Contacts of the helix formed by residues 414 - 425 (chain C) in PDB entry 3GXM
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 414 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C VAL 5.1 0.2 - - - -
15C VAL* 3.7 6.4 - - + +
352C VAL* 4.0 1.6 - - - +
353C ARG 2.9 18.3 + - - +
354C LEU* 3.2 8.9 - - + -
355C GLY* 2.7 32.9 + - - -
356C SER* 4.0 0.5 + - - -
399C ASP* 2.7 32.3 + - - -
400C SER 3.7 7.4 - - - +
401C PRO* 2.9 21.1 + - + +
403C ILE* 3.6 18.6 - - + +
412C TYR 4.6 1.6 - - - +
413C LYS* 1.3 74.9 - - - +
415C PRO* 1.3 73.3 - - + +
416C MET* 4.0 17.5 - - + +
417C PHE* 3.0 17.0 + - - +
418C TYR* 3.4 7.3 - - - -
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Residues in contact with PRO 415 (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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13C SER* 4.5 0.2 - - - -
14C VAL 3.7 19.1 - - - +
48C ARG* 3.8 11.9 - - - +
355C GLY* 3.7 30.7 - - - +
356C SER 3.5 22.0 - - - +
357C TRP* 3.8 25.8 - - + +
360C GLY* 4.5 0.7 - - - -
414C GLN* 1.3 85.8 - - + +
416C MET* 1.3 63.5 + - - +
418C TYR* 2.9 12.5 + - + +
419C HIS* 2.9 31.0 + - + -
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C VAL* 5.0 2.0 - - - -
353C ARG 5.5 0.2 - - - +
356C SER* 4.7 2.6 + - - +
359C ARG* 3.7 35.4 - - + +
360C GLY* 3.6 11.8 - - - +
363C TYR* 3.6 35.3 - - + -
399C ASP* 3.3 46.4 - - + +
400C SER 3.7 13.2 - - - +
401C PRO* 4.2 18.8 - - + -
414C GLN* 3.3 15.4 - - + +
415C PRO* 1.3 75.4 - - - +
417C PHE* 1.3 56.4 + - - +
419C HIS* 3.5 3.2 + - - +
420C LEU* 3.0 32.2 + - - +
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Residues in contact with PHE 417 (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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26C PHE* 6.0 1.6 - + - -
107C SER 3.7 21.8 - - - -
108C TYR* 3.6 37.0 - + - -
114C ILE* 3.6 33.3 - - + +
401C PRO* 3.6 21.3 - - + +
402C ILE* 3.9 22.2 - - + -
413C LYS* 3.5 28.5 - - + -
414C GLN 3.0 16.4 + - - +
415C PRO 3.0 0.2 + - - -
416C MET* 1.3 77.4 - - - +
418C TYR* 1.3 86.2 + + - +
420C LEU* 3.6 3.6 - - - +
421C GLY* 3.1 19.1 + - - -
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Residues in contact with TYR 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C CYS* 3.0 32.1 - - - +
24C ASP* 2.7 30.8 + - - -
26C PHE* 5.4 4.9 - + - -
42C SER* 4.0 17.3 - - - +
48C ARG* 3.7 32.8 - - + -
49C MET* 3.8 28.1 - - + +
357C TRP* 6.2 0.9 - - + -
413C LYS* 3.5 26.1 - - + +
414C GLN 3.4 11.9 - - - -
415C PRO* 2.9 6.6 + - + +
417C PHE* 1.3 95.4 - + - +
419C HIS* 1.3 61.6 + - + +
420C LEU 3.3 0.2 - - - -
421C GLY* 3.1 1.8 + - - +
422C HIS* 2.9 36.3 + - - -
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Residues in contact with HIS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 5.8 0.2 - - - -
357C TRP* 3.2 47.8 - + - -
360C GLY* 3.4 26.8 + - - +
361C MET* 3.7 21.4 + - + -
363C TYR* 4.6 1.1 - - + -
364C SER* 2.8 30.9 + - - +
367C ILE* 4.7 0.2 - - - +
415C PRO* 2.9 27.7 + - + +
416C MET 3.7 7.2 - - - +
418C TYR* 1.3 77.8 - - + +
420C LEU* 1.3 57.4 + - - +
422C HIS* 3.5 5.9 + - - +
423C PHE* 3.1 29.7 - - - -
461C LEU* 4.1 4.7 - - + -
489C ILE* 3.9 20.4 - - + +
