Contacts of the helix formed by residues 491 - 506 (chain C) in PDB entry 5MG3
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 GLN 491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C MET 4.7 8.1 - - - +
383C MET* 3.8 32.3 - - + +
384C ARG* 4.2 7.4 - - - +
418C ASN 5.8 0.4 - - - +
420C LEU* 3.6 43.3 - - + +
489C PRO 3.3 4.6 + - - -
490C MET* 1.3 78.3 - - + +
492C GLN* 1.4 62.9 + - - +
493C LYS 3.5 2.2 - - - -
494C ILE* 3.3 46.0 + - - +
495C MET 4.4 0.9 + - - -
1Y MET* 3.7 19.1 - - - +
91Y ILE* 5.1 7.3 - - - +
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Residues in contact with GLN 492 (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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380C MET 6.0 0.6 + - - -
383C MET* 5.1 7.6 + - - +
384C ARG* 2.8 25.9 + - - +
484C THR 4.5 6.3 + - - -
485C THR* 4.4 4.8 - - - +
486C VAL* 3.5 47.2 - - + +
488C ASP 3.3 25.1 - - - +
489C PRO 4.4 1.7 + - - +
490C MET 2.9 14.0 + - - +
491C GLN* 1.4 72.1 - - - +
493C LYS* 1.3 60.9 + - + +
494C ILE 3.2 0.2 - - - -
495C MET* 3.2 32.2 + - - +
496C THR* 4.0 3.5 + - - +
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Residues in contact with LYS 493 (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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489C PRO 5.5 1.2 + - - -
491C GLN 3.5 0.4 - - - -
492C GLN* 1.3 76.4 - - + +
494C ILE* 1.4 58.9 + - - +
495C MET 3.3 1.1 - - - -
496C THR* 3.4 18.2 - - - +
497C PHE* 2.8 72.6 + - + +
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Residues in contact with ILE 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C MET* 3.7 32.0 - - + +
383C MET* 6.1 0.4 - - + -
491C GLN* 3.4 48.7 - - - +
492C GLN 3.2 0.8 - - - -
493C LYS* 1.4 74.6 - - - +
495C MET* 1.4 62.0 + - - +
497C PHE* 4.1 8.2 + - + +
498C MET* 4.1 17.6 + - + +
1Y MET* 4.4 19.3 - - + -
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Residues in contact with MET 495 (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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377C TYR* 3.8 33.2 - - + +
380C MET* 3.6 41.7 - - + +
381C ALA* 4.3 5.8 - - + -
479C GLN* 3.0 42.7 + - + +
483C PRO* 3.8 40.4 - - + +
491C GLN 5.1 0.2 - - - +
492C GLN* 3.2 16.7 + - - +
494C ILE* 1.4 78.5 - - - +
496C THR* 1.3 67.1 + - + +
497C PHE 3.6 0.4 + - - -
498C MET* 4.0 6.2 + - - +
499C PRO* 4.6 0.3 - - - +
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Residues in contact with THR 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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476C PHE* 5.7 9.6 - - + -
479C GLN* 6.0 2.9 - - + -
485C THR* 6.6 0.4 - - + -
492C GLN 4.1 1.9 + - - +
493C LYS* 3.3 28.9 + - - +
495C MET* 1.3 84.0 - - + +
497C PHE* 1.3 64.8 + - - +
498C MET 3.2 1.1 - - - -
499C PRO* 3.1 16.5 - - - +
500C VAL* 4.1 9.5 - - - +
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Residues in contact with PHE 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LYS* 2.8 62.2 + - + +
494C ILE* 4.1 7.4 + - + +
495C MET 3.6 0.2 - - - -
496C THR* 1.3 72.8 + - - +
498C MET* 1.3 63.2 + - - +
500C VAL* 3.3 20.2 + - + +
501C ILE* 3.0 35.7 + - + +
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Residues in contact with MET 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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376C GLN* 4.4 10.3 - - - +
380C MET* 4.2 26.9 - - + -
475C MET* 5.9 0.9 - - + +
479C GLN* 3.5 32.3 - - + +
