Contacts of the helix formed by residues 349 - 360 (chain B) in PDB entry 3GNI
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 SER 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B GLU* 2.6 33.5 + - - -
348B PHE* 1.3 74.1 - - - +
350B PRO* 1.4 73.4 - - - +
351B HIS* 3.8 11.3 + - - +
352B PHE* 3.1 23.6 + - - +
353B HIS* 3.2 9.0 + - - -
381B GLN* 4.8 3.3 + - - -
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Residues in contact with PRO 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PHE 3.7 2.0 - - - +
349B SER* 1.4 87.4 - - - +
351B HIS* 1.3 69.5 + - + +
353B HIS* 3.2 13.9 + - + +
354B HIS* 3.0 41.7 + - + -
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Residues in contact with HIS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B SER* 3.2 10.9 - - - +
350B PRO* 1.3 84.0 - - + +
352B PHE* 1.3 58.7 + - - +
354B HIS* 3.3 10.4 + - - +
355B PHE* 2.9 25.5 + - - +
376B HIS* 3.2 12.4 - - - -
377B SER* 3.3 38.2 + - - -
378B PHE* 3.9 20.2 - - - +
380B LYS* 5.6 4.5 - - + +
381B GLN* 5.9 0.7 - - - +
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Residues in contact with PHE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B GLU* 3.7 14.4 - - + +
172B ILE* 4.2 15.0 - - + -
269B ALA* 3.8 29.6 - - + -
270B CYS* 5.8 0.2 - - - -
273B ALA* 4.0 13.9 - - + -
348B PHE* 3.5 41.7 - + + -
349B SER* 3.1 13.5 + - - +
351B HIS* 1.3 77.6 - - - +
353B HIS* 1.3 63.9 + + - +
355B PHE* 3.2 5.5 - + - +
356B VAL* 3.0 43.1 + - + +
378B PHE* 3.3 44.5 - + + -
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Residues in contact with HIS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PHE* 3.4 42.0 + + + +
349B SER 3.2 18.0 + - - -
350B PRO* 3.2 12.7 + - + +
352B PHE* 1.3 80.3 - + + +
354B HIS* 1.3 60.7 + - + +
356B VAL* 3.2 6.6 + - - +
357B GLU* 2.9 48.9 + - - +
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Residues in contact with HIS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PRO* 3.0 33.5 + - + +
351B HIS* 3.9 12.3 + - - +
353B HIS* 1.3 75.3 - - + +
355B PHE* 1.3 64.9 + - - +
357B GLU* 3.9 20.6 - - - +
358B GLN* 3.1 29.7 + - + +
376B HIS* 3.8 11.7 - - + +
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.6 23.6 - - + -
180B LEU* 4.3 1.1 - - + -
265B VAL* 3.9 22.4 - - + -
269B ALA* 4.4 5.4 - - + -
351B HIS 2.9 14.5 + - - +
352B PHE* 3.2 13.5 - + - +
354B HIS* 1.3 77.2 - - - +
356B VAL* 1.3 73.9 + - + +
358B GLN* 3.3 5.2 + - - +
359B CYS* 3.3 35.5 + - - -
373B LEU* 3.4 34.0 - - + +
376B HIS* 3.4 21.0 - - + -
378B PHE* 3.9 22.9 - + + -
379B PHE* 3.5 30.5 - + - -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY* 4.4 4.0 - - - +
269B ALA* 3.8 17.0 - - + -
270B CYS* 3.9 19.3 - - - -
352B PHE* 3.0 47.3 + - + +
353B HIS* 3.7 5.8 - - - +
355B PHE* 1.3 79.6 - - + +
357B GLU* 1.3 65.3 + - + +
359B CYS* 3.4 6.0 + - - +
360B LEU* 3.1 46.0 + - + +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B HIS* 2.9 36.0 + - - +
354B HIS* 3.9 21.9 - - - +
356B VAL* 1.3 77.0 - - + +
358B GLN* 1.3 62.0 + - + +
360B LEU* 3.8 9.4 + - - +
361B GLN* 3.5 18.0 + - - +
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Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B HIS* 3.1 17.3 + - + +
355B PHE* 3.6 4.9 - - - +
357B GLU* 1.3 74.5 - - - +
359B CYS* 1.3 65.2 + - - +
360B LEU 3.2 1.9 + - - -
361B GLN* 2.6 36.8 + - - +
366B ALA 5.3 1.8 + - - -
367B ARG* 3.8 5.2 - - - +
368B PRO* 3.7 34.3 - - + +
373B LEU* 5.0 2.9 - - + +
376B HIS* 3.1 31.2 + - - -
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Residues in contact with CYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ILE* 3.3 31.0 - - - +
263B TYR* 3.3 19.3 - - - -
265B VAL* 4.2 1.3 - - - -
266B GLY* 3.7 21.1 - - - -
355B PHE* 3.3 30.6 + - - -
356B VAL 3.7 7.6 - - - +
358B GLN* 1.3 78.2 - - - +
360B LEU* 1.3 57.9 + - - +
361B GLN 3.3 0.2 - - - -
367B ARG* 3.4 17.8 + - - -
368B PRO* 5.2 0.2 - - - -
373B LEU* 3.7 29.2 - - - -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B TYR* 3.6 51.8 - - + +
266B GLY* 4.1 3.6 - - - -
267B ILE* 3.8 24.7 - - + +
270B CYS* 4.6 11.0 - - - -
356B VAL* 3.1 39.3 + - + +
357B GLU* 3.8 7.4 + - - +
358B GLN 3.2 1.0 - - - -
359B CYS* 1.3 75.4 - - - +
361B GLN* 1.3 64.9 + - - +
362B ARG* 3.5 3.6 + - - -
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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