Contacts of the helix formed by residues 405 - 423 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A HIS* 2.7 35.7 + - + +
276A THR 4.4 1.8 + - - +
290A ARG* 5.6 0.2 + - - -
353A LEU 5.4 0.2 - - - +
354A LEU* 3.3 30.2 - - + +
355A ASP 4.7 0.2 - - - -
356A PRO* 3.5 14.2 - - - +
403A THR* 3.3 15.8 + - - +
404A ASN* 1.3 72.5 - - - +
406A PRO* 1.3 64.8 - - - +
407A LEU* 2.9 22.9 + - - +
408A LEU* 2.9 13.9 + - + +
409A GLN* 2.9 28.4 + - - +
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Residues in contact with PRO 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN 3.3 19.1 - - - +
210A ASP* 4.1 8.7 - - + +
211A ALA* 3.3 17.7 + - - +
354A LEU* 3.6 12.8 - - + +
404A ASN 2.8 9.6 - - - +
405A ASP* 1.3 82.3 - - - +
407A LEU* 1.3 61.5 + - - +
409A GLN* 3.9 9.8 - - + +
410A GLY 3.7 6.4 + - - -
497A ARG* 5.6 1.3 - - - -
501A PHE* 3.6 24.2 - - + -
94D SER* 4.7 1.4 + - - -
96D ARG* 3.3 36.6 - - - +
101D GLY 5.7 0.4 - - - +
103D THR* 4.6 3.1 + - - +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 3.7 28.9 - - + -
208A ILE* 3.4 40.8 - - + +
209A GLN 3.2 12.9 + - - +
210A ASP 3.8 1.6 - - - -
211A ALA* 3.7 18.4 - - - +
275A HIS* 3.9 3.8 - - + -
356A PRO* 3.7 10.8 - - + -
405A ASP* 2.9 9.2 + - - +
406A PRO* 1.3 75.6 - - - +
408A LEU* 1.3 66.1 + - - +
410A GLY 3.3 2.4 + - - -
411A ARG* 3.1 23.6 + - - +
760A HDD 3.4 42.6 - - + -
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS* 3.3 44.4 - - + +
276A THR 4.3 2.0 - - - +
277A PHE* 4.0 29.4 - - + -
393A PRO* 4.6 9.4 - - + -
402A PHE* 4.3 7.9 - - + -
403A THR* 3.9 36.1 - - - +
405A ASP* 2.9 12.8 + - - +
407A LEU* 1.3 76.0 - - - +
409A GLN* 1.3 64.2 + - - +
411A ARG* 3.1 14.5 + - + +
412A LEU* 3.2 32.6 + - + +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 4.7 2.6 - - - +
403A THR 2.9 24.0 + - - +
404A ASN* 3.6 13.9 + - - +
405A ASP 2.9 25.0 + - - +
406A PRO* 4.0 5.4 - - + +
407A LEU 3.2 0.4 - - - -
408A LEU* 1.3 76.8 - - - +
410A GLY* 1.3 59.9 + - - +
412A LEU* 3.4 22.4 + - - +
105C LEU* 3.5 17.0 - - - +
106C GLU* 3.1 38.9 + - - +
101D GLY 5.1 0.2 - - - +
102D PRO* 3.4 11.1 - - - +
103D THR* 2.9 49.1 + - - +
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Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA* 3.3 24.0 - - - -
406A PRO 3.7 4.4 + - - -
407A LEU 3.3 4.0 + - - -
409A GLN* 1.3 74.4 - - - +
411A ARG* 1.3 65.3 + - - +
412A LEU 3.2 1.6 - - - -
413A PHE* 3.1 15.1 + - - +
414A SER* 3.4 7.4 + - - -
760A HDD 3.9 7.3 - - - +
105C LEU* 4.1 11.7 - - - -
94D SER* 5.7 0.2 - - - -
103D THR* 4.8 1.5 + - - -
110D LEU* 5.0 8.1 - - - -
114D ILE* 5.0 2.2 - - - +
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 3.0 41.8 + - - +
