Contacts of the helix formed by residues 357 - 371 (chain C) in PDB entry 2GVG
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 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C GLN* 3.9 6.7 - - - -
355C GLY 4.6 1.9 - - - +
356C VAL* 1.3 75.4 - - - +
358C ILE* 1.3 68.8 + - + +
359C ASN* 2.7 25.9 + - - +
360C THR* 2.9 28.1 + - - +
361C LEU* 3.0 23.0 + - - +
382C SER* 4.5 3.6 - - - -
385C GLY* 4.3 10.3 - - - +
389C LYS* 4.1 32.6 + - - +
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Residues in contact with ILE 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 4.0 20.6 - - + +
164C ASN* 3.8 16.0 - - - +
167C GLU* 4.3 10.5 - - + -
168C GLN* 3.2 42.0 + - + +
171C ILE* 3.6 22.7 - - + +
357C ASP* 1.3 76.6 - - + +
359C ASN* 1.3 88.3 + - - +
361C LEU* 3.5 3.3 - - - +
362C GLN* 3.3 18.7 + - - +
385C GLY 5.6 0.6 + - - -
389C LYS* 6.0 2.0 - - - +
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Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ASP* 2.7 15.7 + - - +
358C ILE* 1.3 85.5 - - - +
360C THR* 1.3 65.8 + - + +
361C LEU 3.1 1.6 - - - -
362C GLN* 3.2 8.9 + - - +
363C GLU* 3.0 30.4 + - - +
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Residues in contact with THR 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C PRO* 5.1 8.1 - - + -
355C GLY 2.7 28.7 + - - +
356C VAL* 3.3 3.8 - - - +
357C ASP* 2.9 36.3 + - - +
359C ASN* 1.3 71.1 - - + +
361C LEU* 1.3 64.8 + - - +
363C GLU* 3.7 19.2 - - - +
364C ILE* 3.0 39.2 + - - +
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Residues in contact with LEU 361 (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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168C GLN* 3.3 46.9 - - + +
171C ILE* 4.2 8.7 - - + -
172C LEU* 3.6 22.2 - - + -
190C LEU* 4.2 15.5 - - + -
356C VAL* 4.3 12.1 - - + -
357C ASP 3.0 17.4 + - - +
358C ILE 3.5 5.2 - - - +
360C THR* 1.3 79.0 + - - +
362C GLN* 1.3 64.1 + - - +
364C ILE* 3.3 6.1 + - - +
365C VAL* 3.0 40.7 + - + +
380C PHE* 4.3 11.7 - - + -
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ILE* 3.0 45.4 - - + +
174C LYS* 5.4 0.9 + - - -
175C TYR* 2.8 32.0 + - - -
358C ILE 3.3 9.2 + - - +
359C ASN* 3.2 11.4 + - - +
361C LEU* 1.3 79.5 - - - +
363C GLU* 1.3 59.9 + - + +
365C VAL* 2.9 7.7 - - - +
366C GLU* 2.9 34.3 + - + +
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Residues in contact with GLU 363 (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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318C LEU* 4.3 8.7 - - + +
359C ASN* 3.0 20.8 + - + +
360C THR* 3.7 23.2 - - - +
362C GLN* 1.3 79.8 - - + +
364C ILE* 1.3 53.7 + - + +
366C GLU* 3.1 8.1 + - - +
367C GLY* 2.6 35.3 + - - -
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Residues in contact with ILE 364 (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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317C PRO* 3.5 30.7 - - + -
318C LEU* 3.9 28.5 - - + +
321C VAL* 4.6 13.2 - - + -
352C GLN* 4.1 9.9 - - + -
356C VAL* 4.6 5.8 - - + -
360C THR* 3.0 26.6 + - - +
361C LEU 3.8 3.4 - - - +
363C GLU* 1.3 74.1 - - + +
365C VAL* 1.3 60.9 + - - +
367C GLY* 3.3 0.3 + - - -
368C MET* 2.9 41.8 + - + +
380C PHE* 3.5 34.8 - - + -
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ILE* 3.8 7.0 - - + -
172C LEU* 4.2 9.0 - - + -
175C TYR* 3.4 45.9 - - + -
361C LEU* 3.0 33.1 + - + +
362C GLN* 2.9 26.2 - - - +
364C ILE* 1.3 75.8 - - - +
366C GLU* 1.3 61.4 + - - +
368C MET* 3.6 3.1 + - - +
369C LYS* 3.1 16.6 + - - +
375C ILE* 4.0 21.6 - - + +
380C PHE* 4.0 17.0 - - + -
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Residues in contact with GLU 366 (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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175C TYR* 2.6 35.3 + - - +
362C GLN* 2.9 24.2 + - + +
363C GLU* 3.3 8.3 - - - +
365C VAL* 1.3 75.4 - - - +
367C GLY* 1.3 64.5 + - - +
369C LYS* 3.0 34.6 + - - +
370C GLN* 3.0 39.2 + - - +
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Residues in contact with GLY 367 (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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318C LEU* 3.8 20.9 - - - -
322C LEU* 4.3 3.6 - - - -
363C GLU 2.6 19.8 + - - -
366C GLU* 1.3 74.0 - - - +
368C MET* 1.3 60.8 + - - +
370C GLN* 3.3 14.0 + - - +
371C LYS* 3.1 27.0 + - - +
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Residues in contact with MET 368 (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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318C LEU* 4.4 0.6 - - + +
321C VAL* 4.2 20.6 - - + -
322C LEU* 4.0 12.1 - - + +
325C LEU* 3.6 26.2 - - + -
364C ILE* 2.9 26.4 + - + +
365C VAL* 3.8 4.3 - - - +
367C GLY* 1.3 75.7 - - - +
369C LYS* 1.3 62.0 + - - +
371C LYS* 3.1 2.8 + - - -
372C MET 3.0 4.5 + - - -
373C TRP* 2.8 37.5 + - + +
374C SER 3.6 25.4 - - - +
375C ILE* 4.3 9.4 - - + -
377C ASN* 4.4 4.3 - - + -
378C ILE* 3.5 39.9 - - + -
380C PHE* 4.9 0.2 - - - -
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Residues in contact with LYS 369 (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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174C LYS* 5.8 2.0 - - - +
175C TYR* 4.0 23.9 - - + -
178C GLU* 4.3 16.1 + - + +
179C THR* 4.6 8.5 - - + -
341C TYR* 3.8 26.1 - - + +
365C VAL 3.1 13.6 + - - +
366C GLU* 3.0 33.1 + - - +
368C MET* 1.3 77.4 - - - +
370C GLN* 1.3 61.3 + - + +
372C MET* 2.8 38.7 + - + +
373C TRP 4.3 6.9 + - - -
375C ILE* 5.5 0.4 - - + +
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Residues in contact with GLN 370 (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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366C GLU* 3.0 47.0 + - - +
367C GLY* 3.8 10.7 - - - +
369C LYS* 1.3 81.0 - - + +
371C LYS* 1.3 62.1 - - + +
372C MET* 3.1 11.8 + - - +
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Residues in contact with LYS 371 (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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322C LEU* 3.3 38.4 - - + -
342C LYS* 3.5 11.4 + - - -
367C GLY 3.1 11.3 + - - +
368C MET 3.1 1.3 + - - +
369C LYS 3.1 1.2 - - - -
370C GLN* 1.3 79.6 - - + +
372C MET* 1.3 69.7 + - - +
373C TRP* 3.3 27.9 + - + +
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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