0 + - - +
493C HIS* 3.3 44.1 + - + +
495C GLU* 2.8 16.8 + - + +
497C ALA* 1.3 73.3 - - + +
499C PHE* 1.3 63.7 + - - +
501C TYR* 3.2 33.6 + - - -
502C PHE* 3.2 9.2 + - - +
578C ASN* 2.5 45.3 + - - +
581C TYR* 3.3 47.0 + - - -
620C PHE* 4.4 10.7 - - - -
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Residues in contact with PHE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C MET* 3.6 19.7 - - + -
483C SER* 3.5 28.9 - - - -
484C SER* 3.5 27.1 - - - -
487C TYR* 3.8 35.6 + + + -
488C TRP* 3.5 24.5 - + + +
495C GLU 3.1 6.5 + - - +
496C VAL* 2.8 21.9 + - + +
498C ARG* 1.3 76.5 - - - +
500C GLY* 1.3 67.2 + - - -
502C PHE* 2.8 24.1 + + - +
503C SER* 2.8 25.0 + - - -
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Residues in contact with GLY 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C VAL 2.6 16.5 + - - -
497C ALA* 2.8 8.9 + - - -
499C PHE* 1.3 82.9 - - - +
501C TYR* 1.3 60.2 + - - -
503C SER* 3.3 5.5 + - - -
504C ALA* 3.2 20.3 + - - +
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Residues in contact with TYR 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497C ALA* 2.8 29.5 + - + -
498C ARG* 3.2 40.5 + - - -
500C GLY* 1.3 72.2 - - - +
502C PHE* 1.3 50.5 + - - +
504C ALA* 2.8 24.6 + - + +
505C ALA* 2.8 19.3 + - - +
574C ILE* 5.6 0.4 - - + -
578C ASN* 3.4 15.9 - - + +
620C PHE* 4.1 22.2 - + + -
624C PHE* 3.7 28.3 - + + -
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Residues in contact with PHE 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C LEU* 4.6 4.7 - - + -
426C PHE* 3.5 36.8 - + - -
482C PHE* 4.0 11.9 - + - -
483C SER* 4.2 13.9 - - - -
486C CYS* 6.2 0.2 - - + -
487C TYR* 3.6 47.6 - + + -
492C LEU* 4.0 13.7 - - + -
498C ARG 3.2 12.8 + - - +
499C PHE* 2.8 14.9 + + - +
501C TYR* 1.3 73.7 - - - +
503C SER* 1.3 59.3 + - - +
505C ALA* 3.6 0.9 + - - +
506C LEU* 3.5 41.5 + - + +
575C LEU* 3.7 27.6 - - + -
578C ASN* 3.7 10.5 - - - +
579C GLU* 5.7 0.7 - - + -
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Residues in contact with SER 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C THR* 3.4 26.5 - - - +
480C MET* 3.7 24.8 - - - +
483C SER* 2.6 34.5 + - - -
499C PHE* 2.8 20.6 + - - -
500C GLY* 3.7 11.4 - - - -
502C PHE* 1.3 77.9 - - - +
504C ALA* 1.3 60.9 + - - +
505C ALA 3.4 0.2 - - - -
506C LEU* 4.1 1.1 - - - -
507C LEU* 3.7 5.9 + - - +
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Residues in contact with ALA 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C GLY 3.2 11.4 + - - +
501C TYR* 2.8 11.2 + - + +
503C SER* 1.3 76.4 - - - +
505C ALA* 1.3 65.3 + - - +
506C LEU 3.3 1.0 + - - -
507C LEU* 3.5 5.3 + - - -
508C ALA* 3.7 0.9 + - - +
624C PHE* 3.6 19.5 - - + -
628C TYR* 2.4 40.0 + - + +
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Residues in contact with ALA 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C TYR 2.8 14.3 + - - +
502C PHE 3.9 0.9 - - - +
503C SER 3.4 0.2 - - - -
504C ALA* 1.3 80.0 - - - +
506C LEU* 1.3 58.7 + - - +
509C PRO* 2.9 23.0 - - - +
571C CYS* 3.6 12.6 - - - -
574C ILE* 4.0 19.1 - - + -
575C LEU* 3.7 33.0 - - + -
624C PHE* 4.1 5.3 - - + -
627C LEU* 3.8 10.9 - - + +
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Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C ASN* 4.5 0.2 + - - -
426C PHE* 3.9 26.9 - - + -
427C VAL* 4.4 1.1 - - - +
430C THR* 3.9 26.8 - - + +
479C THR* 3.3 18.8 - - + +
482C PHE* 3.5 29.8 - - + -
502C PHE* 3.5 37.2 + - + +
503C SER 4.1 0.4 + - - -
504C ALA 3.3 0.4 - - - -
505C ALA* 1.3 80.1 - - - +
507C LEU* 1.3 62.2 + - - +
508C ALA 3.4 0.7 - - - -
509C PRO* 3.7 4.5 - - - -
510C HIS* 3.7 15.9 + - - +
571C CYS* 4.5 4.7 - - - -
575C LEU* 3.7 26.5 - - + -
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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