Contacts of the helix formed by residues 437 - 442 (chain K) in PDB entry 3GHG
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 TRP 437 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312K ILE* 4.3 15.0 - - + -
314K MET* 3.4 36.1 - - + -
324K ALA* 3.9 26.5 - - + -
326K TYR* 4.8 1.6 - - - -
349K ALA* 3.3 31.8 + - + +
350K GLY 2.8 28.7 + - - -
352K ALA* 3.8 12.9 - - + +
353K LEU* 4.1 24.9 - - + -
402K TRP* 5.7 1.6 - + - -
409K ALA 3.8 0.4 - - - -
410K ALA* 3.0 31.9 - - + -
412K PRO* 4.8 5.2 - - + -
436K VAL* 1.3 76.1 - - - +
438K MET* 1.3 50.8 + - - +
439K ASN* 2.6 10.4 + - + -
440K TRP* 2.4 39.8 + - + -
441K LYS 3.2 6.8 + - - -
447K MET* 3.3 10.5 - - + +
450K MET* 4.2 10.8 - - + -
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Residues in contact with MET 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K ALA* 4.0 18.2 - - + -
359K GLN* 2.7 42.8 + - + +
360K LEU* 4.3 13.9 - - + -
408K HIS* 3.4 29.4 - - + +
409K ALA* 2.9 22.1 + - - +
432K ASP* 4.5 1.1 - - - +
436K VAL* 3.7 2.3 - - + +
437K TRP* 1.3 71.7 - - - +
439K ASN* 1.3 64.0 + - - +
440K TRP 4.2 0.2 - - - -
441K LYS 3.7 0.3 + - - -
442K GLY* 3.1 23.7 + - - +
443K SER* 3.8 33.7 - - - +
1T GLY* 3.7 17.9 - - - -
2T HIS* 5.6 0.7 - - - +
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Residues in contact with ASN 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349K ALA 3.9 9.4 - - - +
350K GLY* 4.3 8.4 - - - +
351K ASN 3.8 4.2 + - - -
352K ALA* 3.4 25.8 + - - +
356K GLY 3.0 18.9 - - - +
357K ALA* 3.4 22.2 - - - +
358K SER* 3.6 27.1 + - - +
409K ALA 3.7 13.7 + - - -
437K TRP* 2.6 16.8 + - + -
438K MET* 1.3 74.8 - - - +
440K TRP* 1.3 56.0 + - - +
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Residues in contact with TRP 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314K MET* 4.4 4.7 - - + -
315K GLU 4.4 1.6 - - - -
316K ASP* 3.7 33.0 - - + -
320K ASP* 3.7 31.0 - - + -
321K LYS* 4.6 0.2 - - - -
322K VAL* 3.8 44.8 - - + +
348K THR 4.7 8.1 - - - -
349K ALA 3.9 10.3 - - - +
437K TRP* 2.4 29.0 + - + +
438K MET 4.2 0.7 - - - -
439K ASN* 1.3 75.3 - - - +
441K LYS* 1.3 88.9 + - + +
447K MET* 3.7 28.5 - - + -
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Residues in contact with LYS 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316K ASP* 4.1 12.4 + - - -
318K LYS* 3.4 27.5 - - - +
320K ASP* 5.6 1.8 + - - -
437K TRP 3.2 3.2 + - - -
440K TRP* 1.3 128.2 - - + +
442K GLY* 1.3 64.9 + - - +
444K TRP 5.0 0.7 - - - -
445K TYR* 3.5 42.3 + - + +
447K MET* 4.2 7.6 - - + -
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Residues in contact with GLY 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359K GLN* 4.1 13.2 + - - -
436K VAL* 2.7 24.1 - - - +
438K MET* 3.1 23.3 + - - +
441K LYS* 1.3 77.7 - - - +
443K SER* 1.3 51.7 + - - -
444K TRP* 2.7 18.9 + - - -
445K TYR 3.1 6.6 + - - -
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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