273A GLY 4.5 1.0 + - - -
275A HIS* 2.8 44.0 + - - -
277A PHE* 5.3 0.6 - - - -
392A HIS* 3.4 0.6 - - - -
393A PRO* 3.5 23.7 - - + +
407A LEU* 3.1 16.2 + - - +
408A LEU* 3.4 9.0 - - + +
410A GLY* 1.3 76.6 - - - +
412A LEU* 1.3 63.3 + - - +
413A PHE 3.0 1.2 + - - -
414A SER 3.1 10.6 + - - -
415A TYR* 2.7 54.1 + - + -
760A HDD 3.3 59.8 - - + +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A HIS* 3.2 18.4 + - - +
393A PRO* 4.2 1.1 - - + -
394A GLY* 3.5 32.5 - - - +
402A PHE* 3.7 31.0 - - + -
408A LEU* 3.4 26.5 - - + +
409A GLN* 3.5 16.8 - - - +
410A GLY 3.2 0.8 - - - -
411A ARG* 1.3 77.2 - - - +
413A PHE* 1.3 58.8 + - - +
416A THR* 4.6 0.2 + - - -
105C LEU 4.5 2.5 - - - +
106C GLU* 3.4 35.0 - - + +
108C PHE* 6.0 0.2 - - + -
111C ARG* 2.9 33.8 + - - +
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A GLN 4.0 1.2 + - - -
410A GLY* 3.1 11.3 + - - +
412A LEU* 1.3 81.7 - - - +
414A SER* 1.3 63.9 + - - +
415A TYR 3.7 0.2 + - - -
416A THR* 3.8 1.4 + - - -
417A ASP* 3.5 41.8 + - + +
413B PHE* 3.8 26.0 - + - -
417B ASP* 6.3 1.1 - - + -
105C LEU* 3.9 25.0 - - + +
111C ARG* 4.0 12.7 + - - +
110D LEU* 5.9 2.0 - - + -
111D ARG* 3.7 40.4 - - + -
114D ILE* 3.6 29.8 - - + -
115D THR* 3.3 26.9 - - - -
118D ASP* 3.8 0.2 - - - -
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A GLY 3.4 1.0 + - - -
411A ARG 3.1 5.6 + - - -
413A PHE* 1.3 78.0 - - - +
415A TYR* 1.3 61.1 + - - +
417A ASP 3.3 0.2 + - - -
418A THR* 2.9 29.5 + - - -
760A HDD 2.9 41.9 + - - +
114D ILE* 3.6 14.1 - - - -
118D ASP* 2.7 34.3 + - - +
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Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A VAL* 4.1 6.3 - - + -
391A PHE 3.2 21.1 - - - +
392A HIS* 2.0 39.0 - - + +
393A PRO* 3.4 22.7 - - + -
411A ARG* 2.7 53.8 + - + -
414A SER* 1.3 74.6 - - - +
416A THR* 1.3 51.9 + - - +
418A THR* 3.7 2.3 - - - +
419A GLN* 2.5 39.3 + - - +
428A PHE* 5.3 0.2 - - - -
760A HDD 2.1 81.1 + + + -
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A HIS* 3.5 21.4 + - - -
395A HIS* 4.8 5.9 + - - -
413A PHE 3.8 5.5 + - - -
414A SER 3.3 0.6 - - - -
415A TYR* 1.3 75.1 - - - +
417A ASP* 1.3 68.9 + - - +
419A GLN* 3.4 13.6 + - - +
420A ILE* 4.0 9.0 + - - +
428A PHE* 4.4 20.0 - - + -
111C ARG* 4.3 14.7 + - - +
112C GLU* 5.0 15.6 - - + +
115C THR* 4.1 30.5 - - + +
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PHE* 3.5 32.8 + - + +
414A SER 3.6 0.2 - - - +
416A THR* 1.3 80.0 - - - +
418A THR* 1.3 62.1 + - - +
420A ILE* 3.1 18.5 + - - +
413B PHE* 6.3 0.7 - - + -
417B ASP* 4.5 14.0 - - - +
420B ILE* 4.6 3.3 - - - +
115C THR* 6.0 1.6 - - - -
115D THR* 3.4 17.4 + - - +
118D ASP* 2.4 36.3 - - - +
