Contacts of the helix formed by residues 485 - 498 (chain C) in PDB entry 3MSS
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 SER 485 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355C GLU* 3.6 18.4 - - - -
419C LYS* 3.6 13.6 - - - +
422C VAL* 4.8 0.7 - - - -
484C PRO* 1.3 74.8 - - - +
486C PHE* 1.3 59.0 + - - +
487C ALA* 3.4 7.9 + - - +
488C GLU* 3.0 38.1 + - - +
489C ILE* 2.9 27.2 + - - +
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Residues in contact with PHE 486 (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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348C SER* 4.3 8.3 - - - +
351C MET* 3.4 50.7 - - + -
352C GLU* 3.5 22.7 - - - +
355C GLU* 2.8 22.3 + - - +
364C LEU* 4.3 0.2 - - + -
418C ILE* 3.8 10.8 - - + -
421C ASP* 3.6 13.5 - - + -
422C VAL* 3.5 38.1 - - + +
425C PHE* 3.7 27.8 - + + -
484C PRO 4.1 0.4 + - - -
485C SER* 1.3 67.3 - - - +
487C ALA* 1.3 55.9 + - - +
489C ILE* 3.8 18.3 - - + +
490C HIS* 2.7 37.2 + - - +
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Residues in contact with ALA 487 (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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352C GLU* 3.9 25.3 - - + +
355C GLU* 3.1 15.0 + - - +
485C SER* 3.5 9.0 - - - +
486C PHE* 1.3 75.6 - - - +
488C GLU* 1.3 59.2 + - + +
490C HIS* 3.9 1.9 - - - +
491C GLN* 3.0 30.3 + - - +
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Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C PRO* 3.3 17.2 - - + +
485C SER* 3.0 35.2 + - - +
487C ALA* 1.3 74.4 - - + +
489C ILE* 1.3 66.3 + - - +
491C GLN* 3.4 6.9 + - - +
492C ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 489 (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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348C SER* 3.9 7.9 - - - -
422C VAL* 3.7 29.6 - - + -
425C PHE* 3.6 14.1 - - + -
471C LEU* 4.3 12.3 - - + -
475C CYS* 3.9 13.9 - - - -
484C PRO* 3.9 17.0 - - + -
485C SER 2.9 22.2 + - - +
486C PHE* 3.8 24.0 - - + +
488C GLU* 1.3 75.1 - - - +
490C HIS* 1.3 58.4 + - - +
492C ALA* 3.0 8.3 + - - +
493C PHE* 2.9 54.7 + - + -
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Residues in contact with HIS 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C THR* 3.6 24.0 + - + +
348C SER* 3.3 31.3 + - - +
349C SER* 3.8 25.6 + - - -
352C GLU* 2.6 33.7 - - - +
486C PHE 2.7 20.0 + - - +
487C ALA 3.9 0.7 - - - +
489C ILE* 1.3 73.8 - - - +
491C GLN* 1.3 56.6 + - - +
493C PHE* 3.1 1.8 + - - +
494C GLU* 2.6 62.6 + - + +
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Residues in contact with GLN 491 (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 ALA 3.0 19.0 + - - +
488C GLU* 3.6 7.9 - - - +
490C HIS* 1.3 79.2 - - + +
492C ALA* 1.4 58.5 + - - +
494C GLU* 4.3 14.1 - - - +
495C THR* 2.9 42.9 + - - +
244D MET 4.7 12.2 + - - +
245D LYS* 5.4 7.9 + - - +
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Residues in contact with ALA 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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471C LEU* 3.9 27.6 - - + -
488C GLU 2.9 18.1 + - - +
489C ILE 3.0 5.1 + - - +
491C GLN* 1.4 79.0 - - - +
493C PHE* 1.3 61.7 + - - +
495C THR* 3.4 6.0 + - - +
496C MET* 3.2 32.2 + - + +
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Residues in contact with PHE 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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341C LEU* 3.6 22.2 - - + +
344C ALA* 4.1 12.8 - - + -
345C THR* 3.4 22.6 + - - +
348C SER* 3.9 11.0 - - - +
425C PHE* 3.6 17.3 - + - -
429C LEU* 3.6 33.2 - - + -
468C VAL* 4.5 14.6 - - + -
471C LEU* 3.6 14.4 - - + -
489C ILE* 2.9 45.1 + - + -
490C HIS 3.7 4.5 - - - +
492C ALA* 1.3 75.5 - - - +
494C GLU* 1.3 54.9 + - - +
496C MET* 3.2 16.7 + - + +
497C PHE* 2.7 36.7 + - - +
516C MS7 4.9 1.6 - + - -
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Residues in contact with GLU 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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345C THR* 4.2 6.4 - - + +
490C HIS* 2.6 50.1 + - + +
491C GLN* 3.8 15.3 - - - +
493C PHE* 1.3 70.2 - - - +
495C THR* 1.3 65.0 + - - +
497C PHE* 3.1 8.6 + - + +
498C GLN* 2.9 34.6 + - + +
242D ILE 5.0 2.1 - - - +
243D THR* 4.2 24.5 - - + +
244D MET* 4.8 5.8 + - - +
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Residues in contact with THR 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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491C GLN* 2.9 28.4 + - - +
492C ALA* 3.5 7.2 - - - +
493C PHE 3.1 0.2 - - - -
494C GLU* 1.3 80.7 - - - +
496C MET* 1.3 65.9 + - + +
498C GLN* 3.2 20.9 + - - +
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Residues in contact with MET 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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341C LEU* 4.0 17.6 - - + +
467C LYS* 3.9 42.6 - - + +
468C VAL* 4.0 21.8 - - + +
471C LEU* 4.3 20.2 - - + -
492C ALA* 3.2 19.0 + - + +
493C PHE* 3.2 20.2 + - + +
495C THR* 1.3 81.0 - - + +
497C PHE* 1.3 63.4 + - - +
498C GLN 3.1 9.4 - - - +
516C MS7 4.0 27.3 - - + +
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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
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338C VAL* 4.2 17.7 - - + -
341C LEU* 3.7 23.5 - - + +
342C TYR* 3.5 49.6 - + + -
345C THR* 4.0 20.4 - - + +
493C PHE 2.7 21.7 + - - +
494C GLU* 3.1 6.9 + - - +
496C MET* 1.3 75.2 - - - +
498C GLN* 1.3 67.4 + - + +
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Residues in contact with GLN 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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494C GLU* 2.9 26.3 + - + +
495C THR* 3.2 16.6 - - - +
496C MET* 3.1 13.2 - - - +
497C PHE* 1.3 88.5 + - - +
243D THR* 3.4 35.3 + - + +
262D LYS* 3.7 25.6 - - - +
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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