Contacts of the helix formed by residues 465 - 476 (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 PRO 465 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337C ALA* 6.0 0.9 - - + -
463C GLY 3.3 9.9 - - - +
464C CYS* 1.3 88.8 - - - +
466C GLU* 1.3 66.5 + - - +
467C LYS* 4.4 5.8 - - + +
468C VAL* 3.1 17.5 + - + +
469C TYR* 3.0 18.7 + - - +
516C MS7 3.4 61.9 - - + +
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Residues in contact with GLU 466 (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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460C ARG* 4.5 13.6 - - - +
464C CYS 3.5 2.5 + - - -
465C PRO* 1.3 71.2 - - - +
467C LYS* 1.4 58.9 + - + +
469C TYR* 3.3 8.6 + - - +
470C GLU* 2.9 41.4 + - + +
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Residues in contact with LYS 467 (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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465C PRO* 3.3 4.6 - - + +
466C GLU* 1.4 75.3 - - + +
468C VAL* 1.3 66.6 + - + +
470C GLU* 3.4 22.6 + - - +
471C LEU* 3.1 23.9 + - - +
496C MET* 3.9 30.1 - - + +
516C MS7 6.3 0.2 - - + -
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Residues in contact with VAL 468 (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* 5.5 0.2 - - + -
429C LEU* 4.3 15.9 - - + +
464C CYS* 3.7 17.3 - - - -
465C PRO* 3.1 20.0 + - + +
467C LYS* 1.3 78.1 - - - +
469C TYR* 1.3 63.6 + - - +
471C LEU* 3.2 7.5 + - - +
472C MET* 3.0 23.7 + - + +
493C PHE* 4.5 6.3 - - + -
496C MET* 4.0 22.7 - - + -
516C MS7 3.6 49.8 - - + +
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Residues in contact with TYR 469 (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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458C MET 2.5 26.8 + - - -
459C GLU* 3.6 5.6 - - - -
460C ARG* 3.3 62.9 + - + -
464C CYS* 3.8 4.8 - - - -
465C PRO 3.0 8.1 + - - +
466C GLU* 3.7 7.6 - - - +
468C VAL* 1.3 74.7 - - - +
470C GLU* 1.3 66.0 + - + +
472C MET* 3.2 26.1 + - + +
473C ARG* 2.9 65.8 + - + +
476C TRP* 4.5 1.6 - + - -
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Residues in contact with GLU 470 (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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466C GLU* 2.9 34.5 + - + +
467C LYS* 3.6 28.7 + - - +
468C VAL 3.3 0.2 - - - -
469C TYR* 1.3 77.2 - - + +
471C LEU* 1.3 64.8 + - + +
473C ARG* 3.4 8.9 + - - +
474C ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 471 (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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429C LEU* 4.5 5.8 - - + -
467C LYS 3.1 10.6 + - - +
468C VAL* 3.4 10.1 - - - +
469C TYR 3.2 0.2 - - - -
470C GLU* 1.3 81.0 - - + +
472C MET* 1.3 63.3 + - - +
474C ALA* 3.2 10.8 + - + +
475C CYS* 3.0 28.0 + - - -
484C PRO* 5.6 3.6 - - + -
489C ILE* 4.2 19.7 - - + +
492C ALA* 3.9 31.2 - - + -
493C PHE* 3.6 39.3 - - + -
496C MET* 4.3 8.1 - - + -
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Residues in contact with MET 472 (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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426C GLY* 4.0 5.4 - - - +
429C LEU* 3.8 30.0 - - + +
430C TRP* 3.7 33.4 - - - +
433C ALA* 4.3 1.8 - - + -
461C PRO* 4.2 9.2 - - + -
464C CYS* 3.9 28.3 - - - -
468C VAL* 3.0 16.6 + - + +
469C TYR* 3.3 21.8 - - + +
471C LEU* 1.3 76.7 - - - +
473C ARG* 1.3 57.7 + - - +
475C CYS* 3.2 10.3 + - - +
476C TRP* 3.1 60.0 + - + -
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Residues in contact with ARG 473 (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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455C ASP 5.2 3.4 + - - -
457C ARG* 3.7 34.3 + - - +
458C MET 4.4 0.4 + - - -
469C TYR* 2.9 60.2 + - + +
470C GLU* 3.6 8.5 - - - +
471C LEU 3.3 0.2 - - - -
472C MET* 1.3 76.5 - - - +
474C ALA* 1.3 64.7 - - - +
476C TRP* 3.1 29.4 + - - +
477C GLN* 3.3 18.2 + - - +
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Residues in contact with ALA 474 (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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470C GLU 3.0 14.0 + - - +
471C LEU* 3.2 14.3 + - + +
473C ARG* 1.3 74.3 - - - +
475C CYS* 1.3 63.7 + - - +
477C GLN* 3.3 30.3 + - + +
482C ASP 5.6 0.7 - - - +
483C ARG* 3.6 2.4 - - - -
484C PRO* 3.3 31.1 - - + +
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Residues in contact with CYS 475 (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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422C VAL* 3.3 41.7 - - - +
423C TRP* 3.4 11.6 - - - -
425C PHE* 4.1 8.7 - - - -
426C GLY* 3.8 18.8 - - - -
429C LEU* 5.3 0.4 - - - -
471C LEU* 3.0 22.1 + - - -
472C MET* 3.2 8.9 + - - +
474C ALA* 1.3 77.6 - - - +
476C TRP* 1.3 60.0 + - + +
477C GLN 3.4 0.4 - - - -
483C ARG* 3.3 22.5 + - - -
484C PRO* 4.3 2.9 - - - -
489C ILE* 3.9 18.6 - - - -
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Residues in contact with TRP 476 (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 TRP* 3.3 38.5 + + + -
426C GLY* 3.3 24.2 - - - -
427C VAL* 3.3 25.6 - - + +
430C TRP* 4.0 6.5 - + + -
440C TYR* 5.1 3.8 - - - -
457C ARG* 2.8 53.2 + - + +
458C MET* 3.7 55.6 - - + -
469C TYR* 4.5 0.9 - + - -
472C MET* 3.1 38.6 + - + -
473C ARG* 3.1 29.9 + - - +
475C CYS* 1.3 78.1 - - - +
477C GLN* 1.3 59.9 + - - +
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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
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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