Contacts of the helix formed by residues 405 - 423 (chain C) in PDB entry 1GGE
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 ASP 405 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275C HIS* 2.6 37.9 + - + +
276C THR 4.5 2.0 + - - +
290C ARG* 5.6 0.3 + - - -
353C LEU 5.3 0.3 - - - +
354C LEU* 3.3 29.5 - - - +
355C ASP 4.7 0.2 - - - -
356C PRO* 3.6 13.2 - - - +
403C THR* 3.3 16.5 + - - +
404C ASN* 1.3 70.0 - - - +
406C PRO* 1.3 66.4 - - - +
407C LEU* 2.8 21.5 + - - +
408C LEU* 3.1 13.6 + - + +
409C GLN* 2.8 30.5 + - - +
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Residues in contact with PRO 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 4.7 0.9 + - - -
96B ARG* 3.3 36.6 - - - +
101B GLY 5.7 0.2 - - - +
103B THR* 4.6 3.7 + - - +
209C GLN 3.3 20.4 - - - +
210C ASP* 4.0 8.9 - - + +
211C ALA* 3.3 18.3 + - - +
354C LEU* 3.6 10.8 - - + +
404C ASN 2.8 9.6 - - - +
405C ASP* 1.3 87.4 - - - +
407C LEU* 1.3 61.8 + - - +
409C GLN* 4.0 8.2 - - + +
410C GLY* 3.6 6.1 + - - -
497C ARG* 5.6 1.3 - - - -
501C PHE* 3.6 24.5 - - + -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 3.6 28.3 - - + -
208C ILE* 3.5 43.3 - - + +
209C GLN 3.4 10.9 + - - +
210C ASP 3.9 0.9 - - - -
211C ALA* 3.6 17.9 - - - +
275C HIS* 3.8 3.6 - - + -
356C PRO* 3.6 12.6 - - + -
405C ASP* 2.8 9.9 + - - +
406C PRO* 1.3 75.1 - - - +
408C LEU* 1.3 67.3 + - - +
410C GLY 3.2 2.3 + - - -
411C ARG* 2.9 24.3 + - - +
760C HDD 3.4 41.7 - - + -
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C HIS* 3.4 46.3 - - + +
276C THR 4.3 3.8 - - - +
277C PHE* 3.9 32.3 - - + -
393C PRO* 4.5 10.1 - - + -
402C PHE* 4.2 7.2 - - + -
403C THR* 4.1 30.5 - - - +
405C ASP* 3.1 11.3 + - + +
407C LEU* 1.3 79.7 - - - +
409C GLN* 1.3 65.4 + - - +
411C ARG* 3.0 17.5 + - + +
412C LEU* 3.1 32.2 + - + +
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Residues in contact with GLN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.5 16.6 - - - +
106A GLU* 3.0 40.5 + - - +
101B GLY 5.0 0.4 - - - +
102B PRO* 3.5 8.0 - - - +
103B THR* 2.8 50.6 + - - +
402C PHE* 4.9 2.8 - - - +
403C THR 3.0 19.5 + - - +
404C ASN* 3.7 18.1 + - - +
405C ASP 2.8 25.0 + - - +
406C PRO* 4.0 4.7 - - + +
408C LEU* 1.3 77.2 - - - +
410C GLY* 1.3 60.3 + - - +
412C LEU* 3.3 21.9 + - - +
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Residues in contact with GLY 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.1 11.2 - - - -
94B SER* 5.6 0.4 - - - -
103B THR* 4.7 1.5 + - - -
110B LEU* 5.1 8.5 - - - -
114B ILE* 5.1 2.3 - - - +
211C ALA* 3.3 24.0 - - - -
406C PRO 3.6 4.2 + - - -
407C LEU 3.2 3.8 + - - -
409C GLN* 1.3 73.5 - - - +
411C ARG* 1.3 66.4 + - - +
412C LEU 3.2 1.6 - - - -
413C PHE* 3.2 15.4 + - - +
414C SER* 3.5 7.3 + - - -
760C HDD 3.9 6.9 - - - +
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Residues in contact with ARG 411 (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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199C VAL* 3.1 45.3 + - - +
273C GLY 4.5 1.0 + - - -
275C HIS* 3.0 41.3 + - - -
277C PHE* 5.3 1.2 - - - -
393C PRO* 3.5 24.3 - - + +
407C LEU 2.9 16.0 + - - +
408C LEU* 3.3 10.1 - - + +