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Residues in contact with LEU 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 4.9 11.7 - - + -
82C GLY 5.2 2.9 - - - +
108C TYR* 5.4 0.4 - - + -
114C ILE* 4.5 3.1 - - + -
116C TYR* 3.0 33.7 - - + +
312C TRP* 5.9 1.1 - - + -
341C ALA* 6.5 0.7 - - + -
363C TYR* 4.0 19.2 - - + +
367C ILE* 3.9 23.6 - - + -
378C TRP* 5.6 5.4 - - + -
380C ASP* 4.2 14.1 - - + +
401C PRO* 3.9 27.1 - - + -
416C MET 3.0 17.6 + - - +
417C PHE* 3.6 6.7 - - - +
419C HIS* 1.3 75.1 - - - +
421C GLY* 1.3 57.7 + - - +
423C PHE* 3.1 8.3 + - - +
424C SER* 2.8 28.0 + - - -
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Residues in contact with GLY 421 (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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49C MET* 3.4 9.4 - - - +
114C ILE* 3.6 24.2 - - - +
417C PHE 3.1 5.2 + - - -
418C TYR 3.1 7.7 + - - -
420C LEU* 1.3 73.9 - - - +
422C HIS* 1.3 62.1 + - - +
423C PHE 3.0 5.4 + - - -
424C SER* 3.6 12.8 - - - -
425C LYS* 3.1 26.3 + - - +
426C PHE* 3.7 0.3 - - - -
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Residues in contact with HIS 422 (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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40C TYR* 3.2 31.6 - - + -
42C SER* 2.8 30.8 + - - -
49C MET* 3.8 16.2 - - + +
418C TYR 2.9 25.5 + - - -
419C HIS 3.7 4.3 - - - +
420C LEU 3.2 0.6 - - - -
421C GLY* 1.3 75.1 - - - +
423C PHE* 1.3 60.2 + - + +
426C PHE* 3.4 12.0 - - - +
427C ILE* 5.1 0.2 - - - +
459C VAL* 3.7 10.8 - - + +
489C ILE* 3.0 57.8 + - + +
490C HIS 3.8 1.6 - - - -
491C THR* 2.9 39.3 + - - +
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Residues in contact with PHE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 3.7 21.3 - - + -
364C SER* 3.5 28.7 - - - -
367C ILE* 3.6 32.5 - - + -
368C ILE* 3.6 27.6 - - + -
371C LEU* 4.2 3.8 - - + -
419C HIS 3.1 28.0 - - - -
420C LEU 3.1 4.9 + - - +
422C HIS* 1.3 79.3 - - - +
424C SER* 1.3 60.1 + - - +
425C LYS 3.2 1.8 - - - -
426C PHE 3.1 2.3 + - - -
427C ILE* 2.9 52.8 + - + +
447C VAL* 4.2 7.2 - - + -
459C VAL* 3.5 35.2 - - + -
489C ILE* 4.1 1.8 - - + -
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Residues in contact with SER 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 3.4 39.1 - - - -
114C ILE* 2.7 31.0 + - - +
115C GLY 3.7 3.1 - - - +
116C TYR* 3.9 10.4 - - - -
170C ARG* 2.7 30.8 + - - -
420C LEU* 2.8 20.9 + - - -
421C GLY* 3.6 7.6 - - - -
423C PHE* 1.3 73.8 - - - +
425C LYS* 1.3 52.2 + - - +
426C PHE 3.5 0.3 + - - -
427C ILE 4.1 5.2 + - - +
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Residues in contact with LYS 425 (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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26C PHE* 3.4 42.7 - - + +
27C ASP 5.0 1.8 + - - -
29C PRO* 5.1 8.4 - - - +
40C TYR* 5.0 3.6 - - - -
49C MET* 4.2 3.4 - - + -
111C GLU* 2.7 30.9 + - - +
113C GLY 2.8 21.4 + - - +
114C ILE* 3.4 16.8 - - - +
170C ARG* 2.9 20.8 + - - +
421C GLY 3.1 18.1 + - - +
424C SER* 1.3 82.7 + - - +
426C PHE* 1.3 88.7 + - + +
427C ILE 3.7 0.4 - - - -
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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