Contacts of the helix formed by residues 289 - 297 (chain C) in PDB entry 3GZN
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 PRO 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C GLN* 3.4 12.0 - - + +
288C ILE* 1.3 86.1 - - + +
290C SER* 1.3 57.9 + - - +
291C SER* 3.1 11.7 - - - +
292C ILE* 3.0 17.7 + - + +
293C GLU 3.0 22.2 + - - -
330C LEU* 4.0 19.5 - - + -
395C ALA* 3.9 26.7 - - + +
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Residues in contact with SER 290 (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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288C ILE 3.4 3.2 + - - -
289C PRO* 1.3 71.1 - - - +
291C SER* 1.3 57.3 + - - +
293C GLU* 3.6 12.2 - - - +
294C ASP* 3.0 34.5 + - - +
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Residues in contact with SER 291 (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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289C PRO* 4.0 7.3 - - - +
290C SER* 1.3 81.6 + - - +
292C ILE* 1.3 74.4 + - - +
294C ASP* 3.2 11.9 + - - +
295C ILE* 3.2 27.9 + - - +
395C ALA 4.4 3.5 + - - -
397C LEU 4.2 8.1 + - - -
398C ARG* 5.2 10.5 - - - -
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Residues in contact with ILE 292 (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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288C ILE* 4.5 1.8 - - + -
289C PRO* 3.0 19.1 + - + +
291C SER* 1.3 81.4 + - - +
293C GLU* 1.3 65.4 + - - +
295C ILE* 3.2 8.1 + - + +
296C PHE* 3.2 52.3 + - + -
318C LEU* 6.1 0.2 - - + -
330C LEU* 4.3 7.6 - - + -
394C SER 3.5 25.8 - - - +
395C ALA* 3.6 26.9 - - - +
397C LEU* 3.6 41.7 - - + +
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Residues in contact with GLU 293 (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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288C ILE* 4.2 20.4 - - + +
289C PRO 3.0 12.7 + - - +
290C SER* 3.6 16.4 - - - +
292C ILE* 1.3 76.1 - - - +
294C ASP* 1.3 63.5 + - - +
296C PHE* 3.4 18.6 + - - +
297C ASN* 3.1 47.2 + - - +
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Residues in contact with ASP 294 (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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290C SER* 3.0 20.2 + - - +
291C SER* 3.4 13.0 - - - +
292C ILE 3.2 0.2 - - - -
293C GLU* 1.3 77.4 - - - +
295C ILE* 1.3 64.4 + - + +
297C ASN* 3.5 8.8 + - - +
298C ASP* 3.3 20.8 + - - +
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Residues in contact with ILE 295 (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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291C SER* 3.2 14.2 + - - +
292C ILE* 3.2 14.3 + - + +
294C ASP* 1.3 72.7 - - + +
296C PHE* 1.3 75.1 + - + +
298C ASP* 3.1 22.4 + - - +
301C CYS* 3.6 6.8 - - - +
311C PHE* 4.7 5.2 - - + -
312C TRP* 3.7 20.8 - - + -
315C ALA* 4.2 16.4 - - + -
397C LEU* 3.7 48.7 - - + +
398C ARG* 4.4 1.6 - - - +
399C VAL* 4.1 24.9 - - + +
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Residues in contact with PHE 296 (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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288C ILE* 4.6 12.1 - - + -
292C ILE* 3.2 38.9 + - + -
293C GLU* 3.5 18.2 - - - +
295C ILE* 1.3 83.8 - - + +
297C ASN* 1.3 60.3 + - - +
298C ASP 3.1 12.1 + - - +
301C CYS* 3.7 13.3 - - - +
302C ILE* 3.7 1.0 - - - +
315C ALA* 3.5 22.7 - - - -
318C LEU* 4.0 13.2 - - + -
319C LYS* 3.2 62.7 + - + -
322C VAL* 4.1 19.1 - - + -
330C LEU* 4.2 11.0 - - + -
397C LEU* 6.0 0.9 - - + -
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Residues in contact with ASN 297 (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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293C GLU* 3.1 38.6 + - - +
294C ASP* 3.8 10.1 + - - +
295C ILE 3.3 0.4 - - - -
296C PHE* 1.3 77.7 - - - +
298C ASP* 1.3 61.8 + - - +
299C ASP 3.7 1.0 + - - -
302C ILE* 3.6 15.6 - - + +
319C LYS* 4.4 9.5 + - - -
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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