Contacts of the helix formed by residues 482 - 495 (chain C) in PDB entry 1M7X
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 ASN 482 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C LYS 3.2 2.0 + - - -
481C TRP* 1.3 70.2 - - - +
483C LEU* 1.3 60.4 + - - +
484C GLY 3.7 2.6 + - - -
485C TRP* 3.0 25.5 + - + +
486C MET* 3.4 12.8 + - - +
510C GLY 4.8 4.4 + - - -
513C TYR* 2.8 32.9 + - - -
514C ASN* 5.0 2.6 - - - +
519C PHE* 3.0 49.8 - - + +
520C VAL 3.1 18.0 + - - +
521C LEU* 4.2 10.3 - - + +
522C PRO* 3.4 14.6 - - + +
560C PHE* 5.6 1.4 - - - -
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C GLU* 3.2 27.8 - - - +
459C GLU 4.0 8.1 - - - +
460C SER* 3.8 25.8 - - - +
481C TRP* 3.0 42.7 + - + +
482C ASN* 1.3 70.5 - - - +
484C GLY* 1.3 61.1 + - - +
486C MET* 3.3 24.2 + - + +
487C HIS* 2.9 43.3 + - + -
522C PRO* 4.8 3.6 - - + -
524C SER* 6.1 0.2 - - - +
527C GLU* 5.3 2.2 - - - +
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Residues in contact with GLY 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ASN* 3.3 4.8 + - - -
483C LEU* 1.3 76.8 - - - +
485C TRP* 1.3 65.7 + - - +
487C HIS* 3.4 7.5 + - - +
488C ASP* 3.0 34.7 + - - +
513C TYR* 3.7 8.7 - - - -
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Residues in contact with TRP 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ASN* 3.0 30.2 + - + +
484C GLY* 1.3 74.5 - - - +
486C MET* 1.3 70.5 + - + +
488C ASP* 4.1 2.2 - - - +
489C THR* 2.4 64.5 + - + +
506C LYS 5.5 1.3 - - - -
507C LEU* 5.8 1.3 + - - -
510C GLY* 4.7 9.6 - - - -
513C TYR* 3.1 8.5 + - - +
521C LEU* 4.0 29.8 - - + -
522C PRO* 4.4 2.7 - - + -
523C LEU* 4.3 7.2 - - + -
553C TYR* 3.6 27.1 - + - -
556C TRP* 4.2 11.8 - + - +
557C MET* 3.2 55.2 - - + -
560C PHE* 3.8 40.2 - + + -
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Residues in contact with MET 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ASN 3.4 8.9 + - - +
483C LEU* 3.3 28.9 + - + +
485C TRP* 1.3 87.0 - - + +
487C HIS* 1.3 91.8 + - + +
489C THR* 3.5 4.7 - - - -
490C LEU* 2.9 51.5 + - + +
522C PRO* 3.6 26.9 - - + +
523C LEU* 4.3 1.8 - - + -
527C GLU* 3.2 46.0 - - + +
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Residues in contact with HIS 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LEU* 2.9 30.5 + - + +
484C GLY* 3.9 7.1 - - - +
485C TRP 3.3 0.2 - - - -
486C MET* 1.3 109.9 - - + +
488C ASP* 1.3 54.2 + - - +
490C LEU* 3.5 2.3 - - - +
491C ASP* 2.6 48.4 + - - +
527C GLU* 4.4 7.9 + - - -
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Residues in contact with ASP 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C GLY* 3.0 21.5 + - - +
485C TRP* 4.1 2.2 - - - +
487C HIS* 1.3 81.1 - - - +
489C THR* 1.3 52.5 + - - +
491C ASP* 2.9 17.7 + - - +
492C TYR 2.7 30.5 + - - -
506C LYS* 3.2 43.0 + - + +
509C PHE* 4.7 16.9 - - - -
513C TYR* 5.4 1.0 + - - -
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Residues in contact with THR 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C TRP* 2.4 64.3 + - + +
486C MET* 3.3 5.5 + - - -
488C ASP* 1.3 71.8 - - - +
490C LEU* 1.3 56.5 + - - +
492C TYR* 2.8 10.7 + - - +
493C MET* 2.8 38.5 + - - +
506C LYS 3.8 15.0 - - - +
507C LEU* 4.3 11.6 - - + +
553C TYR* 3.4 25.0 + - + -
556C TRP* 4.8 6.3 - - + +
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C MET* 2.9 39.8 + - + +
487C HIS* 3.5 4.5 - - + +
489C THR* 1.3 81.4 + - - +
491C ASP* 1.3 60.0 + - - +
493C MET* 3.3 8.3 + - + +
494C LYS* 2.8 36.8 + - + +
523C LEU* 4.0 13.2 - - + -
527C GLU* 4.7 7.2 - - + +
535C ILE* 4.5 10.5 - - + -
538C ARG* 3.4 43.2 - - - +
539C MET* 5.9 0.4 - - + -
553C TYR* 2.8 36.8 - - + +
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Residues in contact with ASP 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C HIS* 2.6 35.5 + - - +
488C ASP* 2.9 19.0 + - - +
490C LEU* 1.3 79.0 - - - +
492C TYR* 1.3 60.8 + - - +
494C LYS* 3.4 25.0 + - - +
495C LEU* 3.2 27.5 + - - +
506C LYS* 3.6 21.0 + - + -
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Residues in contact with TYR 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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488C ASP 2.7 13.1 + - - +
489C THR 2.8 7.6 + - - +
491C ASP* 1.3 76.0 - - - +
493C MET* 1.3 72.7 + - - +
495C LEU* 3.3 11.6 + - + +
500C ARG* 3.0 77.3 + - + +
503C HIS* 3.5 28.5 - - + -
504C HIS* 4.0 4.7 - - - -
506C LYS* 4.0 5.8 - - + -
507C LEU* 3.2 48.5 - - + +
637C SER* 3.2 23.0 + - - -
639C LEU* 4.4 1.7 - - - +
657C PHE* 3.3 20.2 - + + -
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Residues in contact with MET 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C THR 2.8 18.4 + - - +
490C LEU* 3.7 5.6 - - - +
492C TYR* 1.3 89.1 - - - +
494C LYS* 1.3 52.8 - - - +
500C ARG* 3.4 12.9 + - - +
539C MET* 3.4 34.8 - - + -
540C PRO* 2.8 34.8 - - - +
549C ASN* 2.9 51.4 - - + +
552C ALA* 5.3 1.3 - - + -
553C TYR* 3.4 39.5 - - + +
657C PHE* 5.6 11.0 - - + -
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C LEU* 2.8 23.6 + - - +
491C ASP* 3.7 29.3 + - - +
492C TYR 3.2 0.4 - - - -
493C MET* 1.3 77.0 - - - +
495C LEU* 1.3 65.3 + - - +
496C ASP 3.3 2.1 + - - -
538C ARG* 3.3 50.6 - - + +
540C PRO* 3.8 11.8 - - - +
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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
----------------------------------------------------------
491C ASP 3.2 17.8 + - - +
492C TYR* 3.3 20.2 + - + +
494C LYS* 1.3 79.0 - - - +
496C ASP* 1.3 62.5 + - - +
497C PRO 3.3 0.2 - - - -
499C TYR* 3.8 17.3 - - + -
500C ARG* 2.6 38.2 + - - -
503C HIS* 3.2 58.3 - - + +
506C LYS* 4.2 5.6 - - - -
540C PRO* 3.7 2.9 - - - +
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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