Contacts of the helix formed by residues 211 - 221 (chain Y) in PDB entry 1GNG
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 ASN 211 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B GLU* 3.6 9.0 - - - -
206Y LEU* 2.8 20.9 + - + +
209Y SER* 2.9 37.1 + - - +
210Y GLY* 1.3 75.3 - - - +
212Y LEU* 1.3 65.9 + - - +
213Y ILE 3.5 1.3 - - - -
214Y LYS* 3.1 30.4 + - + +
215Y GLU* 3.0 25.3 + - + +
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Residues in contact with LEU 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ILE* 3.5 21.1 - - + +
229B PHE* 3.5 33.9 - - + -
263B VAL* 4.7 9.4 - - + +
266B LEU* 3.4 26.9 - - + -
288B TYR* 3.0 17.3 + - + +
203Y LEU* 3.7 24.2 - - + -
206Y LEU* 3.4 26.2 + - + +
207Y VAL* 4.2 6.3 - - + -
211Y ASN* 1.3 77.5 - - - +
213Y ILE* 1.3 58.9 + - - +
215Y GLU* 3.8 1.6 - - - +
216Y ALA* 2.9 30.0 + - + +
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Residues in contact with ILE 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 3.7 29.4 - - + -
266B LEU* 5.0 3.1 - - + -
270B ILE* 4.5 4.9 - - + -
275B THR* 4.2 10.1 - - + -
276B PRO* 4.1 11.7 - - + -
281B ILE* 3.2 36.3 - - + -
288B TYR* 4.8 0.4 - - + -
290B GLU* 3.0 18.3 + - - +
293B PHE* 3.5 33.7 - - + -
212Y LEU* 1.3 72.0 - - - +
214Y LYS* 1.3 60.4 + - - +
216Y ALA* 4.3 4.9 - - - -
217Y VAL* 2.9 47.8 + - + +
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Residues in contact with LYS 214 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 2.7 62.6 + - - +
291B PHE 5.4 0.4 - - - +
292B LYS* 2.9 29.6 - - - +
293B PHE* 4.1 6.7 - - + +
294B PRO* 4.3 16.5 - - + +
210Y GLY 3.2 2.8 + - - -
211Y ASN* 3.1 34.1 + - + +
213Y ILE* 1.3 74.8 - - - +
215Y GLU* 1.3 60.2 + - - +
217Y VAL* 4.0 2.8 - - - +
218Y ARG* 3.2 22.0 + - - +
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Residues in contact with GLU 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B VAL* 4.8 0.9 - - + -
202Y LEU* 6.0 1.1 - - + -
206Y LEU* 3.9 31.5 - - + +
211Y ASN* 3.0 19.8 + - + +
212Y LEU 4.0 2.2 - - - +
214Y LYS* 1.3 74.9 - - - +
216Y ALA* 1.3 66.0 + - - +
218Y ARG* 2.6 47.8 + - - +
219Y ARG* 3.2 44.1 + - - +
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Residues in contact with ALA 216 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B VAL* 4.7 9.1 - - + +
266B LEU* 4.3 13.2 - - + -
267B VAL* 3.7 24.2 - - + +
270B ILE* 4.3 19.3 - - + -
212Y LEU 2.9 18.6 + - - +
213Y ILE* 3.7 5.2 - - - +
215Y GLU* 1.3 79.1 - - - +
217Y VAL* 1.3 63.3 + - - +
218Y ARG 3.2 0.2 + - - -
219Y ARG* 3.2 6.5 + - - +
220Y LEU* 3.0 20.3 + - - +
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Residues in contact with VAL 217 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE* 4.7 6.3 - - + -
275B THR* 3.8 21.1 - - + -
294B PRO* 3.3 47.3 - - + +
296B ILE* 3.9 10.8 - - + -
213Y ILE* 2.9 26.1 + - + +
214Y LYS 4.0 0.9 - - - +
216Y ALA* 1.3 74.6 - - - +
218Y ARG* 1.3 64.3 + - - +
220Y LEU* 2.9 23.1 - - - +
221Y HIS* 3.3 30.8 + - + +
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Residues in contact with ARG 218 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 5.4 0.2 - - - +
214Y LYS 3.2 16.9 + - - +
215Y GLU* 2.6 41.9 + - - +
216Y ALA 3.1 0.4 - - - -
217Y VAL* 1.3 77.7 - - - +
219Y ARG* 1.3 77.0 + - - +
220Y LEU 2.9 1.2 + - - -
221Y HIS* 3.1 15.5 + - - +
222Y SER* 2.9 31.6 + - - +
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Residues in contact with ARG 219 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B SER* 3.8 12.9 + - - -
263B VAL* 3.6 35.1 - - - +
264B ASP* 4.2 7.6 - - - +
267B VAL* 4.4 15.2 - - + +
199Y PRO* 5.1 4.2 - - - +
202Y LEU* 3.2 32.9 - - - +
215Y GLU* 3.2 37.1 + - - +
216Y ALA 3.7 5.2 - - - +
218Y ARG* 1.3 85.6 - - - +
220Y LEU* 1.3 62.1 + - - +
222Y SER* 3.3 23.1 - - - -
223Y ARG 4.2 1.9 + - - -
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Residues in contact with LEU 220 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B VAL* 3.7 22.7 - - + +
270B ILE* 4.2 10.5 - - + +
271B LYS* 3.3 36.8 - - + -
296B ILE* 3.6 45.3 - - + -
216Y ALA 3.0 11.8 + - - +
217Y VAL* 2.9 17.5 - - - +
218Y ARG 2.9 0.4 - - - -
219Y ARG* 1.3 79.1 - - - +
221Y HIS* 1.3 63.0 + - + +
222Y SER 3.0 4.2 + - - -
223Y ARG 3.9 5.9 + - - -
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Residues in contact with HIS 221 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 5.7 2.7 - - + -
296B ILE* 3.2 35.1 - - + +
217Y VAL* 3.7 20.1 + - + +
218Y ARG* 3.1 8.6 + - - +
220Y LEU* 1.3 82.6 - - + +
222Y SER* 1.3 62.8 + - - +
223Y ARG 3.5 0.7 - - - -
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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