Contacts of the helix formed by residues 429 - 442 (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 429 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366C ARG* 3.4 13.8 + - - +
369C MET* 3.4 21.9 - - + +
372C LEU* 3.7 14.8 - - + -
373C THR* 2.7 41.7 + - - +
376C GLN* 3.9 29.0 - - + +
426C LEU* 4.5 8.0 + - - +
427C LEU 3.4 0.2 - - - -
428C ILE* 1.3 75.2 - - + +
430C MET* 1.4 64.3 + - - +
431C PRO 3.4 2.0 - - - -
432C ILE* 3.5 19.2 + - - +
433C PHE* 3.6 28.3 - - + -
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Residues in contact with MET 430 (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 LEU* 4.0 13.8 + - + +
427C LEU* 3.5 10.5 + - + +
428C ILE 3.4 0.6 - - - -
429C GLN* 1.4 76.4 - - - +
431C PRO* 1.4 64.1 - - + +
433C PHE* 3.8 4.3 + - - +
434C LEU* 3.2 51.9 + - + +
129Y ILE* 4.7 8.5 - - - -
130Y PHE* 3.9 27.1 - - + -
133Y ILE* 3.4 37.5 - - + -
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Residues in contact with PRO 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU* 3.5 14.5 - - + +
427C LEU* 3.7 12.3 - - + +
428C ILE 3.6 15.0 - - - +
430C MET* 1.4 89.3 - - + +
432C ILE* 1.4 65.3 + - + +
434C LEU* 4.0 1.7 - - + +
435C ALA* 2.9 29.6 + - - +
149Y VAL 5.6 1.3 - - - +
150Y ILE* 3.9 32.0 - - + +
158Y PHE* 5.9 7.2 - - + -
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Residues in contact with ILE 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU* 4.5 9.2 - - + -
344C LEU* 4.2 24.5 - - + -
365C VAL* 4.0 24.9 - - + -
369C MET* 4.2 21.5 - - + -
428C ILE* 4.0 14.6 - - + +
429C GLN* 3.7 13.2 - - - +
430C MET 3.5 0.4 - - - -
431C PRO* 1.4 80.7 - - + +
433C PHE* 1.4 59.6 + - + +
435C ALA* 3.2 7.2 + - - +
436C LEU* 2.9 44.1 + - + +
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Residues in contact with PHE 433 (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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362C THR* 4.2 15.9 - - + -
365C VAL* 4.3 22.9 - - + -
366C ARG* 3.3 53.8 - - - -
369C MET* 4.9 5.2 - - + -
429C GLN* 3.6 34.8 - - + -
430C MET* 3.8 5.2 + - - +
432C ILE* 1.4 70.8 - - + +
434C LEU* 1.3 58.6 + - - +
436C LEU* 3.8 14.6 - - + -
437C TYR* 3.0 25.1 + - - +
516C TYR* 3.2 29.2 + + - +
520C SER* 4.2 8.1 - - - -
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Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C MET* 3.2 45.1 + - + +
431C PRO* 4.0 3.6 - - + +
433C PHE* 1.3 74.0 - - - +
435C ALA* 1.3 60.2 + - - +
437C TYR* 3.2 18.8 + - + +
438C TYR* 2.8 66.3 + - + +
133Y ILE* 6.0 3.6 - - + -
148Y LEU* 5.9 2.2 - - + -
149Y VAL* 6.2 1.8 - - + -
150Y ILE* 4.2 22.2 - - + -
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Residues in contact with ALA 435 (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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340C LEU* 3.5 28.5 - - + -
341C PHE* 3.7 22.5 - - + -
344C LEU* 3.9 9.9 - - + -
431C PRO 2.9 20.1 + - - +
432C ILE 3.2 4.9 + - - +
434C LEU* 1.3 76.2 - - - +
436C LEU* 1.4 50.4 + - - +
438C TYR 3.4 0.3 + - - -
439C MET* 2.9 41.3 + - - +
150Y ILE* 4.2 3.2 - - + +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 4.3 7.2 - - + -
358C ILE* 3.8 31.0 - - + +
361C ILE* 4.6 9.2 - - + -
362C THR* 3.7 24.0 - - - +
365C VAL* 5.7 1.3 - - + -
432C ILE* 2.9 36.4 + - + +
433C PHE* 3.8 23.3 - - + -
435C ALA* 1.4 52.3 - - - +
437C TYR* 1.3 63.4 + - - +
439C MET* 3.5 23.4 - - + +
440C LEU* 3.3 30.2 + - + +
516C TYR* 3.6 23.1 - - + +
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Residues in contact with TYR 437 (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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433C PHE 3.0 21.7 + - - +
434C LEU* 3.2 18.6 + - + +
436C LEU* 1.3 73.8 - - - +
438C TYR* 1.3 85.9 + + - +
440C LEU* 3.8 1.0 - - - +
441C MET* 2.9 65.6 + - + +
505C PHE* 4.1 20.5 - + - -
506C PHE* 4.8 14.4 - + - -
513C LEU* 3.9 4.2 - - + +
516C TYR* 4.3 8.0 - - + -
517C TYR* 3.8 21.8 - - + +
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Residues in contact with TYR 438 (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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335C PHE* 5.2 5.0 - - - -
336C ILE* 4.6 23.4 - - + +
341C PHE* 3.6 26.0 - + + -
434C LEU* 2.8 49.5 + - + +
436C LEU 3.4 0.2 - - - -
437C TYR* 1.3 95.9 - + - +
439C MET* 1.3 64.8 + - - +
441C MET* 3.9 5.4 - - + +
442C GLY* 3.5 14.7 + - - -
148Y LEU* 4.3 25.2 - - + +
150Y ILE* 4.1 13.7 - - + -
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Residues in contact with MET 439 (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 PHE* 3.3 48.0 - - + +
344C LEU* 3.5 22.4 - - + -
345C LYS* 4.1 22.9 - - - +
358C ILE* 3.9 13.5 - - + -
435C ALA 2.9 24.8 + - - +
436C LEU* 3.5 33.7 - - + +
438C TYR* 1.3 73.4 - - - +
440C LEU* 1.4 58.7 + - + +
442C GLY 4.0 0.9 - - - -
443C SER* 3.2 29.0 + - - -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ILE* 3.8 31.4 - - + -
436C LEU 3.3 15.7 + - - +
439C MET* 1.4 76.2 - - + +
441C MET* 1.3 63.4 + - - +
443C SER* 3.6 15.3 - - - +
446C LEU* 4.0 35.7 - - + +
510C PRO* 5.8 0.9 - - - +
512C GLY 3.9 14.1 - - - +
513C LEU* 3.6 25.2 - - + +
516C TYR* 3.3 49.1 - - + -
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Residues in contact with MET 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C TYR* 2.9 59.3 + - + +
438C TYR* 3.9 9.0 - - + +
439C MET 3.4 0.2 - - - -
440C LEU* 1.3 78.2 - - - +
442C GLY* 1.3 57.9 - - - +
443C SER 3.6 0.7 + - - +
509C PHE* 3.9 40.8 - - + -
510C PRO* 5.7 3.3 - - - +
513C LEU* 3.6 25.2 - - + +
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Residues in contact with GLY 442 (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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236C ASP 4.0 16.1 - - - +
237C THR* 5.4 2.6 - - - +
239C ALA* 6.4 2.0 - - - -
438C TYR 3.5 10.0 + - - -
439C MET 4.0 2.0 - - - -
441C MET* 1.3 76.7 - - - +
443C SER* 1.4 65.3 + - - +
444C VAL* 3.7 3.8 + - - +
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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