410C GLY* 1.3 76.1 - - - +
412C LEU* 1.3 61.8 + - - +
414C SER 3.0 12.6 + - - -
415C TYR* 2.7 51.7 + - + -
760C HDD 3.3 60.7 - - + +
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 4.5 2.5 - - - +
106A GLU* 3.5 34.5 - - + +
108A PHE* 6.2 0.2 - - + -
111A ARG* 2.9 31.4 + - - +
392C HIS* 3.1 20.7 + - - +
393C PRO* 4.2 1.1 - - + -
394C GLY* 3.5 34.1 - - - +
402C PHE* 3.6 31.0 - - + -
408C LEU* 3.1 26.7 + - + +
409C GLN* 3.4 16.8 - - - +
410C GLY 3.2 0.8 - - - -
411C ARG* 1.3 76.2 - - - +
413C PHE* 1.3 56.3 + - - +
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Residues in contact with PHE 413 (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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105A LEU* 3.9 24.1 - - + +
111A ARG* 3.9 10.6 + - - +
110B LEU* 6.2 1.3 - - + -
111B ARG* 3.7 37.0 - - + -
114B ILE* 3.6 31.0 - - + -
115B THR* 3.2 29.6 - - - -
409C GLN 4.1 1.0 + - - -
410C GLY 3.2 10.1 + - - +
411C ARG 3.1 1.0 - - - -
412C LEU* 1.3 78.6 - - - +
414C SER* 1.3 67.5 + - - +
415C TYR 3.6 0.2 + - - -
416C THR* 3.7 3.6 + - - -
417C ASP* 3.4 38.3 + - + +
413D PHE* 3.7 31.0 - + - -
417D ASP* 6.3 0.7 - - + -
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Residues in contact with SER 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 3.9 6.3 - - - -
118B ASP* 2.6 34.2 + - - +
410C GLY 3.5 0.6 + - - -
411C ARG 3.0 8.4 + - - -
413C PHE* 1.3 82.2 - - - +
415C TYR* 1.3 59.0 + - - -
416C THR 3.3 0.2 + - - -
417C ASP 3.3 0.5 + - - -
418C THR* 3.0 28.9 + - - -
760C HDD 2.9 48.8 + - - +
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Residues in contact with TYR 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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199C VAL* 4.0 5.8 - - + -
391C PHE 3.2 20.6 - - - +
392C HIS* 2.1 39.9 + - + +
393C PRO* 3.5 16.4 - - + -
411C ARG* 2.7 59.0 + - + -
414C SER* 1.3 74.8 - - - +
416C THR* 1.3 51.5 + - - +
418C THR* 3.8 2.4 - - - +
419C GLN* 2.5 37.8 + - - +
428C PHE* 5.2 0.2 - - - -
760C HDD 2.0 83.4 + + + -
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Residues in contact with THR 416 (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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108A PHE* 6.1 1.0 - - - +
111A ARG* 4.2 14.7 + - - +
112A GLU* 4.9 15.4 + - + +
115A THR* 4.0 31.4 - - + +
392C HIS* 3.5 21.2 + - - -
395C HIS* 5.0 4.6 + - - -
413C PHE 3.7 5.3 + - - -
414C SER 3.3 0.8 - - - -
415C TYR* 1.3 75.9 - - - +
417C ASP* 1.3 68.3 + - - +
419C GLN* 3.3 15.4 + - - +
420C ILE* 4.0 8.0 + - - +
428C PHE* 4.5 19.6 - - + -
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Residues in contact with ASP 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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115A THR* 6.0 0.9 - - - -
115B THR* 3.4 20.1 + - - +
118B ASP* 2.4 34.7 - - - +
119B HIS* 2.8 33.7 + - - -
413C PHE* 3.4 32.4 + - + +
414C SER 3.3 0.4 + - - +
416C THR* 1.3 80.6 - - - +
418C THR* 1.3 63.2 + - - +
420C ILE* 3.0 19.6 + - - +
413D PHE* 6.4 0.7 - - + -
417D ASP* 4.4 14.4 - - - +
420D ILE* 4.6 3.6 - - - +