494C ILE* 4.1 13.2 + - + +
495C MET 4.0 6.2 + - - +
496C THR 3.2 2.0 + - - -
497C PHE* 1.3 76.6 - - - +
499C PRO* 1.4 64.2 - - + +
501C ILE* 3.4 9.9 + - + +
502C PHE* 3.1 56.6 + - + -
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Residues in contact with PRO 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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472C GLY 3.9 20.9 - - - +
475C MET* 4.0 18.8 - - + +
476C PHE* 3.9 35.9 - - + +
479C GLN* 4.7 4.7 - - + -
495C MET 4.6 1.3 - - - +
496C THR* 3.1 29.2 - - - +
498C MET* 1.4 85.0 - - + +
500C VAL* 1.4 55.6 + - + +
502C PHE* 4.3 1.3 - - + -
503C THR* 2.9 37.4 + - - +
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Residues in contact with VAL 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 THR 4.1 14.1 - - - +
497C PHE* 3.4 20.4 - - + +
499C PRO* 1.4 80.2 - - + +
501C ILE* 1.4 68.7 + - + +
503C THR* 4.5 1.2 - - - -
504C VAL* 3.8 23.6 + - + +
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Residues in contact with ILE 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 PHE* 3.0 26.9 + - + +
498C MET* 3.5 16.4 - - + +
500C VAL* 1.4 81.6 - - + +
502C PHE* 1.3 79.1 + - + +
504C VAL* 4.2 1.6 - - - +
505C PHE* 3.1 26.6 + - - +
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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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471C MET* 4.3 1.3 - - - -
475C MET* 3.6 40.4 - - + -
498C MET* 3.1 49.2 + - + +
499C PRO 4.1 2.5 - - - +
500C VAL 3.5 0.2 - - - -
501C ILE* 1.3 87.4 - - + +
503C THR* 1.4 63.5 + - - +
505C PHE* 3.3 6.0 + + - +
506C PHE* 3.0 66.8 + + + +
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Residues in contact with THR 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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468C PRO* 4.3 17.8 - - + +
469C ILE* 5.6 2.2 - - + -
471C MET* 3.8 12.1 - - - +
472C GLY* 3.2 24.0 - - - -
499C PRO* 2.9 25.0 + - - +
500C VAL* 4.5 2.7 - - - -
502C PHE* 1.4 71.5 - - - +
504C VAL* 1.4 63.7 + - + +
506C PHE 4.2 0.2 - - - -
507C LEU* 3.1 33.3 + - + +
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Residues in contact with VAL 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 VAL* 3.8 17.2 + - + +
501C ILE* 3.6 3.7 + - - +
502C PHE 3.4 0.2 - - - -
503C THR* 1.4 82.1 - - + +
505C PHE* 1.4 60.9 + - - +
506C PHE 3.5 0.2 - - - -
507C LEU* 3.8 10.1 - - + +
508C TRP* 3.4 35.3 - - + -
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Residues in contact with PHE 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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437C TYR* 4.1 22.4 - + - -
501C ILE* 3.1 20.0 + - + +
502C PHE* 3.8 7.6 - + - +
504C VAL* 1.4 77.5 - - - +
506C PHE* 1.4 94.0 + + - +
507C LEU 3.4 2.0 + - - -
508C TRP* 4.0 12.7 + - - +
509C PHE* 5.5 2.6 - - - -
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Residues in contact with PHE 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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437C TYR* 4.8 10.8 - + - -
468C PRO* 4.9 0.2 - - - +
471C MET* 3.7 18.4 - - + -
475C MET* 4.2 7.4 - - + -
502C PHE* 3.0 64.2 + + + +
503C THR 4.2 0.4 - - - -
505C PHE* 1.4 104.7 - + - +
507C LEU* 1.3 55.8 + - - +
508C TRP 3.1 18.3 - - - +
509C PHE 4.2 0.7 - - - +
514C VAL* 3.5 22.6 - - + +
517C TYR* 3.5 54.5 - + + -
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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