Contacts of the helix formed by residues 491 - 506 (chain C) in PDB entry 4MNE
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 THR 491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489C ALA 2.8 10.2 + - - -
490C PRO* 1.3 71.5 - - - +
492C PRO* 1.3 69.9 - - + +
493C GLN* 2.8 28.5 - - + +
494C GLN* 2.6 53.7 + - + +
495C LEU* 2.9 11.1 + - - +
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Residues in contact with PRO 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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490C PRO 3.4 5.1 - - - +
491C THR* 1.3 90.4 - - + +
493C GLN* 1.3 58.2 + - + +
495C LEU* 4.1 12.2 - - + +
496C GLN* 3.4 22.5 + - - +
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Residues in contact with GLN 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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491C THR* 2.8 15.9 - - + +
492C PRO* 1.3 82.0 - - + +
494C GLN* 1.3 59.9 + - + +
495C LEU 3.4 0.4 - - - -
496C GLN* 3.7 12.8 - - - +
497C ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 494 (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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485C LEU* 3.7 43.7 - - + +
487C VAL* 4.6 16.6 - - - +
489C ALA 3.1 10.0 - - - +
490C PRO* 3.8 3.5 - - + +
491C THR* 2.6 49.3 + - - +
493C GLN* 1.3 72.6 - - + +
495C LEU* 1.3 62.0 + - - +
497C ALA* 3.2 7.1 + - - +
498C PHE* 3.1 24.9 + - - +
525C LEU* 4.3 2.1 - - - +
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Residues in contact with LEU 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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490C PRO* 4.8 11.8 - - + -
491C THR 2.9 12.6 + - - +
492C PRO* 4.2 10.5 - - + +
494C GLN* 1.3 75.3 - - - +
496C GLN* 1.3 64.3 + - - +
498C PHE* 3.7 7.1 - - + +
499C LYS* 3.0 50.1 + - - +
521C THR* 6.1 2.5 - - + -
525C LEU* 4.2 24.0 - - + +
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Residues in contact with GLN 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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492C PRO 3.4 18.1 + - - +
493C GLN* 3.7 17.5 - - - +
494C GLN 3.2 0.4 - - - -
495C LEU* 1.3 79.1 - - - +
497C ALA* 1.3 63.2 + - - +
499C LYS* 3.3 20.4 + - - +
500C ASN* 2.7 58.5 + - - +
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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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493C GLN 3.1 15.0 + - - +
494C GLN* 3.2 13.0 + - - +
496C GLN* 1.3 75.8 - - - +
498C PHE* 1.3 63.1 + - - +
500C ASN* 3.0 9.4 + - - +
501C GLU* 3.0 24.9 + - - +
596C GLY 6.1 0.9 - - - +
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Residues in contact with PHE 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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485C LEU* 5.8 2.9 - - + -
494C GLN 3.1 13.4 + - - +
495C LEU* 3.7 8.5 - - + +
497C ALA* 1.3 79.1 - - - +
499C LYS* 1.3 67.8 + - - +
501C GLU* 3.9 7.2 - - - +
502C VAL* 3.1 32.3 + - + +
519C TYR* 3.9 26.7 - + + -
520C SER 3.6 13.2 - - - -
521C THR* 4.2 4.9 - - + -
525C LEU* 3.4 37.5 - - + -
526C ALA* 3.2 44.2 - - - -
527C ILE* 3.9 14.1 - - + -
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Residues in contact with LYS 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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495C LEU* 3.0 49.5 + - - +
496C GLN* 3.5 22.4 + - - +
497C ALA 3.3 0.2 - - - -
498C PHE* 1.3 80.7 - - - +
500C ASN* 1.3 65.9 + - - +
502C VAL* 4.0 4.0 - - - +
503C GLY* 3.0 22.9 + - - -
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Residues in contact with ASN 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 GLN* 2.7 45.6 + - - +
497C ALA* 3.0 7.6 + - - +
499C LYS* 1.3 79.1 - - - +
501C GLU* 1.3 58.1 + - - +
503C GLY* 3.2 2.5 + - - +
504C VAL* 2.7 41.9 + - + +
598C ALA 5.3 7.2 - - - +
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Residues in contact with GLU 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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483C LYS* 2.4 41.1 + - - +
497C ALA 3.0 16.4 + - - +
498C PHE* 3.9 6.7 - - - +
500C ASN* 1.3 74.9 - - - +
502C VAL* 1.3 59.5 + - - +
504C VAL* 3.2 6.7 + - - +
505C LEU* 2.9 37.5 + - + +
527C ILE* 3.5 22.0 - - + +
595C PHE* 3.5 28.3 + - + +
596C GLY* 3.6 20.1 + - - -
598C ALA 5.5 1.8 + - - -
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Residues in contact with VAL 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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498C PHE* 3.1 24.5 + - + +
499C LYS* 4.0 4.0 - - - +
501C GLU* 1.3 78.7 - - - +
503C GLY* 1.3 59.7 + - - +
504C VAL 3.0 0.5 + - - -
505C LEU* 3.1 8.7 + - - +
506C ARG* 2.8 52.0 + - + +
516C PHE* 4.3 9.9 - - + -
519C TYR* 3.9 45.8 - - + -
527C ILE* 4.1 19.3 - - + -
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Residues in contact with GLY 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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499C LYS 3.0 17.7 + - - -
500C ASN* 3.2 5.1 + - - -
502C VAL* 1.3 75.9 - - - +
504C VAL* 1.3 62.2 + - - +
506C ARG* 3.7 19.5 + - - +
507C LYS* 3.5 22.5 + - - +
600C VAL* 5.5 0.8 - - - +
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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 ASN* 2.7 24.8 + - + +
501C GLU* 3.6 6.1 - - - +
503C GLY* 1.3 72.7 - - - +
505C LEU* 1.3 67.5 + - - +
507C LYS* 2.9 25.9 + - - +
508C THR* 4.1 3.9 + - - +
572C ILE* 3.9 26.5 - - + -
595C PHE* 3.7 27.6 - - + -
598C ALA* 4.0 27.1 - - + +
599C THR* 4.3 3.6 - - - -
600C VAL* 4.1 22.0 - - + +
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Residues in contact with LEU 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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509B ARG* 3.8 2.4 + - - -
501C GLU* 2.9 37.6 + - + +
502C VAL* 3.5 4.3 - - - +
504C VAL* 1.3 74.3 - - - +
506C ARG* 1.3 55.2 + - - +
507C LYS 2.8 4.5 + - - -
508C THR* 2.6 34.4 + - - +
514C LEU* 4.9 9.9 - - + +
516C PHE* 3.8 34.1 - - + +
527C ILE* 3.7 33.0 - - + -
529C THR* 4.9 6.7 - - + -
595C PHE* 3.9 37.0 - - + -
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Residues in contact with ARG 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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450B TRP* 3.3 22.0 - - - -
509B ARG* 3.3 11.0 + - - +
449C ASP* 3.8 24.7 + - - +
450C TRP* 4.1 26.8 + - + +
502C VAL* 2.8 37.5 + - + +
503C GLY* 3.7 19.1 - - - +
504C VAL 3.1 0.2 + - - -
505C LEU* 1.3 70.7 - - - +
507C LYS* 1.3 58.4 + - + +
508C THR 3.2 1.8 - - - -
516C PHE* 4.2 15.4 - - + -
519C TYR* 4.5 12.7 - - - -
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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