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Residues in contact with THR 418 (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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118B ASP* 2.7 36.0 + - - -
119B HIS* 3.9 2.5 - - - -
126C ILE* 3.8 14.0 + - - +
414C SER 3.0 22.2 + - - +
415C TYR 3.8 0.2 - - - +
417C ASP* 1.3 72.3 - - - +
419C GLN* 1.3 89.6 + - + +
420C ILE 3.2 0.7 + - - -
421C SER* 3.4 7.6 + - - -
422C ARG* 3.1 23.7 + - - +
760C HDD 3.5 28.9 - - + +
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Residues in contact with GLN 419 (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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390C ALA* 4.0 12.2 - - - +
391C PHE 4.3 8.7 + - - -
392C HIS* 5.6 1.0 - - - +
415C TYR 2.5 31.3 + - - +
416C THR 3.3 7.2 + - - +
417C ASP 3.1 2.0 + - - -
418C THR* 1.3 80.8 - - - +
420C ILE* 1.3 60.7 + - - +
422C ARG* 3.7 21.8 - - - +
423C LEU* 2.8 54.8 + - + +
424C GLY 3.5 1.0 + - - -
425C GLY 3.9 4.8 + - - +
428C PHE* 3.9 30.4 - - + -
760C HDD 2.7 27.7 + - - -
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Residues in contact with ILE 420 (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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115A THR* 3.8 25.4 - - + -
119A HIS* 3.6 42.0 - - + +
119B HIS* 4.2 4.9 - - + -
416C THR 4.0 7.6 + - - +
417C ASP* 3.0 19.4 + - - +
419C GLN* 1.3 76.0 - - - +
421C SER* 1.3 58.0 + - - +
424C GLY* 3.2 6.9 - - - -
425C GLY* 3.0 47.2 + - - +
426C PRO* 3.7 6.7 - - + -
428C PHE* 5.1 3.6 - - + -
417D ASP* 4.5 3.4 - - - +
420D ILE* 3.9 14.4 - - + -
421D SER* 4.8 6.3 - - - +
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Residues in contact with SER 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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448A MET* 3.7 10.6 - - - +
118B ASP 4.0 1.4 + - - -
119B HIS* 2.7 41.5 + - - -
121B ARG 5.0 6.0 + - - -
123C PRO* 3.8 13.8 - - - +
126C ILE* 5.8 0.3 - - - +
418C THR 3.4 5.2 + - - -
419C GLN 3.2 0.2 - - - -
420C ILE* 1.3 79.6 - - - +
422C ARG* 1.3 70.2 + - - +
423C LEU 3.4 0.2 + - - -
424C GLY* 3.4 7.2 + - - -
420D ILE* 4.8 5.8 - - - -
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Residues in contact with ARG 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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448A MET* 3.4 15.1 - - - +
122C ILE* 3.7 9.7 - - + +
123C PRO* 3.4 28.2 - - + +
124C GLU 4.2 2.0 - - - +
125C ARG* 3.5 47.7 - - - +
126C ILE* 5.3 0.4 - - - +
387C GLU* 2.8 30.5 + - - -
389C ALA 2.8 23.2 + - - -
390C ALA* 3.6 14.1 - - - +
418C THR* 3.1 17.7 + - - +
419C GLN* 3.7 17.9 - - - +
421C SER* 1.3 85.4 + - - +
423C LEU* 1.3 74.8 + - + +
760C HDD 3.8 20.5 + - - -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A MET* 3.3 15.3 - - - +
449A HIS* 4.5 9.9 + - - +
122C ILE* 4.0 9.2 - - + -
388C GLN* 3.4 38.4 - - + +
390C ALA* 3.7 11.7 - - + -
419C GLN* 2.8 40.0 + - + +
422C ARG* 1.3 98.6 - - - +
424C GLY* 1.3 60.4 + - - +
425C GLY 3.3 6.0 + - - +
428C PHE* 3.6 28.9 - - + +
431C ILE* 4.0 17.4 - - + +
434C ASN* 4.0 3.1 - - - +
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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