Contacts of the helix formed by residues 269 - 278 (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 GLU 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C LYS 5.1 0.2 - - - +
216C HIS* 2.7 41.2 + - - +
217C SER* 3.4 30.6 + - - -
258C ILE* 3.7 7.2 - - + +
259C LEU* 3.5 25.0 + - - +
267C GLU* 3.0 20.7 + - + +
268C ASP* 1.3 73.0 - - - +
270C GLU* 1.3 59.7 + - - +
271C ASN* 3.1 13.2 - - - +
272C PHE* 2.9 36.6 + - + +
273C GLU* 3.1 18.0 + - - +
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Residues in contact with GLU 270 (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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268C ASP* 3.7 18.1 + - + +
269C GLU* 1.3 71.4 - - - +
271C ASN* 1.3 53.6 + - - +
273C GLU* 3.1 14.3 + - + +
274C GLU* 2.7 41.3 + - + +
340C ILE* 3.4 31.4 - - + +
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Residues in contact with ASN 271 (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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216C HIS 3.0 24.4 + - - -
217C SER* 2.9 30.6 + - - +
219C THR 3.4 17.3 + - - +
221C TRP* 3.6 10.5 - - - +
224C ILE* 3.4 23.3 - - - +
269C GLU* 3.4 14.7 - - - +
270C GLU* 1.3 79.8 + - - +
272C PHE* 1.3 63.6 + - - +
274C GLU* 3.6 5.9 + - - +
275C ALA* 3.1 25.1 + - - +
340C ILE* 3.8 23.6 - - + +
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Residues in contact with PHE 272 (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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208C LEU* 5.1 4.5 - - + -
216C HIS* 3.4 37.7 - + - -
219C THR* 6.1 0.2 - - - -
224C ILE* 3.8 33.2 - - + -
228C TYR* 3.6 27.4 - + - -
254C ILE* 3.6 31.3 - - + +
257C GLY 4.1 5.2 - - - -
258C ILE* 4.0 23.1 - - + -
269C GLU* 2.9 23.7 + - + +
271C ASN* 1.3 97.4 - - - +
273C GLU* 1.3 66.0 + - - +
275C ALA* 3.4 6.3 + - - +
276C ILE* 3.1 29.0 + - - +
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Residues in contact with GLU 273 (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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255C ARG* 4.2 17.1 + - - -
258C ILE* 4.1 18.9 - - - +
267C GLU 5.3 4.2 - - - +
268C ASP* 6.0 1.2 - - - -
269C GLU 3.1 18.8 + - - +
270C GLU* 3.1 16.6 + - + +
272C PHE* 1.3 75.9 - - - +
274C GLU* 1.3 58.0 + - - +
276C ILE* 2.9 26.1 + - - +
277C LYS* 3.0 20.9 + - + +
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Residues in contact with GLU 274 (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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221C TRP* 3.1 23.9 - - + +
270C GLU* 2.7 20.8 + - + +
271C ASN* 3.6 6.1 - - - +
273C GLU* 1.3 72.3 - - + +
275C ALA* 1.3 62.8 + - - +
277C LYS* 3.3 9.9 + - + +
278C ASN* 3.0 35.4 + - - +
338C ASP 5.7 0.2 - - - -
339C MET* 3.6 4.9 - - - -
340C ILE* 3.0 49.8 + - - +
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Residues in contact with ALA 275 (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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221C TRP* 3.7 17.9 - - + +
224C ILE* 4.0 23.8 - - + -
225C ILE* 3.3 33.1 - - + +
254C ILE* 4.5 6.3 - - + -
271C ASN 3.1 14.9 + - - +
272C PHE 3.4 10.1 - - - +
273C GLU 3.2 0.2 - - - -
274C GLU* 1.3 76.8 - - - +
276C ILE* 1.3 60.4 + - - +
278C ASN 3.4 0.9 + - - -
279C VAL* 3.3 13.2 + - - +
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Residues in contact with ILE 276 (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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251C ARG* 2.9 52.0 + - + +
254C ILE* 3.7 27.1 - - + -
255C ARG* 3.7 52.9 - - + +
258C ILE* 4.6 6.3 - - + -
272C PHE 3.1 19.7 + - - +
273C GLU* 2.9 14.7 + - - +
275C ALA* 1.3 75.3 - - - +
277C LYS* 1.3 61.9 + - + +
279C VAL* 3.5 13.2 - - - +
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Residues in contact with LYS 277 (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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251C ARG* 3.7 5.8 + - - +
273C GLU* 3.0 17.7 + - + +
274C GLU* 3.3 13.4 + - + +
276C ILE* 1.3 78.4 - - + +
278C ASN* 1.3 60.1 + - - +
279C VAL 3.2 3.7 + - - -
280C ASN* 3.5 18.9 + - - +
28J GLU* 5.4 0.5 - - - +
31J GLU* 4.9 3.3 - - - +
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Residues in contact with ASN 278 (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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221C TRP* 3.5 51.6 - - + +
225C ILE* 4.2 2.5 - - - -
274C GLU* 3.0 31.1 + - - +
275C ALA 3.4 2.4 + - - +
276C ILE 3.3 0.2 - - - -
277C LYS* 1.3 79.1 - - - +
279C VAL* 1.3 60.4 + - - +
280C ASN* 2.9 6.7 + - - -
281C THR* 3.3 14.4 + - - +
282C ALA* 3.0 26.2 + - - +
31J GLU* 4.2 10.8 - - - +
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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