119D HIS* 2.8 36.4 + - - -
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.7 13.5 + - - +
414A SER 2.9 17.2 + - - +
415A TYR 3.7 0.2 - - - +
417A ASP* 1.3 73.8 - - - +
419A GLN* 1.3 88.6 + - + +
420A ILE 3.2 1.0 + - - -
421A SER* 3.3 7.3 + - - -
422A ARG* 3.1 23.1 + - - +
760A HDD 3.5 34.3 - - + +
118D ASP* 2.6 37.2 + - - -
119D HIS* 3.8 2.2 - - - -
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ALA* 3.9 16.2 - - - +
391A PHE 4.2 7.5 + - - -
392A HIS* 5.5 0.4 - - - +
415A TYR 2.5 31.4 + - - +
416A THR 3.4 5.4 + - - +
417A ASP 3.2 1.4 + - - -
418A THR* 1.3 77.2 - - - +
420A ILE* 1.3 61.2 + - - +
421A SER 3.2 0.4 - - - -
422A ARG* 3.6 32.3 - - - +
423A LEU* 2.8 49.0 + - + +
424A GLY 3.5 1.2 + - - -
425A GLY 3.8 5.3 - - - +
428A PHE* 3.9 22.6 - - + -
760A HDD 2.9 25.7 + - - -
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A THR 4.0 8.5 + - - +
417A ASP* 3.1 16.2 + - - +
419A GLN* 1.3 77.1 - - - +
421A SER* 1.3 57.8 + - - +
424A GLY* 3.3 6.9 - - - -
425A GLY* 3.1 44.7 + - - +
426A PRO* 3.5 12.3 - - + -
428A PHE* 4.9 3.6 - - + -
417B ASP* 4.7 3.4 - - - +
420B ILE* 3.8 18.8 - - + +
421B SER* 4.8 7.6 - - - -
115C THR* 3.8 21.8 - - + -
119C HIS* 3.7 40.6 - - + +
119D HIS* 4.3 0.4 - - + -
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Residues in contact with SER 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 3.8 14.1 - - - +
126A ILE* 5.9 0.3 - - - +
418A THR 3.3 4.8 + - - -
419A GLN 3.2 0.4 - - - -
420A ILE* 1.3 78.4 - - - +
422A ARG* 1.3 69.6 + - - +
423A LEU 3.3 0.4 - - - -
424A GLY* 3.3 8.5 + - - -
420B ILE* 4.9 5.2 - - - -
448C MET* 3.6 10.7 - - - +
118D ASP 4.0 1.2 + - - -
119D HIS* 2.7 43.2 + - - -
121D ARG 5.1 5.2 + - - -
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Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 3.7 9.3 - - + +
123A PRO* 3.3 30.3 - - + +
124A GLU 4.1 2.0 - - - +
125A ARG* 3.3 51.2 - - - +
126A ILE* 5.3 0.7 - - - +
387A GLU* 2.8 30.5 + - - -
389A ALA 2.7 24.4 + - - -
390A ALA* 3.6 8.7 - - - +
418A THR* 3.1 17.7 + - - +
419A GLN* 3.6 27.6 - - - +
421A SER* 1.3 84.6 + - - +
423A LEU* 1.3 72.4 + - + +
760A HDD 3.8 14.5 + - - -
448C MET* 3.4 15.4 - - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 4.1 9.0 - - + -
388A GLN* 3.4 41.5 - - + +
390A ALA* 3.7 11.9 - - + -
419A GLN* 2.8 37.3 + - + +
422A ARG* 1.3 91.7 - - - +
424A GLY* 1.3 61.0 + - - +
425A GLY* 3.3 5.7 + - - +
428A PHE* 3.6 31.0 + - + +
431A ILE* 3.9 15.0 - - + +
434A ASN* 4.0 1.3 - - - +
448C MET* 3.4 14.8 - - - +
449C HIS* 4.4 14.9 + - - +
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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